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Arana, M.E., K. Takata, M. Garcia-Diaz, R.D. Wood, and T.A. Kunkel (2007) A unique error signature for human DNA polymerase nu. DNA Repair 6:213-223 Human DNA polymerase nu (pol nu) is one of three A family polymerases conserved in vertebrates. Although its biological functions are unknown, pol nu has been implicated in DNA repair and in translesion DNA synthesis (TLS). Pol nu lacks intrinsic exonucleolytic proofreading activity and discriminates poorly against misinsertion of dNTP opposite template thymine or guanine, implying that it should copy DNA with low base substitution fidelity. To test this prediction and to comprehensively examine pol nu DNA synthesis fidelity as a clue to its function, here we describe human pol nu error rates for all 12 single base-base mismatches and for insertion and deletion errors during synthesis to copy the lacZ alpha-complementation sequence in M13mp2 DNA. Pol nu copies this DNA with average single-base insertion and deletion error rates of 7 x 10(-5) and 17 x 10(-5), respectively. This accuracy is comparable to that of replicative polymerases in the B family, lower than that of its A family homolog, human pol ga Masuda, K., R. Ouchida, M. Hikida, T. Kurosaki, M. Yokoi, C. Masutani, M. Seki, R.D. Wood, F. Hanaoka, and J. O-Wang (2007) DNA Polymerases {eta} and {theta} Function in the Same Genetic Pathway to Generate Mutations at A/T during Somatic Hypermutation of Ig Genes. J. Biol. Chem. 282:17387-17394 Somatic hypermutation of the Ig genes requires the activity of multiple DNA polymerases to ultimately introduce mutations at both A/T and C/G base pairs. Mice deficient for DNA polymerase eta (POLH) exhibited an approximately 80% reduction of the mutations at A/T, whereas absence of polymerase (POLQ) resulted in approximately 20% reduction of both A/T and C/G mutations. To investigate whether the residual A/T mutations observed in the absence of POLH are generated by POLQ and how these two polymerases might cooperate or compete with each other to generate A/T mutations, here we have established mice deficient for both POLH and POLQ. Polq(-/-)Polh(-/-) mice, however, did not show a further decrease of A/T mutations as compared with Polh(-/-) mice, suggesting that POLH and POLQ function in the same genetic pathway in the generation of these mutations. Frequent misincorporation of nucleotides, in particular opposite template T, is a known feature of POLH, but the efficiency of extension beyond the misincor Friedberg, E.C., and R.D. Wood (2007) New insights into the combined Cockayne/xeroderma pigmentosum complex: human XPG protein can function in transcription factor stability. Mol. Cell 26:162-164 A new study provides evidence supporting a function for XPG protein in maintaining the integrity and function of TFIIH (Ito et al. [2007], this issue of Molecular Cell). This observation likely explains some of the clinical features of individuals with both defective DNA repair and development. Friedberg, E.C., A. Aguilera, M. Gellert, P.C. Hanawalt, J.B. Hays, A.R. Lehmann, T. Lindahl, N. Lowndes, A. Sarasin, and R.D. Wood (2006) DNA repair: from molecular mechanism to human disease. DNA Repair 5:986-996 Yoshimura, M., M. Kohzaki, J. Nakamura, K. Asagoshi, E. Sonoda, E. Hou, R. Prasad, S.H. Wilson, K. Tano, A. Yasui, L. Lan, M. Seki, R.D. Wood, H. Arakawa, J.M. Buerstedde, H. Hochegger, T. Okada, M. Hiraoka, and S. Takeda (2006) Vertebrate POLQ and POLbeta cooperate in base excision repair of oxidative DNA damage. Mol. Cell 24:115-125 Base excision repair (BER) plays an essential role in protecting cells from mutagenic base damage caused by oxidative stress, hydrolysis, and environmental factors. POLQ is a DNA polymerase, which appears to be involved in translesion DNA synthesis (TLS) past base damage. We disrupted POLQ, and its homologs HEL308 and POLN in chicken DT40 cells, and also created polq/hel308 and polq/poln double mutants. We found that POLQ-deficient mutants exhibit hypersensitivity to oxidative base damage induced by H(2)O(2), but not to UV or cisplatin. Surprisingly, this phenotype was synergistically increased by concomitant deletion of the major BER polymerase, POLbeta. Moreover, extracts from a polq null mutant cell line show reduced BER activity, and POLQ, like POLbeta, accumulated rapidly at sites of base damage. Accordingly, POLQ and POLbeta share an overlapping function in the repair of oxidative base damage. Taken together, these results suggest a role for vertebrate POLQ in BER. Biggerstaff, M., and R.D. Wood (2006) Repair synthesis assay for nucleotide excision repair activity using fractionated cell extracts and UV-damaged plasmid DNA. Methods Mol Biol 314:417-434 Methods are described for measuring nucleotide excision repair (NER) of damaged plasmid DNA using fractionated mammalian cell extracts. NER creates a single-stranded gap of approx 25-30 nt. Filling of this gap by repair synthesis can be monitored by the incorporation of radioactive nucleotides. We first describe the preparation of ultraviolet light (UV)-damaged and control plasmid DNA substrates and purification of their closed-circular forms. To increase the specificity for NER, plasmid molecules containing pyrimidine hydrates and other lesions sensitive to Escherichia coli Nth protein are eliminated. The preparation of whole cell extracts active in NER is described, both for cells grown as attached cultures and those grown in suspension. Cell extracts are partially purified on phosphocellulose to produce a fraction that can carry out the full NER reaction when combined with purified RPA and PCNA proteins. This enables NER to be quantified in an assay with exceptionally low background in nondamaged DNA. Shivji, M.K., J.G. Moggs, I. Kuraoka, and R.D. Wood (2006) Assaying for the dual incisions of nucleotide excision repair using DNA with a lesion at a specific site. Methods Mol. Biol. 314:435-456 Analysis of the mechanism of nucleotide excision repair (NER) using cell-free extract systems and purified proteins requires DNA substrates containing chemically defined lesions that are placed at a unique site in a DNA duplex. In this way, NER can be readily specifically measured by detecting the 24-32 nucleotide products of the dual-incision reaction. This chapter describes several methods for detection of repair of a specific lesion in closed-circular DNA. As a model lesion, we use the well-repaired 1,3-intrastrand d(GpTpG)-cisplatin crosslink. Three methods are given for analysis of repair. One is to incorporate a radioactive label internally near the lesion and measure excision by detecting radioactive excised oligomers. Two other methods use DNA that is not internally labeled so that it can be stored and used when convenient. The first method for detection of repair of such unlabeled DNA is to detect excision products with a labeled complementary oligonucleotide by Southern blot hybridization. The second method is to 3'- end-label the excised oligonucleotide directly with radiolabeled dNTP and a DNA polymerase, using a complementary oligonucleotide with a 5'-overhang that serves as a template. This protocol is fast and sensitive, but relies on accurate foreknowledge of the site of 3'-incision for the particular lesion being used. Takata, K., T. Shimizu, S. Iwai, R.D. Wood, J.Y. Kim, W. Zeng, K. Kiselyov, J.P. Yuan, M.H. Dehoff, K. Mikoshiba, P.F. Worely, and S. Muallem (2006) Human DNA polymerase N (POLN) is a low fidelity enzyme capable of error-free bypass of 5S-thymine glycol. J. Biol. Chem. 281:23445-23455 Human DNA polymerase N (POLN or pol nu) is the most recently discovered nuclear DNA polymerase in the human genome. It is an A-family DNA polymerase related to Escherichia coli pol I, human POLQ, and Drosophila Mus308. We report the first purification of the recombinant enzyme and examination of its biochemical properties, as a step toward understanding the functions of POLN. Unusual for an A-family DNA polymerase, POLN is a low fidelity enzyme incorporating T opposite template G with a frequency of 0.45 and G opposite template T with a frequency of 0.021. The frequency of misincorporation of T opposite template G is higher than any other known DNA polymerase. POLN has a processivity of DNA synthesis (1-100 nucleotides) similar to the exonuclease-deficient Klenow fragment of E. coli pol I, is inhibited by dideoxynucleotides, and resistant to aphidicolin. The strand displacement activity of POLN was higher than exonuclease-deficient Klenow fragment. Furthermore, POLN can perform translesion synthesis past thymine glycol, a common endogenous and radiation-induced product of reactive oxygen species damage to DNA. Thymine glycol blocks DNA synthesis by most DNA polymerases, but POLN was particularly adept at efficient and accurate translesion synthesis past a 5S-thymine glycol. Wood, R.D., M. Mitchell, and T. Lindahl (2005) Human DNA repair genes, 2005. Mutat. Res. 577:275-283 An updated inventory of about 150 human DNA repair genes is described. The compilation includes genes encoding DNA repair enzymes, some genes associated with cellular responses to DNA damage, and other genes associated with genetic instability or sensitivity to DNA damaging agents. The updated human DNA repair genes table (http://www.cgal.icnet.uk/DNA_Repair_Genes.htmlhttp://www.cgal.icnet.uk/DN A_Repair_Genes.html) is a research and reference tool that directly links to several databases: Gene Cards, Online Mendelian Inheritance in Man, the NCBI MapViewer for chromosome position, and the NCBI Entrez database for the reference nucleotide sequence. This article discusses the approximately 25 genes added, since the original version of the table was first produced in 2001, and some other revisions. Wittschieben, B.O., S. Iwai, and R.D. Wood (2005) DDB1-DDB2 (XPE) protein complex recognizes a cyclobutane pyrimidine dimer, mismatches, AP sites and compound lesions in DNA. J. Biol. Chem. 280:39982-39989 The DDB protein complex, comprising the subunits DDB1 and DDB2, binds tightly to UV-irradiated DNA. Mutations in DDB2 are responsible for xeroderma pigmentosum group E, a disorder with a defect in nucleotide excision repair of DNA. Both subunits are also components of a complex involved in ubiquitin-mediated proteolysis. Cellular defects in DDB2 disable repair of the major UV radiation photoproduct in DNA, a cyclobutane pyrimidine dimer, but no significant direct binding of DDB to this photoproduct in DNA has ever been demonstrated. Thus, it has been uncertain how DDB could play a specific role in DNA repair of such damage. We investigated DDB function using highly purified proteins. Co-purified DDB1-DDB2, or DDB reconstituted with individual DDB1 and DDB2 subunits, binds to damaged DNA as a ternary complex. We find that DDB can indeed recognize a cyclobutane pyrimidine dimer in DNA, with an affinity (Ka(app)) 6-fold higher than nondamaged DNA. DDB1-DDB2 complex also binds with high specificity to a UV radiation-induced (6-4) photoproduct and to an apurinic site in DNA. Unexpectedly, DDB also binds avidly to DNA containing a 2 bp or 3 bp mismatch (and does not bind well to DNA containing more mismatches). These data indicate that DDB does not detect lesions per se. It instead recognizes other structural features, acting as a sensor that probes damaged DNA for a subset of conformational changes. Lesions recognized may include those arising when translesion DNA polymerases such as POLH incorporate bases across from DNA lesions caused by UV radiation.
Thorel, F., A. Constantinou, I. Dunand-Sauthier, T. Nouspikel, P. Lalle, A. Raams, N.G. Jaspers, W. Vermeulen, M.K. Shivji, R.D. Wood, and S.G. Clarkson (2004) Definition of a short region of XPG necessary for TFIIH interaction and stable recruitment to sites of UV damage. Mol. Cell Biol. 24:10670-10680 XPG is the human endonuclease that cuts 3' to DNA lesions during nucleotide excision repair. Missense mutations in XPG can lead to xeroderma pigmentosum (XP), whereas truncated or unstable XPG proteins cause Cockayne syndrome (CS), normally yielding life spans of <7 years. One XP-G individual who had advanced XP/CS symptoms at 28 years has been identified. The genetic, biochemical, and cellular defects in this remarkable case provide insight into the onset of XP and CS, and they reveal a previously unrecognized property of XPG. Both of this individual's XPG alleles produce a severely truncated protein, but an infrequent alternative splice generates an XPG protein lacking seven internal amino acids, which can account for his very slight cellular UV resistance. Deletion of XPG amino acids 225 to 231 does not abolish structure-specific endonuclease activity. Instead, this region is essential for interaction with TFIIH and for the stable recruitment of XPG to sites of local UV damage after the prior recruitment of TFIIH. These results define a new functional domain of XPG, and they demonstrate that recruitment of DNA repair proteins to sites of damage does not necessarily lead to productive repair reactions. This observation has potential implications that extend beyond nucleotide excision repair.
Welsh, C., R. Day, C. McGurk, J.R. Masters, R.D. Wood, and B. Koberle (2004) Reduced levels of XPA, ERCC1 and XPF DNA repair proteins in testis tumor cell lines. Int. J. Cancer 110:352-361 Over 80% of patients with advanced metastatic testis tumors can be cured using cisplatin-based combination chemotherapy. This is unusual as metastatic cancer in adults is usually incurable. Cell lines derived from testis tumors retain sensitivity to cisplatin in vitro. We previously investigated 2 testis tumor cell lines with a low capacity to remove cisplatin-induced DNA damage and found that they had low levels of the DNA nucleotide excision repair proteins XPA, ERCC1 and XPF. To determine whether low levels of XPA, ERCC1 and XPF proteins are characteristic of testis tumor cell lines, we investigated 35 cell lines derived from cancers to determine whether groups of cell lines from diverse tissue origins differ from one another in constitutive levels of these NER proteins. Quantitative immunoblotting was used to compare groups of cell lines representing prostate, bladder, breast, lung, cervical, ovarian and testis cancers. Only the 6 testis tumor cell lines showed significantly lower mean levels of XPA (p = 0.001), XPF (p = 0.001) and ERCC1 (p = 0.004) proteins from the other groups. Our results encourage further investigation of the possibility that low levels of these nucleotide excision repair proteins could be related to the favorable response of testis tumors to cisplatin-based chemotherapy. Seki, M., C. Masutani, L.W. Yang, A. Schuffert, S. Iwai, I. Bahar, and R.D. Wood (2004) High-efficiency bypass of DNA damage by human DNA polymerase Q. EMBO J 23:4484-4494 Endogenous DNA damage arises frequently, particularly apurinic (AP) sites. These must be dealt with by cells in order to avoid genotoxic effects. DNA polymerase theta; is a newly identified enzyme encoded by the human POLQ gene. We find that POLQ has an exceptional ability to bypass an AP site, inserting A with 22% of the efficiency of a normal template, and continuing extension as avidly as with a normally paired base. POLQ preferentially incorporates A opposite an AP site and strongly disfavors C. On nondamaged templates, POLQ makes frequent errors, incorporating G or T opposite T about 1% of the time. This very low fidelity distinguishes POLQ from other A-family polymerases. POLQ has three sequence insertions between conserved motifs in its catalytic site. One insert of approximately 22 residues into the tip of the polymerase thumb subdomain is predicted to confer considerable flexibility and additional DNA contacts to affect enzyme fidelity. POLQ is the only known enzyme that efficiently carries out both the insertion and extension steps for bypass of AP sites, commonly formed as endogenous genomic lesions.
Thorel, F., A. Constantinou, I. Dunand-Sauthier, T. Nouspikel, P. Lalle, A. Raams, N.G. Jaspers, W. Vermeulen, M.K. Shivji, R.D. Wood, and S.G. Clarkson (2004) Definition of a short region of XPG necessary for TFIIH interaction and stable recruitment to sites of UV damage. Mol Cell Biol. 24:10670-10680 XPG is the human endonuclease that cuts 3' to DNA lesions during nucleotide excision repair. Missense mutations in XPG can lead to xeroderma pigmentosum (XP), whereas truncated or unstable XPG proteins cause Cockayne syndrome (CS), normally yielding life spans of <7 years. One XP-G individual who had advanced XP/CS symptoms at 28 years has been identified. The genetic, biochemical, and cellular defects in this remarkable case provide insight into the onset of XP and CS, and they reveal a previously unrecognized property of XPG. Both of this individual's XPG alleles produce a severely truncated protein, but an infrequent alternative splice generates an XPG protein lacking seven internal amino acids, which can account for his very slight cellular UV resistance. Deletion of XPG amino acids 225 to 231 does not abolish structure-specific endonuclease activity. Instead, this region is essential for interaction with TFIIH and for the stable recruitment of XPG to sites of local UV damage after the prior recruitment of TFIIH. These results define a new functional domain of XPG, and they demonstrate that recruitment of DNA repair proteins to sites of damage does not necessarily lead to productive repair reactions. This observation has potential implications that extend beyond nucleotide excision repair. Wittschieben, B. .B.O., and R.D. Wood (2003) DDB complexities. DNA Repair 2:1065-1069 A group of recent publications contribute new insights concerning the role of the DNA damage-binding protein complex (DDB) in DNA repair. Mutations in the 48kDa DDB2 subunit are now found in all confirmed cases of xeroderma pigmentosum complementation group E. Several studies have reported a connection between the 127kDa DDB1 subunit and proteins involved in ubiquitin-mediated proteolysis. One such multiprotein complex containing DDB1 and DDB2 is closely related to a complex containing DDB1 and the Cockayne syndrome group A (CSA) protein. There is accumulating evidence for several levels of cellular regulation of DDB, including translocation to the nucleus, proteolytic degradation of DDB2 protein, and transcriptional induction of DDB2 mRNA. Although the mechanism is not yet known, it appears that DDB assists in nucleotide excision repair in chromatin. Seki, M., F. Marini, and R.D. Wood (2003) POLQ (Pol theta), a DNA polymerase and DNA-dependent ATPase in human cells. Nucleic Acids Res. 31:6117-6126 The genomes of eukaryotic cells predict the existence of multiple DNA polymerases, which are proposed to serve specialized roles in DNA replication and repair. We report here the isolation of the full-length human DNA POLQ gene, and an initial characterization of its gene product, DNA polymerase theta. POLQ is of particular interest as it is orthologous to Drosophila Mus308, a gene implicated in cellular resistance to interstrand DNA cross-linking agents. The POLQ cDNA encodes a polypeptide of 2592 amino acids with an ATPase-helicase domain in the N-terminal part of the protein, a central spacer domain, and a DNA polymerase domain in the C-terminal portion. This arrangement is conserved with Mus308. Expression of an mRNA of approximately 8.5 kb was detected in human cell lines. In a survey of human and mouse tissues, expression was highest in testis. Immunoblotting with POLQ antibodies detected a protein of >250 kDa in extracts from HeLa cells. Prominent fragments of approximately 100 kDa suggest that POLQ is readily proteolyzed. Full-length human POLQ was expressed from a baculovirus system. Purified POLQ showed DNA polymerase activity on nicked double-stranded DNA and on a singly primed DNA template. The enzyme activity was resistant to aphidicolin, consistent with its membership of the A family of DNA polymerases, and inhibited by dideoxynucleotides. POLQ further exhibited a single-stranded DNA-dependent ATPase activity.
Marini, F., N. Kim, A. Schuffert, and R.D. Wood (2003) POLN, a nuclear polA family DNA polymerase homologous to the DNA cross-link sensitivity protein Mus308. J. Biol. Chem. 278:32014-32019 The Drosophila Mus308 gene is unusual in encoding both a family A DNA polymerase domain and a DNA/RNA helicase domain. A mus308 mutation was shown to result in increased sensitivity to DNA cross-linking agents, leading to the hypothesis that Mus308 functions in the repair of DNA interstrand cross-links. Recently a mammalian ortholog of Mus308, POLQ, has been identified. We report here the identification, cloning, and characterization of POLN and its gene product, a new mammalian DNA polymerase also related to Mus308. The human cDNA encodes a protein of 900 amino acid residues. The region starting from residue 419 shares 33% identity (48% similarity) with the equivalent region of Escherichia coli DNA polymerase I. POLN is expressed in human cell lines with numerous alternatively spliced transcripts, and a full-length human coding region that comprises 24 exons within 160 kilobases of genomic DNA. Expression analysis by northern blotting and in situ hybridization showed highest expression of full-length POLN in human and mouse testis. POLN localized to the nucleus when expressed as a enhanced green fluorescent protein (GFP)-tagged protein in human fibroblasts. GFP-tagged recombinant POLN had DNA polymerase activity on activated calf thymus DNA and on a singly primed template.
Marini, F., and R.D. Wood (2002) A human DNA helicase homologous to the DNA cross-link sensitivity protein Mus308. J. Biol. Chem. 277:8716-8723 Repair of DNA interstrand cross-links is a challenging problem for cells. Many human gene products influence sensitivity to DNA cross-linking agents, but the mechanisms of cross-link repair are unknown. In Drosophila melanogaster, the mus308 mutation leads to marked sensitivity to DNA cross-linking agents. The C-terminal portion of the Mus308 polypeptide encodes a DNA polymerase, whereas a putative DNA helicase is encoded by the N-terminal portion. As a step toward isolating proteins involved in DNA cross-link repair, we searched for mammalian genes similar to the DNA helicase portion of Mus308. Human and mouse homologs were isolated from cDNA expression libraries and designated HEL308. Human HEL308 is on chromosome 4q21 and encodes a polypeptide of 1101 amino acids. The protein was expressed in insect cells and purified. HEL308 is a single-stranded DNA-dependent ATPase and DNA helicase. Mutation of a highly conserved lysine to methionine in helicase domain I eliminated both activities. The protein readily displaces 20- to 40-mer duplex oligonucleotides. Displacement of longer substrates was less efficient but was stimulated by the single-stranded DNA-binding protein RPA. Activity was supported by ATP or dATP but not other nucleotide triphosphates. The enzyme translocates on DNA with 3' to 5' polarity and behaves as a multimer upon gel filtration.
Yang, H., I.T. Phan, S. Fitz-Gibbon, M.K. Shivji, R.D. Wood, W.M. Clendenin, E.C. Hyman, and J.H. Miller (2001) A thermostable endonuclease III homolog from the archaeon Pyrobaculum aerophilum. Nucleic Acids Res. 29:604-613 Pyrimidine adducts in cellular DNA arise from modification of the pyrimidine 5,6-double bond by oxidation, reduction or hydration. The biological outcome includes increased mutation rate and potential lethality. A major DNA N:-glycosylase responsible for the excision of modified pyrimidine bases is the base excision repair (BER) glycosylase endonuclease III, for which functional homologs have been identified and characterized in Escherichia coli, yeast and humans. So far, little is known about how hyperthermophilic Archaea cope with such pyrimidine damage. Here we report characterization of an endonuclease III homolog, PaNth, from the hyperthermophilic archaeon Pyrobaculum aerophilum, whose optimal growth temperature is 100 degrees C. The predicted product of 223 amino acids shares significant sequence homology with several [4Fe-4S]-containing DNA N:-glycosylases including E.coli endonuclease III (EcNth). The histidine-tagged recombinant protein was expressed in E.coli and purified. Under optimal conditions of 80-160 mM NaCl and 70 degrees C, PaNth displays DNA glycosylase/ss-lyase activity with the modified pyrimidine base 5,6-dihydrothymine (DHT). This activity is enhanced when DHT is paired with G. Our data, showing the structural and functional similarity between PaNth and EcNth, suggests that BER of modified pyrimidines may be a conserved repair mechanism in Archaea. Conserved amino acid residues are identified for five subfamilies of endonuclease III/UV endonuclease homologs clustered by phylogenetic analysis.
Kuraoka, I., P. Robins, C. Masutani, F. Hanaoka, D. Gasparutto, J. Cadet, R.D. Wood, and T. Lindahl (2001) Oxygen free radical damage to DNA. Translesion synthesis by human DNA polymerase eta and resistance to exonuclease action at cyclopurine deoxynucleoside residues. J. Biol. Chem. 276:49283-49288 Cyclopurine deoxynucleosides are common DNA lesions generated by exposure to reactive oxygen species under hypoxic conditions. The S and R diastereoisomers of cyclodeoxyadenosine on DNA were investigated separately for their ability to block 3' to 5' exonucleases. The mammalian DNA-editing enzyme DNase III (TREX1) was blocked by both diastereoisomers, whereas only the S diastereoisomer was highly efficient in preventing digestion by the exonuclease function of T4 DNA polymerase. Digestion in both cases was frequently blocked one residue before the modified base. Oligodeoxyribonucleotides containing a cyclodeoxyadenosine residue were further employed as templates for synthesis by human DNA polymerase eta (pol eta). pol eta could catalyze translesion synthesis on the R diastereoisomer of cyclodeoxyadenosine. On the S diastereoisomer, pol eta could catalyze the incorporation of one nucleotide opposite the lesion but could not continue elongation. Although pol eta preferentially incorporated dAMP opposite the R diastereoisomer, elongation continued only when dTMP was incorporated, suggesting bypass of this lesion by pol eta with reasonable fidelity. With the S diastereoisomer, pol eta mainly incorporated dAMP or dTMP opposite the lesion but could not elongate even after incorporating a correct nucleotide. These data suggest that the S diastereoisomer may be a more cytotoxic DNA lesion than the R diastereoisomer.
Gearhart, P.J., and R.D. Wood (2001) Emerging links between hypermutation of antibody genes and DNA polymerases. Nat. Rev. Immunol. 1:187-192 Substantial antibody variability is created when nucleotide substitutions are introduced into immunoglobulin variable genes by a controlled process of hypermutation. Evidence points to a mechanism involving DNA repair events at sites of targeted breaks. In vertebrate cells, there are many recently identified DNA polymerases that inaccurately copy templates. Some of these are candidates for enzymes that introduce base changes during hypermutation. Recent research has focused on possible roles for DNA polymerases zeta (POLZ), eta (POLH), iota (POLI), and mu (POLM) in the process. Gaillard, P.H., and R.D. Wood (2001) Activity of individual ERCC1 and XPF subunits in DNA nucleotide excision repair. Nucleic Acids Res. 29:872-879 ERCC1-XPF is a structure-specific nuclease with two subunits, ERCC1 and XPF. The enzyme cuts DNA at junctions where a single strand moves 5' to 3' away from a branch point with duplex DNA. This activity has a central role in nucleotide excision repair (NER), DNA cross-link repair and recombination. To dissect the activities of the nuclease it is necessary to investigate the subunits individually, as studies of the enzyme so far have only used the heterodimeric complex. We produced recombinant ERCC1 and XPF separately in Escherichia coli as soluble proteins. Activity was monitored by a sensitive dual incision assay for NER by complementation of cell extracts. XPF and ERCC1 are unstable in mammalian cells in the absence of their partners but we found, surprisingly, that ERCC1 alone could confer some repair to extracts from ERCC1-defective cells. A version of ERCC1 lacking the first 88 non- conserved amino acids was also functional. This indicated that a small amount of active XPF was present in ERCC1 extracts, and immunoassays showed this to be the case. Some repair in XPF-defective extracts could be achieved by adding ERCC1 and XPF proteins together, but not by adding only XPF. The results show for the first time that functional ERCC1-XPF can be formed from separately produced subunits. Protein sequence comparison revealed similarity between the ERCC1 family and the C-terminal region of the XPF family, including the regions of both proteins that are necessary for the ERCC1-XPF heterodimeric interaction. This suggests that the ERCC1 and XPF families are related via an ancient duplication.
Wood, R.D., M. Mitchell, J. Sgouros, and T. Lindahl (2001) Human DNA repair genes. Science 291:1284-1289 Cellular DNA is subjected to continual attack, both by reactive species inside cells and by environmental agents. Toxic and mutagenic consequences are minimized by distinct pathways of repair, and 130 known human DNA repair genes are described here. Notable features presently include four enzymes that can remove uracil from DNA, seven recombination genes related to RAD51, and many recently discovered DNA polymerases that bypass damage, but only one system to remove the main DNA lesions induced by ultraviolet light. More human DNA repair genes will be found by comparison with model organisms and as common folds in three-dimensional protein structures are determined. Modulation of DNA repair should lead to clinical applications including improvement of radiotherapy and treatment with anticancer drugs and an advanced understanding of the cellular aging process. Araujo, S.J., E.A. Nigg, and R.D. Wood (2001) Strong functional interactions of TFIIH with XPC and XPG in human DNA nucleotide excision repair, without a preassembled repairosome. Mol. Cell. Biol. 21:2281-2291 In mammalian cells, the core factors involved in the damage recognition and incision steps of DNA nucleotide excision repair are XPA, TFIIH complex, XPC-HR23B, replication protein A (RPA), XPG, and ERCC1-XPF. Many interactions between these components have been detected, using different physical methods, in human cells and for the homologous factors in Saccharomyces cerevisiae. Several human nucleotide excision repair (NER) complexes, including a high-molecular-mass repairosome complex, have been proposed. However, there have been no measurements of activity of any mammalian NER protein complex isolated under native conditions. In order to assess relative strengths of interactions between NER factors, we captured TFIIH from cell extracts with an anti- cdk7 antibody, retaining TFIIH in active form attached to magnetic beads. Coimmunoprecipitation of other NER proteins was then monitored functionally in a reconstituted repair system with purified proteins. We found that all detectable TFIIH in gently prepared human cell extracts was present in the intact nine-subunit form. There was no evidence for a repair complex that contained all of the NER components. At low ionic strength TFIIH could associate with functional amounts of each NER factor except RPA. At physiological ionic strength, TFIIH associated with significant amounts of XPC-HR23B and XPG but not other repair factors. The strongest interaction was between TFIIH and XPC- HR23B, indicating a coupled role of these proteins in early steps of repair. A panel of antibodies was used to estimate that there are on the order of 10(5) molecules of each core NER factor per HeLa cell.
Winkler, G.S., S.J. Araujo, U. Fiedler, W. Vermeulen, F. Coin, J.M. Egly, J.H. Hoeijmakers, R.D. Wood, H.T. Timmers, and G. Weeda (2000) TFIIH with inactive XPD helicase functions in transcription initiation but is defective in DNA repair. J. Biol. Chem. 275:4258-4266 TFIIH is a multisubunit protein complex involved in RNA polymerase II transcription and nucleotide excision repair, which removes a wide variety of DNA lesions including UV-induced photoproducts. Mutations in the DNA-dependent ATPase/helicase subunits of TFIIH, XPB and XPD, are associated with three inherited syndromes as follows: xeroderma pigmentosum with or without Cockayne syndrome and trichothiodystrophy. By using epitope-tagged XPD we purified mammalian TFIIH carrying a wild type or an active-site mutant XPD subunit. Contrary to XPB, XPD helicase activity was dispensable for in vitro transcription, catalytic formation of trinucleotide transcripts, and promoter opening. Moreover, in contrast to XPB, microinjection of mutant XPD cDNA did not interfere with in vivo transcription. These data show directly that XPD activity is not required for transcription. However, during DNA repair, neither 5' nor 3' incisions in defined positions around a DNA adduct were detected in the presence of TFIIH containing inactive XPD, although substantial damage-dependent DNA synthesis was induced by the presence of mutant XPD both in cells and cell extracts. The aberrant damage- dependent DNA synthesis caused by the mutant XPD does not lead to effective repair, consistent with the discrepancy between repair synthesis and survival in cells from a number of XP-D patients.
George, H., I. Kuraoka, D.A. Nauman, W.R. Kobertz, R.D. Wood, and S.C. West (2000) RuvAB-mediated branch migration does not involve extensive DNA opening within the RuvB hexamer. Curr. Biol. 10:103-106 The Escherichia coli RuvA and RuvB proteins promote the branch migration of Holliday junctions during the late stages of homologous recombination and DNA repair (reviewed in [1]). Biochemical and structural studies of the RuvAB-Holliday junction complex have shown that RuvA binds directly to the Holliday junction [2] [3] [4] [5] [6] and acts as a specificity factor that promotes the targeting of RuvB [7] [8], a hexameric ring protein that drives branch migration [9] [10] [11]. Electron microscopic visualisation of the RuvAB complex revealed that RuvA is flanked by two RuvB hexamers, which bind DNA arms that lie diametrically opposed across the junction [8]. ATP-dependent branch migration occurs as duplex DNA is pumped out through the centre of each ring. Because RuvB possesses well-conserved helicase motifs and RuvAB exhibits a 5'-3' DNA helicase activity in vitro [12], the mechanism of branch migration is thought to involve DNA opening within the RuvB ring, which provides a single strand for the unidirectional translocation of the protein along DNA. We have investigated whether the RuvB ring can translocate along duplex DNA containing a site- directed interstrand psoralen crosslink. Surprisingly, we found that the crosslink failed to inhibit branch migration. We interpret these data as evidence against a base-by-base tracking model and suggest that extensive DNA opening within the RuvB ring is not required for DNA translocation by RuvB. Araujo, S.J., F. Tirode, F. Coin, H. Pospiech, J.E. Syvaoja, M. Stucki, U. Hubscher, J.M. Egly, and R.D. Wood (2000) Nucleotide excision repair of DNA with recombinant human proteins: definition of the minimal set of factors, active forms of TFIIH, and modulation by CAK. Genes Dev. 14:349-359 During human nucleotide excision repair, damage is recognized, two incisions are made flanking a DNA lesion, and residues are replaced by repair synthesis. A set of proteins required for repair of most lesions is RPA, XPA, TFIIH, XPC-hHR23B, XPG, and ERCC1-XPF, but additional components have not been excluded. The most complex and difficult to analyze factor is TFIIH, which has a 6-subunit core (XPB, XPD, p44, p34, p52, p62) and a 3-subunit kinase (CAK). TFIIH has roles both in basal transcription initiation and in DNA repair, and several inherited human disorders are associated with mutations in TFIIH subunits. To identify the forms of TFIIH that can function in repair, recombinant XPA, RPA, XPC-hHR23B, XPG, and ERCC1-XPF were combined with TFIIH fractions purified from HeLa cells. Repair activity coeluted with the peak of TFIIH and with transcription activity. TFIIH from cells with XPB or XPD mutations was defective in supporting repair, whereas TFIIH from spinal muscular atrophy cells with a deletion of one p44 gene was active. Recombinant TFIIH also functioned in repair, both a 6- and a 9- subunit form containing CAK. The CAK kinase inhibitor H-8 improved repair efficiency, indicating that CAK can negatively regulate NER by phosphorylation. The 15 recombinant polypeptides define the minimal set of proteins required for dual incision of DNA containing a cisplatin adduct. Complete repair was achieved by including highly purified human DNA polymerase delta or epsilon, PCNA, RFC, and DNA ligase I in reaction mixtures, reconstituting adduct repair for the first time with recombinant incision factors and human replication proteins.
Batty, D.P., and R.D. Wood (2000) Damage recognition in nucleotide excision repair of DNA. Gene 241:193-204 Nucleotide excision repair (NER) is found throughout nature, in eubacteria, eukaryotes and archaea. In human cells it is the main pathway for the removal of damage caused by UV light, but it also acts on a wide variety of other bulky helix-distorting lesions caused by chemical mutagens. An ongoing challenge is to understand how a site of DNA damage is located during NER and distinguished from non-damaged sites. This article reviews information on damage recognition in mammalian cells and the bacterium Escherichia coli. In mammalian cells the XPC-hHR23B, XPA, RPA and TFIIH factors may all have a role in damage recognition. XPC-hHR23B has the strongest affinity for damaged DNA in some assays, as does the similar budding yeast complex Rad4- Rad23. There is current discussion as to whether XPC or XPA acts first in the repair process to recognise damage or distortions. TFIIH may play a role in distinguishing the damaged strand from the non-damaged one, if translocation along a DNA strand by the TFIIH DNA helicases is interrupted by encountering a lesion. The recognition and incision steps of human NER use 15 to 18 polypeptides, whereas E. coli requires only three proteins to obtain a similar result. Despite this, many remarkable similarities in the NER mechanism have emerged between eukaryotes and bacteria. These include use of a distortion-recognition factor, a strand separating helicase to create an open preincision complex, participation of structure-specific endonucleases and the lack of a need for certain factors when a region containing damage is already sufficiently distorted. Berneburg, M., J.E. Lowe, T. Nardo, S. Araujo, M.I. Fousteri, M.H. Green, J. Krutmann, R.D. Wood, M. Stefanini, and A.R. Lehmann (2000) UV damage causes uncontrolled DNA breakage in cells from patients with combined features of XP-D and Cockayne syndrome. EMBO J 19:1157-1166 Nucleotide excision repair (NER) removes damage from DNA in a tightly regulated multiprotein process. Defects in NER result in three different human disorders, xeroderma pigmentosum (XP), trichothiodystrophy (TTD) and Cockayne syndrome (CS). Two cases with the combined features of XP and CS have been assigned to the XP-D complementation group. Despite their extreme UV sensitivity, these cells appeared to incise their DNA as efficiently as normal cells in response to UV damage. These incisions were, however, uncoupled from the rest of the repair process. Using cell-free extracts, we were unable to detect any incision activity in the neighbourhood of the damage. When irradiated plasmids were introduced into unirradiated XP- D/CS cells, the ectopically introduced damage triggered the induction of breaks in the undamaged genomic DNA. XP-D/CS cells thus have a unique response to sensing UV damage, which results in the introduction of breaks into the DNA at sites distant from the damage. We propose that it is these spurious breaks that are responsible for the extreme UV sensitivity of these cells.
Kuraoka, I., C. Bender, A. Romieu, J. Cadet, R.D. Wood, and T. Lindahl (2000) Removal of oxygen free-radical-induced 5',8-purine cyclodeoxynucleosides from DNA by the nucleotide excision-repair pathway in human cells. Proc Natl Acad Sci U S A 97:3832-3837 Exposure of cellular DNA to reactive oxygen species generates several classes of base lesions, many of which are removed by the base excision- repair pathway. However, the lesions include purine cyclodeoxynucleoside formation by intramolecular crosslinking between the C-8 position of adenine or guanine and the 5' position of 2- deoxyribose. This distorting form of DNA damage, in which the purine is attached by two covalent bonds to the sugar-phosphate backbone, occurs as distinct diastereoisomers. It was observed here that both diastereoisomers block primer extension by mammalian and microbial replicative DNA polymerases, using DNA with a site-specific purine cyclodeoxynucleoside residue as template, and consequently appear to be cytotoxic lesions. Plasmid DNA containing either the 5'R or 5'S form of 5',8-cyclo-2-deoxyadenosine was a substrate for the human nucleotide excision-repair enzyme complex. The R diastereoisomer was more efficiently repaired than the S isomer. No correction of the lesion by direct damage reversal or base excision repair was detected. Dual incision around the lesion depended on the core nucleotide excision- repair protein XPA. In contrast to several other types of oxidative DNA damage, purine cyclodeoxynucleosides are chemically stable and would be expected to accumulate at a slow rate over many years in the DNA of nonregenerating cells from xeroderma pigmentosum patients. High levels of this form of DNA damage might explain the progressive neurodegeneration seen in XPA individuals.
Winter, D.B., Q.H. Phung, R.D. Wood, and P.J. Gearhart (2000) Differential expression of DNA polymerase epsilon in resting and activated B lymphocytes is consistent with an in vivo role in replication and not repair. Mol. Immunol. 37:125-131 DNA polymerases may be differentially expressed by cells during periods of quiescence and proliferation. Murine B cells are an ideal population to study because their division time varies widely in vivo, and different subsets can be easily isolated. Consequently, we analyzed RNA from resting cells (B220(+)peanut agglutinin(-)) and activated germinal center cells (B220(+)peanut agglutinin(+)) from spleens by reverse transcriptase-PCR using primers for five nuclear polymerases and their associated subunits. Gel analyses of the amplified products showed that the rapidly-dividing germinal center B cells expressed DNA polymerases alpha, beta, delta, epsilon, and zeta. The resting B cells did not express polymerases alpha or epsilon at detectable levels, although they did express polymerases beta, delta, and zeta. Thus, polymerase epsilon, as well as alpha, appears to have a primary role in chromosomal replication of murine B lymphocytes. Further, the lack of expression of polymerase epsilon in resting cells indicates that this enzyme is not used in any DNA repair pathways by these cells. The expression of polymerase zeta by resting cells suggests that it has another role in DNA repair, perhaps recombination, in addition to its function of bypassing damage during chromosomal replication. Batty, D., V. Rapic'-Otrin, A.S. Levine, and R.D. Wood (2000) Stable binding of human XPC complex to irradiated DNA confers strong discrimination for damaged sites. J. Mol. Biol. 300:275-290 Nucleotide excision repair (NER) of DNA damage requires an efficient means of discrimination between damaged and non-damaged DNA. Cells from humans with xeroderma pigmentosum group C do not perform NER in the bulk of the genome and are corrected by XPC protein, which forms a complex with hHR23B protein. This complex preferentially binds to some types of damaged DNA, but the extent of discrimination in comparison to other NER proteins has not been clear. Recombinant XPC, hHR23B, and XPC- hHR23B complex were purified. In a reconstituted repair system, hHR23B stimulated XPC activity tenfold. Electrophoretic mobility-shift competition measurements revealed a 400-fold preference for binding of XPC-hHR23B to UV damaged over non-damaged DNA. This damage preference is much greater than displayed by the XPA protein. The discrimination power is similar to that determined here in parallel for the XP-E factor UV-DDB, despite the considerably greater molar affinity of UV- DDB for DNA. Binding of XPC-hHR23B to UV damaged DNA was very fast. Damaged DNA-XPC-hHR23B complexes were stable, with half of the complexes remaining four hours after challenge with excess UV-damaged DNA at 30 degrees C. XPC-hHR23B had a higher level of affinity for (6- 4) photoproducts than cyclobutane pyrimidine dimers, and some affinity for DNA treated with cisplatin and alkylating agents. XPC-hHR23B could bind to single-stranded M13 DNA, but only poorly to single-stranded homopolymers. The strong preference of XPC complex for structures in damaged duplex DNA indicates its importance as a primary damage recognition factor in non-transcribed DNA during human NER. Kuraoka, I., W.R. Kobertz, R.R. Ariza, M. Biggerstaff, J.M. Essigmann, and R.D. Wood (2000) Repair of an interstrand DNA cross-link initiated by ERCC1-XPF repair/recombination nuclease. J. Biol. Chem. 275:26632-26636 Interstrand DNA cross-link damage is a severe challenge to genomic integrity. Nucleotide excision repair plays some role in the repair of DNA cross-links caused by psoralens and other agents. However, in mammalian cells there is evidence that the ERCC1-XPF nuclease has a specialized additional function during interstrand DNA cross-link repair, beyond its role in nucleotide excision repair. We placed a psoralen monoadduct or interstrand cross-link in a duplex, 4-6 bases from a junction with unpaired DNA. ERCC1-XPF endonucleolytically cleaved within the duplex on either side of the adduct, on the strand having an unpaired 3' tail. Cross-links that were cleaved only on the 5' side were purified and reincubated with ERCC1-XPF. A second cleavage was then observed on the 3' side. Relevant partially unwound structures near a cross-link may be expected to arise frequently, for example at stalled DNA replication forks. The results show that the single enzyme ERCC1-XPF can release one arm of a cross-link and suggest a novel mechanism for interstrand cross-link repair.
Wittschieben, J., M.K. Shivji, E. Lalani, M.A. Jacobs, F. Marini, P.J. Gearhart, I. Rosewell, G. Stamp, and R.D. Wood (2000) Disruption of the developmentally regulated Rev3l gene causes embryonic lethality. Curr. Biol. 10:1217-1220 The REV3 gene encodes the catalytic subunit of DNA polymerase (pol) zeta, which can replicate past certain types of DNA lesions [1]. Saccharomyces cerevisiae rev3 mutants are viable and have lower rates of spontaneous and DNA-damage-induced mutagenesis [2]. Reduction in the level of Rev31, the presumed catalytic subunit of mammalian pol zeta, decreased damage-induced mutagenesis in human cell lines [3]. To study the function of mammalian Rev31, we inactivated the gene in mice. Two exons containing conserved DNA polymerase motifs were replaced by a cassette encoding G418 resistance and beta-galactosidase, under the control of the Rev3l promoter. Surprisingly, disruption of Rev3l caused mid-gestation embryonic lethality, with the frequency of Rev3l(-/-) embryos declining markedly between 9.5 and 12.5 days post coitum (dpc). Rev3l(-/-) embryos were smaller than their heterozygous littermates and showed retarded development. Tissues in many areas were disorganised, with significantly reduced cell density. Rev3l expression, traced by beta-galactosidase staining, was first detected during early somitogenesis and gradually expanded to other tissues of mesodermal origin, including extraembryonic membranes. Embryonic death coincided with the period of more widely distributed Rev3l expression. The data demonstrate an essential function for murine Rev31 and suggest that bypass of specific types of DNAlesions by pol zeta is essential for cell viability during embryonic development in mammals. Klungland, A., M. Hoss, D. Gunz, A. Constantinou, S.G. Clarkson, P.W. Doetsch, P.H. Bolton, R.D. Wood, and T. Lindahl (1999) Base excision repair of oxidative DNA damage activated by XPG protein. Mol. Cell 3:33-42 Oxidized pyrimidines in DNA are removed by a distinct base excision repair pathway initiated by the DNA glycosylase--AP lyase hNth1 in human cells. We have reconstituted this single-residue replacement pathway with recombinant proteins, including the AP endonuclease HAP1/APE, DNA polymerase beta, and DNA ligase III-XRCC1 heterodimer. With these proteins, the nucleotide excision repair enzyme XPG serves as a cofactor for the efficient function of hNth1. XPG protein promotes binding of hNth1 to damaged DNA. The stimulation of hNth1 activity is retained in XPG catalytic site mutants inactive in nucleotide excision repair. The data support the model that development of Cockayne syndrome in XP-G patients is related to inefficient excision of endogenous oxidative DNA damage. Constantinou, A., D. Gunz, E. Evans, P. Lalle, P.A. Bates, R.D. Wood, and S.G. Clarkson (1999) Conserved residues of human XPG protein important for nuclease activity and function in nucleotide excision repair. J. Biol. Chem. 274:5637-5648 The human XPG endonuclease cuts on the 3' side of a DNA lesion during nucleotide excision repair. Mutations in XPG can lead to the disorders xeroderma pigmentosum (XP) and Cockayne syndrome. XPG shares sequence similarities in two regions with a family of structure-specific nucleases and exonucleases. To begin defining its catalytic mechanism, we changed highly conserved residues and determined the effects on the endonuclease activity of isolated XPG, its function in open complex formation and dual incision reconstituted with purified proteins, and its ability to restore cellular resistance to UV light. The substitution A792V present in two XP complementation group G (XP-G) individuals reduced but did not abolish endonuclease activity, explaining their mild clinical phenotype. Isolated XPG proteins with Asp-77 or Glu-791 substitutions did not cleave DNA. In the reconstituted repair system, alanine substitutions at these positions permitted open complex formation but were inactive for 3' cleavage, whereas D77E and E791D proteins retained considerable activity. The function of each mutant protein in the reconstituted system was mirrored by its ability to restore UV resistance to XP-G cell lines. Hydrodynamic measurements indicated that XPG exists as a monomer in high salt conditions, but immunoprecipitation of intact and truncated XPG proteins showed that XPG polypeptides can interact with each other, suggesting dimerization as an element of XPG function. The mutation results define critical residues in the catalytic center of XPG and strongly suggest that key features of the strand cleavage mechanism and active site structure are shared by members of the nuclease family.
Koberle, B., J.R. Masters, J.A. Hartley, and R.D. Wood (1999) Defective repair of cisplatin-induced DNA damage caused by reduced XPA protein in testicular germ cell tumours. Curr. Biol. 9:273-276 Metastatic cancer in adults usually has a fatal outcome. In contrast, advanced testicular germ cell tumours are cured in over 80% of patients using cisplatin-based combination chemotherapy [1]. An understanding of why these cells are sensitive to chemotherapeutic drugs is likely to have implications for the treatment of other types of cancer. Earlier measurements indicate that testis tumour cells are hypersensitive to cisplatin and have a low capacity to remove cisplatin-induced DNA damage from the genome [2] [3]. We have investigated the nucleotide excision repair (NER) capacity of extracts from the well-defined 833K and GCT27 human testis tumour cell lines. Both had a reduced ability to carry out the incision steps of NER in comparison with extracts from known repair-proficient cells. Immunoblotting revealed that the testis tumour cells had normal amounts of most NER proteins, but low levels of the xeroderma pigmentosum group A protein (XPA) and the ERCC1-XPF endonuclease complex. Addition of XPA specifically conferred full NER capacity on the testis tumour extracts. These results show that a low XPA level in the testis tumour cell lines is sufficient to explain their poor ability to remove cisplatin adducts from DNA and might be a major reason for the high cisplatin sensitivity of testis tumours. Targeted inhibition of XPA could sensitise other types of cells and tumours to cisplatin and broaden the usefulness of this chemotherapeutic agent. Wood, R.D. (1999) DNA damage recognition during nucleotide excision repair in mammalian cells. Biochimie 81:39-44 For the bulk of mammalian DNA, the core protein factors needed for damage recognition and incision during nucleotide excision repair (NER) are the XPA protein, the heterotrimeric RPA protein, the 6 to 9-subunit TFIIH, the XPC-hHR23B complex, the XPG nuclease, and the ERCC1-XPF nuclease. With varying efficiencies, NER can repair a very wide range of DNA adducts, from bulky helical distortions to subtle modifications on sugar residues. Several of the NER factors have an affinity for damaged DNA. The strongest binding factor appears to be XPC-hHR23B but preferential binding to damage is also a property of XPA, RPA, and components of TFIIH. It appears that in order to be repaired by NER, an adduct in DNA must have two features: it must create a helical distortion, and there must be a change in DNA chemistry. Initial recognition of the distortion is the most likely function for XPC- hHR23B and perhaps XPA and RPA, whereas TFIIH is well-suited to locate the damaged DNA strand by locating altered DNA chemistry that blocks translocation of the XPB and XPD components. Sgouros, J., P.H. Gaillard, and R.D. Wood (1999) A relationship between a DNA-repair/recombination nuclease family and archaeal helicases. Trends Biochem Sci. 24:95-97 The main pathway by which mammalian cells remove DNA damage caused by UV light and some other mutagens is nucleotide excision repair (NER). The best characterised components of the human NER process are those proteins defective in the inherited disorder xeroderma pigmentosum (XP). The proteins known to be involved in the first steps of the NER reaction (damage recognition and incision-excision) are heterotrimeric RPA, XPA, the 6 to 9 subunit TFIIH, XPC-hHR23B, XPG, and ERCC1-XPF. Many interactions between these proteins have been found in recent years using different methods both in mammalian cells and for the homologous proteins in yeast. There are virtually no quantitative measurements of the relative strengths of these interactions. Higher order associations between these proteins in solution and even the existence of a complete "repairosome" complex have been reported, which would have implications both for the mechanism of repair and for the interplay between NER and other cellular processes. Nevertheless, evidence for a completely pre-assembled functional repairosome in solution is inconclusive and the order of action of repair factors on damaged DNA is uncertain. Wood, R.D. (1999) DNA repair. Variants on a theme. Nature 399:639-640 The main pathway by which mammalian cells remove DNA damage caused by UV light and some other mutagens is nucleotide excision repair (NER). The best characterised components of the human NER process are those proteins defective in the inherited disorder xeroderma pigmentosum (XP). The proteins known to be involved in the first steps of the NER reaction (damage recognition and incision-excision) are heterotrimeric RPA, XPA, the 6 to 9 subunit TFIIH, XPC-hHR23B, XPG, and ERCC1-XPF. Many interactions between these proteins have been found in recent years using different methods both in mammalian cells and for the homologous proteins in yeast. There are virtually no quantitative measurements of the relative strengths of these interactions. Higher order associations between these proteins in solution and even the existence of a complete "repairosome" complex have been reported, which would have implications both for the mechanism of repair and for the interplay between NER and other cellular processes. Nevertheless, evidence for a completely pre-assembled functional repairosome in solution is inconclusive and the order of action of repair factors on damaged DNA is uncertain. Biggerstaff, M., and R.D. Wood (1999) Assay for nucleotide excision repair protein activity using fractionated cell extracts and UV-damaged plasmid DNA. Methods Mol. Biol. 113:357-372 The main pathway by which mammalian cells remove DNA damage caused by UV light and some other mutagens is nucleotide excision repair (NER). The best characterised components of the human NER process are those proteins defective in the inherited disorder xeroderma pigmentosum (XP). The proteins known to be involved in the first steps of the NER reaction (damage recognition and incision-excision) are heterotrimeric RPA, XPA, the 6 to 9 subunit TFIIH, XPC-hHR23B, XPG, and ERCC1-XPF. Many interactions between these proteins have been found in recent years using different methods both in mammalian cells and for the homologous proteins in yeast. There are virtually no quantitative measurements of the relative strengths of these interactions. Higher order associations between these proteins in solution and even the existence of a complete "repairosome" complex have been reported, which would have implications both for the mechanism of repair and for the interplay between NER and other cellular processes. Nevertheless, evidence for a completely pre-assembled functional repairosome in solution is inconclusive and the order of action of repair factors on damaged DNA is uncertain. Shivji, M.K., J.G. Moggs, I. Kuraoka, and R.D. Wood (1999) Dual-incision assays for nucleotide excision repair using DNA with a lesion at a specific site. Methods Mol Biol 113:373-392 The main pathway by which mammalian cells remove DNA damage caused by UV light and some other mutagens is nucleotide excision repair (NER). The best characterised components of the human NER process are those proteins defective in the inherited disorder xeroderma pigmentosum (XP). The proteins known to be involved in the first steps of the NER reaction (damage recognition and incision-excision) are heterotrimeric RPA, XPA, the 6 to 9 subunit TFIIH, XPC-hHR23B, XPG, and ERCC1-XPF. Many interactions between these proteins have been found in recent years using different methods both in mammalian cells and for the homologous proteins in yeast. There are virtually no quantitative measurements of the relative strengths of these interactions. Higher order associations between these proteins in solution and even the existence of a complete "repairosome" complex have been reported, which would have implications both for the mechanism of repair and for the interplay between NER and other cellular processes. Nevertheless, evidence for a completely pre-assembled functional repairosome in solution is inconclusive and the order of action of repair factors on damaged DNA is uncertain. Araujo, S.J., and R.D. Wood (1999) Protein complexes in nucleotide excision repair. Mutat Res 435:23-33 The main pathway by which mammalian cells remove DNA damage caused by UV light and some other mutagens is nucleotide excision repair (NER). The best characterised components of the human NER process are those proteins defective in the inherited disorder xeroderma pigmentosum (XP). The proteins known to be involved in the first steps of the NER reaction (damage recognition and incision-excision) are heterotrimeric RPA, XPA, the 6 to 9 subunit TFIIH, XPC-hHR23B, XPG, and ERCC1-XPF. Many interactions between these proteins have been found in recent years using different methods both in mammalian cells and for the homologous proteins in yeast. There are virtually no quantitative measurements of the relative strengths of these interactions. Higher order associations between these proteins in solution and even the existence of a complete "repairosome" complex have been reported, which would have implications both for the mechanism of repair and for the interplay between NER and other cellular processes. Nevertheless, evidence for a completely pre-assembled functional repairosome in solution is inconclusive and the order of action of repair factors on damaged DNA is uncertain. Lindahl, T., and R.D. Wood (1999) Quality control by DNA repair. Science 286:1897-1905 Faithful maintenance of the genome is crucial to the individual and to species. DNA damage arises from both endogenous sources such as water and oxygen and exogenous sources such as sunlight and tobacco smoke. In human cells, base alterations are generally removed by excision repair pathways that counteract the mutagenic effects of DNA lesions. This serves to maintain the integrity of the genetic information, although not all of the pathways are absolutely error-free. In some cases, DNA damage is not repaired but is instead bypassed by specialized DNA polymerases. Lin, Y.L., M.K. Shivji, C. Chen, R. Kolodner, R.D. Wood, and A. Dutta (1998) The evolutionarily conserved zinc finger motif in the largest subunit of human replication protein A is required for DNA replication and mismatch repair but not for nucleotide excision repair. J Biol Chem 273:1453-1461 The largest subunit of the replication protein A (RPA) contains an evolutionarily conserved zinc finger motif that lies outside of the domains required for binding to single-stranded DNA or forming the RPA holocomplex. In previous studies, we showed that a point mutation in this motif (RPAm) cannot support SV40 DNA replication. We have now investigated the role of this motif in several steps of DNA replication and in two DNA repair pathways. RPAm associates with T antigen, assists the unwinding of double-stranded DNA at an origin of replication, stimulates DNA polymerases alpha and delta, and supports the formation of the initial short Okazaki fragments. However, the synthesis of a leading strand and later Okazaki fragments is impaired. In contrast, RPAm can function well during the incision step of nucleotide excision repair and in a full repair synthesis reaction, with either UV-damaged or cisplatin-adducted DNA. Two deletion mutants of the Rpa1 subunit (eliminating amino acids 1-278 or 222-411) were not functional in nucleotide excision repair. We report for the first time that wild type RPA is required for a mismatch repair reaction in vitro. Neither the deletion mutants nor RPAm can support this reaction. Therefore, the zinc finger of the largest subunit of RPA is required for a function that is essential for DNA replication and mismatch repair but not for nucleotide excision repair.
Rapic, O.t.r.i.n., I. Kuraoka, T. Nardo, M. McLenigan, A.P. Eker, M. Stefanini, A.S. Levine, and R.D. Wood (1998) Relationship of the xeroderma pigmentosum group E DNA repair defect to the chromatin and DNA binding proteins UV-DDB and replication protein A. Mol Cell Biol 18:3182-3190 Cells from complementation groups A through G of the heritable sun- sensitive disorder xeroderma pigmentosum (XP) show defects in nucleotide excision repair of damaged DNA. Proteins representing groups A, B, C, D, F, and G are subunits of the core recognition and incision machinery of repair. XP group E (XP-E) is the mildest form of the disorder, and cells generally show about 50% of the normal repair level. We investigated two protein factors previously implicated in the XP-E defect, UV-damaged DNA binding protein (UV-DDB) and replication protein A (RPA). Three newly identified XP-E cell lines (XP23PV, XP25PV, and a line formerly classified as an XP variant) were defective in UV-DDB binding activity but had levels of RPA in the normal range. The XP-E cell extracts did not display a significant nucleotide excision repair defect in vitro, with either UV-irradiated DNA or a uniquely placed cisplatin lesion used as a substrate. Purified UV-DDB protein did not stimulate repair of naked DNA by DDB- XP-E cell extracts, but microinjection of the protein into DDB- XP-E cells could partially correct the repair defect. RPA stimulated repair in normal, XP-E, or complemented extracts from other XP groups, and so the effect of RPA was not specific for XP-E cell extracts. These data strengthen the connection between XP-E and UV-DDB. Coupled with previous results, the findings suggest that UV-DDB has a role in the repair of DNA in chromatin.
Wood, R.D. (1998) DNA repair: knockouts still mutating after first round. Curr Biol 8:R757-R760 Recent studies have investigated whether particular DNA repair pathways are involved in the somatic hypermutation mechanism that increases antibody diversity. The primary mutation mechanism still functions in mice carrying knockouts of all repair genes examined, but mismatch repair defects affect the final outcome. Shivji, M.K., E. Ferrari, K. Ball, U. Hubscher, and R.D. Wood (1998) Resistance of human nucleotide excision repair synthesis in vitro to p21Cdn1. Oncogene 17:2827-2838 The p21Cdn1 protein (cip1/waf1/sdi1) plays an important role as an inhibitor of mammalian cell proliferation in response to DNA damage. By interacting with and inhibiting the function of cyclin-Cdk complexes, p21 can block entry into S phase. p21 can also directly inhibit replicative DNA synthesis by binding to the DNA polymerase sliding clamp factor PCNA. When cells are damaged and p21 is induced, DNA nucleotide excision repair (NER) continues, even though this pathway is PCNA-dependent. We investigated features of p21-resistant NER using human cell extracts. A direct end-labelling approach was used to measure the excision of damaged oligonucleotides by NER and no inhibition by p21 was found. By contrast, filling of the approximately 30 nt gaps created by NER could be inhibited by pre-binding p21 to PCNA, but only when gap filling was uncoupled from incision. Binding p21 to PCNA could also inhibit filling of model 30 nt gaps by both purified DNA polymerases delta and epsilon. When p21 was incubated in a cell extract before addition of PCNA, inhibition of repair synthesis was gradually relieved with time. This incubation gives p21 the opportunity to associate with other targets. As p21 blocks association of DNA polymerases with PCNA but does not prevent loading of PCNA onto DNA, repair gap filling can occur rapidly as soon as p21 dissociates from PCNA. A synthetic PCNA-binding p21 peptide was an efficient inhibitor of NER synthesis in cell extracts. Yagi, T., R.D. Wood, and H. Takebe (1997) A low content of ERCC1 and a 120 kDa protein is a frequent feature of group F xeroderma pigmentosum fibroblast cells. Mutagenesis 12:41-44 The ERCC1 protein has been predicted to form part of a tight complex with a protein partner, the yet-unidentified XPF/ERCC4 protein, in normal human cells. We used an anti-ERCC1 antibody to detect the complex by immunoprecipitation and immunoblotting. The amount of ERCC1 protein expressed in five different XP-F cell strains was 1/ 5-1/34 of that of the protein in normal and XP cell strains representing other complementation groups. A 120 kDa protein was co-immunoprecipitated with ERCC1 by the anti-ERCC1 antibody, and the amount of the 120 kDa protein in XP-F cell strains was 1/5-1/8 of that of the protein in normal and XP cell strains representing other complementation groups. The XPA protein was not co-immunoprecipitated with ERCC1 in any cell strain. These results demonstrate that a low level of ERCC1 and the 120 kDa protein is a frequent feature of XP-F cell extracts and that a lower amount of a complex between these proteins occurs in XP-F cells than in normal cells. Moggs, J.G., D.E. Szymkowski, M. Yamada, P. Karran, and R.D. Wood (1997) Differential human nucleotide excision repair of paired and mispaired cisplatin-DNA adducts. Nucleic Acids Res 25:480-491 In order to understand the action of the chemotherapeutic drug cisplatin, it is necessary to determine why some types of cisplatin-DNA intrastrand crosslinks are repaired better than others. Using cell extracts and circular duplex DNA, we compared nucleotide excision repair of uniquely placed 1,2-GG, 1,2-AG, and 1,3-GTG cisplatin- crosslinks, and a 2-acetylaminofluorene lesion. The 1,3 crosslink and the acetylaminofluorene lesion were repaired by normal cell extracts approximately 15-20 fold better than the 1,2 crosslinks. No evidence was found for selective shielding of 1,2 cisplatin crosslinks from repair by cellular proteins. Fractionation of cell extracts to remove putative shielding proteins did not improve repair of the 1,2-GG crosslink, and cell extracts did not selectively inhibit access of UvrABC incision nuclease to 1,2-GG crosslinks. The poorer repair of 1,2 crosslinks in comparison to the 1,3 crosslink is more likely a consequence of different structural alterations of the DNA helix. In support of this, a 1,2-GG-cisplatin crosslink was much better repaired when it was opposite one or two non-complementary thymines. Extracts from cells defective in the hMutSalpha mismatch binding activity also showed preferential repair of the 1,3 crosslink over the 1,2 crosslink, and increased repair of the 1,2 adduct when opposite thymines, showing that hMutSalphais not involved in the differential NER of these substrates in vitro. Mismatched cisplatin adducts could arise by translesion DNA synthesis, and improved repair of such adducts could promote cisplatin-induced mutagenesis in some cases.
Evans, E., J. Fellows, A. Coffer, and R.D. Wood (1997) Open complex formation around a lesion during nucleotide excision repair provides a structure for cleavage by human XPG protein. EMBO J 16:625-638 Human XPG nuclease makes the 3' incision during nucleotide excision repair of DNA. The enzyme cleaves model DNA bubble structures specifically near the junction of unpaired DNA with a duplex region. It is not yet known, however, whether an unpaired structure is an intermediate during actual DNA repair. We find here that XPG requires opening of >5 bp for efficient cleavage. To seek direct evidence for formation of an open structure around a lesion in DNA during a nucleotide excision repair reaction in vitro, KMnO4 footprinting experiments were performed on a damaged DNA molecule bearing a uniquely placed cisplatin adduct. An unwound open complex spanning approximately 25 nucleotides was observed that extended to the positions of 5' and 3' incision sites and was dependent on XPA protein and on ATP. Opening during repair occurred prior to strand incision by XPG.
Wood, R.D., and M.K. Shivji (1997) Which DNA polymerases are used for DNA-repair in eukaryotes? Carcinogenesis 18:605-610 There are five well-characterized nuclear DNA polymerases in eukaryotes (DNA polymerases alpha, beta, delta, epsilon and zeta) and this short review summarizes our current knowledge concerning the participation of each in DNA-repair. The three major DNA excision-repair pathways involve a DNA synthesis step that replaces altered bases or nucleotides removed during repair. Base excision-repair removes many modified bases and abasic sites, and in mammalian cells this mainly involves DNA polymerase beta. An alternative means for completion of base excision- repair, involving DNA polymerases delta or epsilon, may also operate and be even more important in yeast. Nucleotide excision-repair uses DNA polymerases delta or epsilon to resynthesize the bases removed during repair of pyrimidine dimers and other bulky adducts in DNA. Similarly, mismatch-repair of replication errors appears to involve DNA polymerases delta or epsilon. DNA polymerase alpha is required for semi- conservative replication of DNA but not for repair of DNA. A more recently discovered enzyme, DNA polymerase zeta, appears to be involved in the bypass of damage, without excision, and occurs during DNA replication of a damaged template. Lindahl, T., P. Karran, and R.D. Wood (1997) DNA excision repair pathways. Curr Opin Genet Dev 7:158-169 The major DNA excision repair pathways of base excision repair for endogenous DNA lesions and nucleotide excision repair for DNA damage inflicted by ultraviolet light have been reconstructed with purified mammalian proteins and details of these repair mechanisms are emerging. Similar data are becoming available with regard to mismatch repair for correction of replication errors. Deletion of individual DNA repair proteins in knockout mice provides information on the roles of such factors in vivo and recent three-dimensional structures of several repair enzymes explain their detailed modes of action. Wood, R.D. (1997) Nucleotide excision repair in mammalian cells. J Biol Chem 272:23465-23468 To restore full genomic integrity in a eukaryotic cell, DNA repair processes have to be coordinated with the resetting of nucleosomal organization. We have established a cell-free system using Drosophila embryo extracts to investigate the mechanism linking de novo nucleosome formation to nucleotide excision repair (NER). Closed-circular DNA containing a uniquely placed cisplatin-DNA adduct was used to follow chromatin assembly specifically from a site of NER. Nucleosome formation was initiated from a target site for NER. The assembly of nucleosomes propagated bidirectionally, creating a regular nucleosomal array extending beyond the initiation site. Furthermore, this chromatin assembly was still effective when the repair synthesis step in the NER process was inhibited.
Gaillard, P.H., J.G. Moggs, D.M. Roche, J.P. Quivy, P.B. Becker, R.D. Wood, and G. Almouzni (1997) Initiation and bidirectional propagation of chromatin assembly from a target site for nucleotide excision repair. EMBO J 16:6281-6289 To restore full genomic integrity in a eukaryotic cell, DNA repair processes have to be coordinated with the resetting of nucleosomal organization. We have established a cell-free system using Drosophila embryo extracts to investigate the mechanism linking de novo nucleosome formation to nucleotide excision repair (NER). Closed-circular DNA containing a uniquely placed cisplatin-DNA adduct was used to follow chromatin assembly specifically from a site of NER. Nucleosome formation was initiated from a target site for NER. The assembly of nucleosomes propagated bidirectionally, creating a regular nucleosomal array extending beyond the initiation site. Furthermore, this chromatin assembly was still effective when the repair synthesis step in the NER process was inhibited.
Evans, E., J.G. Moggs, J.R. Hwang, J.M. Egly, and R.D. Wood (1997) Mechanism of open complex and dual incision formation by human nucleotide excision repair factors. EMBO J 16:6559-6573 During nucleotide excision repair in human cells, a damaged DNA strand is cleaved by two endonucleases, XPG on the 3' side of the lesion and ERCC1-XPF on the 5' side. These structure-specific enzymes act at junctions between duplex and single-stranded DNA. ATP-dependent formation of an open DNA structure of approximately 25 nt around the adduct precedes this dual incision. We investigated the mechanism of open complex formation and find that mutations in XPB or XPD, the DNA helicase subunits of the transcription and repair factor TFIIH, can completely prevent opening and dual incision in cell-free extracts. A deficiency in XPC protein also prevents opening. The absence of RPA, XPA or XPG activities leads to an intermediate level of strand separation. In contrast, XPF or ERCC1-defective extracts open normally and generate a 3' incision, but fail to form the 5' incision. This same repair defect was observed in extracts from human xeroderma pigmentosum cells with an alteration in the C-terminal domain of XPB, suggesting that XPB has an additional role in facilitating 5' incision by ERCC1- XPF nuclease. These data support a mechanism in which TFIIH-associated helicase activity and XPC protein catalyze initial formation of the key open intermediate, with full extension to the cleavage sites promoted by the other core nucleotide excision repair factors. Opening is followed by dual incision, with the 3' cleavage made first.
Sugasawa, K., J.M. Ng, C. Masutani, T. Maekawa, A. Uchida, d.e.r. .S. van, A.P. Eker, S. Rademakers, C. Visser, A. Aboussekhra, R.D. Wood, F. Hanaoka, D. Bootsma, and J.H. Hoeijmakers (1997) Two human homologs of Rad23 are functionally interchangeable in complex formation and stimulation of XPC repair activity. Mol Cell Biol 17:6924-6931 XPC-hHR23B protein complex is specifically involved in nucleotide excision repair (NER) of DNA lesions on transcriptionally inactive sequences as well as the nontranscribed strand of active genes. Here we demonstrate that not only highly purified recombinant hHR23B (rhHR23B) but also a second human homolog of the Saccharomyces cerevisiae Rad23 repair protein, hHR23A, stimulates the in vitro repair activity of recombinant human XPC (rhXPC), revealing functional redundancy between these human Rad23 homologs. Coprecipitation experiments with His-tagged rhHR23 as well as sedimentation velocity analysis showed that both rhHR23 proteins in vitro reconstitute a physical complex with rhXPC. Both complexes were more active than free rhXPC, indicating that complex assembly is required for the stimulation. rhHR23B was shown to stimulate an early stage of NER at or prior to incision. Furthermore, both rhHR23 proteins function in a defined NER system reconstituted with purified proteins, indicating direct involvement of hHR23 proteins in the DNA repair reaction via interaction with XPC.
Moggs, J.G., K.J. Yarema, J.M. Essigmann, and R.D. Wood (1996) Analysis of incision sites produced by human cell extracts and purified proteins during nucleotide excision repair of a 1,3-intrastrand d(GpTpG)-cisplatin adduct. J. Biol. Chem. 271:7177-7186 Nucleotide excision repair by mammalian enzymes removes DNA damage as part of approximately 30-mer oligonucleotides by incising phosphodiester bonds on either side of a lesion. We analyzed this dual incision reaction at a single 1,3-intrastrand d(GpTpG)-cisplatin cross-link in a closed circular duplex DNA substrate. Incisions were formed in the DNA with human cell extracts in which DNA repair synthesis was inhibited. The nicks were mapped by restriction fragment end labeling and primer extension analysis. Principal sites of cleavage were identified at the 9th phosphodiester bond 3' to the lesion and at the 16th phosphodiester bond 5' to the lesion. The predominant product was found to be a 26-mer platinated oligonucleotide by hybridization to a 32P-labeled complementary DNA probe. Oligonucleotides were formed at the same rate as the 3' cleavage, suggesting that both incisions are made in a near-synchronous manner. There was, however, a low frequency of 5' incisions in the absence of 3' cleavage. The dual incision reaction was reconstituted using the purified mammalian proteins XPA, RPA, XPC, TFIIH, XPG, and a fraction containing ERCC1-XPF and IF7. All of these components were required in order to observe any cleavage.
Wood, R.D. (1996) DNA repair in eukaryotes. Annu Rev Biochem 65:135-167 Eukaryotic cells have multiple mechanisms for repairing damaged DNA. O6- methylguanine-DNA methyltransferase directly reverses some simple alkylation adducts. However, most repair strategies excise lesions from DNA. Two major pathways are base excision repair (BER), which eliminates single damaged-base residues, and nucleotide excision repair (NER), which excises damage within oligomers that are 25-32 nucleotides long. The specialized DNA glycosylases and AP endonucleases of BER act on spontaneous and induced DNA alterations caused by hydrolysis, oxygen free radicals, and simple alkylating agents. NER utilizes many proteins (including the XP proteins in humans) to remove the major UV-induced photoproducts from DNA, as well as other types of modified nucleotides. Different DNA polymerases and ligases are used to complete the separate pathways. Some organisms have alternative schemes, which include the use of photolyases and a specific UV-endonuclease for repairing UV damage to DNA. Finally, double-strand breaks in DNA are repaired by mechanisms that involve recombination proteins and, in mammalian cells, a DNA protein kinase. Ariza, R.R., S.M. Keyse, J.G. Moggs, and R.D. Wood (1996) Reversible protein phosphorylation modulates nucleotide excision repair of damaged DNA by human cell extracts. Nucleic Acids Res 24:433-440 Nucleotide excision repair of DNA in mammalian cells uses more than 20 polypeptides to remove DNA lesions caused by UV light and other mutagens. To investigate whether reversible protein phosphorylation can significantly modulate this repair mechanism we studied the effect of specific inhibitors of Ser/Thr protein phosphatases. The ability of HeLa cell extracts to carry out nucleotide excision repair in vitro was highly sensitive to three toxins (okadaic acid, microcystin-LR and tautomycin), which block PP1- and PP2A-type phosphatases. Repair was more sensitive to okadaic acid than to tautomycin, suggesting the involvement of a PP2A-type enzyme, and was insensitive to inhibitor-2, which exclusively inhibits PP1-type enzymes. In a repair synthesis assay the toxins gave 70% inhibition of activity. Full activity could be restored to toxin-inhibited extracts by addition of purified PP2A, but not PP1. The p34 subunit of replication protein A was hyperphosphorylated in cell extracts in the presence of phosphatase inhibitors, but we found no evidence that this affected repair. In a coupled incision/synthesis repair assay okadaic acid decreased the production of incision intermediates in the repair reaction. The formation of 25-30mer oligonucleotides by dual incision during repair was also inhibited by okadaic acid and inhibition could be reversed with PP2A. Thus Ser/Thr- specific protein phosphorylation plays an important role in the modulation of nucleotide excision repair in vitro.
Sijbers, A.M., L.a.a.t. . de, R.R. Ariza, M. Biggerstaff, Y.F. Wei, J.G. Moggs, K.C. Carter, B.K. Shell, E. Evans, J.o.n.g. . de, S. Rademakers, R.o.o.i.j. de, N.G. Jaspers, J.H. Hoeijmakers, and R.D. Wood (1996) Xeroderma pigmentosum group F caused by a defect in a structure- specific DNA repair endonuclease. Cell 86:811-822 Nucleotide excision repair, which is defective in xeroderma pigmentosum (XP), involves incision of a DNA strand on each side of a lesion. We isolated a human gene homologous to yeast Rad1 and found that it corrects the repair defects of XP group F as well as rodent groups 4 and 11. Causative mutations and strongly reduced levels of encoded protein were identified in XP-F patients. The XPF protein was purified from mammalian cells in a tight complex with ERCC1. This complex is a structure-specific endonuclease responsible for the 5' incision during repair. These results demonstrate that the XPF, ERCC4, and ERCC11 genes are equivalent, complete the isolation of the XP genes that form the core nucleotide excision repair system, and solve the catalytic function of the XPF-containing complex. Vilpo, J.A., L.M. Vilpo, D.E. Szymkowski, A. O'Donovan, and R.D. Wood (1995) An XPG DNA repair defect causing mutagen hypersensitivity in mouse leukemia L1210 cells. Mol Cell Biol 15:290-297 One of the most widely used antitumor drugs is cis- diamminedichloroplatinum(II) (cisplatin), and mechanisms of cisplatin resistance have been investigated in numerous model systems. Many studies have used mouse leukemia L1210/0 as a reference wild-type cell line, and cisplatin-resistant subclones have been derived from it. Increased DNA excision repair capacity is thought to play a key role in the acquired cisplatin resistance, and this has influenced development of drugs for clinical trials. We report here that the L1210/0 line is in fact severely deficient in nucleotide excision repair of damaged DNA in vivo and in vitro. L1210/0 cell extracts could be complemented by extracts from repair-defective human xeroderma pigmentosum (XP) or rodent excision repair cross-complementing (ERCC) mutant cells, except for XPG/ERCC5 mutants. Purified XPG protein could restore repair proficiency to L1210/0 extracts. Expression of mouse XPG mRNA was similar in all L1210 lines studied, suggesting a point mutation or small alteration of XPG in L1210/0 cells. The DNA repair capacity of a cisplatin-resistant subline, L1210/DDP10, is similar to that of type culture collection L1210 cells and to those of other normal mammalian cell lines. Nucleotide excision repair of DNA is thus clearly important in the intrinsic cellular defense against cisplatin. However, in contrast to what is generally believed, enhancement of DNA repair above the normal level in these rodent cells does not appear to be a mechanism of acquired resistance to the drug.
Wood, R.D. (1995) Proteins that participate in nucleotide excision repair of DNA in mammalian cells. Philos T Roy Soc B 347:69-74 The most versatile strategy for repair of damage to DNA, and the main process for repair of UV-induced damage, is nucleotide excision repair. In mammalian cells, the complete mechanism involves more than 20 polypeptides, and defects in many of these are associated with various forms of inherited disorders in humans. The syndrome xeroderma pigmentosum (XP) is associated with mutagen hypersensitivity and increased cancer frequency, and studies of the nucleotide excision repair defect in this disease have been particularly informative. Many of the XP proteins are now being characterized. XPA binds to DNA, with a preference for damaged base pairs. XPC activity is part of a protein complex with single-stranded DNA binding activity. The XPG protein is a nuclease. Aboussekhra, A., M. Biggerstaff, M.K. Shivji, J.A. Vilpo, V. Moncollin, V.N. Podust, M. Protic, U. Hubscher, J.M. Egly, and R.D. Wood (1995) Mammalian DNA nucleotide excision repair reconstituted with purified protein components. Cell 80:859-868 Nucleotide excision repair is the principal way by which human cells remove UV damage from DNA. Human cell extracts were fractionated to locate active components, including xeroderma pigmentosum (XP) and ERCC factors. The incision reaction was then reconstituted with the purified proteins RPA, XPA, TFIIH (containing XPB and XPD), XPC, UV-DDB, XPG, partially purified ERCC1/XPF complex, and a factor designated IF7. UV- DDB (related to XPE protein) stimulated repair but was not essential. ERCC1- and XPF-correcting activity copurified with an ERCC1-binding polypeptide of 110 kDa that was absent in XP-F cell extract. Complete repair synthesis was achieved by combining these factors with DNA polymerase epsilon, RFC, PCNA, and DNA ligase I. The reconstituted core reaction requires about 30 polypeptides. Shivji, M.K., V.N. Podust, U. Hubscher, and R.D. Wood (1995) Nucleotide excision repair DNA synthesis by DNA polymerase epsilon in the presence of PCNA, RFC, and RPA. Biochemistry 34:5011-5017 In eukaryotes, nucleotide excision repair of DNA is a complex process that requires many polypeptides to perform dual incision and remove a segment of about 30 nucleotides containing the damage, followed by repair DNA synthesis to replace the excised segment. Nucleotide excision repair DNA synthesis is dependent on proliferating cell nuclear antigen (PCNA). To study gap-filling DNA synthesis during DNA nucleotide excision repair, UV-damaged DNA was first incubated with PCNA-depleted human cell extracts to create repair incisions. Purified DNA polymerase delta or epsilon, with DNA ligase, was then used to form the repair patch. DNA polymerase delta could perform repair synthesis and was strictly dependent on the presence of both PCNA and replication factor C, but gave rise to a very low proportion of complete, ligated circles. The presence of replication protein A (which is also required for nucleotide excision repair) did not alter this result, while addition of DNase IV increased the fraction of ligated products. DNA polymerase epsilon, on the other hand, could fill the repair patch in the absence of PCNA and replication factor C, and most of the products were ligated circles. Addition of replication protein A changed the situation dramatically, and synthesis by polymerase epsilon became dependent on both PCNA and replication factor C. A combination of DNA polymerase epsilon, PCNA, replication factor C, replication protein A, and DNA ligase I appears to be well-suited to the task of creating nucleotide excision repair patches. Nagai, A., M. Saijo, I. Kuraoka, T. Matsuda, N. Kodo, Y. Nakatsu, T. Mimaki, M. Mino, M. Biggerstaff, R.D. Wood, and a.l... et (1995) Enhancement of damage-specific DNA binding of XPA by interaction with the ERCC1 DNA repair protein. Biochem Biophys Res Commun 211:960-966 The human XPA and ERCC1 proteins, which are involved in early steps of nucleotide excision repair of DNA, specifically interacted in an in vitro binding assay and a yeast two-hybrid assay. A stretch of consecutive glutamic acid residues in XPA was needed for binding to ERCC1. Binding of XPA to damaged DNA was markedly increased by the interaction of the XPA and ERCC1 proteins. ERCC1 did not enhance binding to DNA when a truncated XPA protein, MF122, was used in place of the XPA protein. MF122 retains damaged DNA binding activity but lacks the region for protein-protein interaction including the E- cluster region. These results suggest that the XPA/ERCC1 interaction may participate in damage-recognition as well as in incision at the 5' site of damage during nucleotide excision repair. Laviola, G., R.D. Wood, C. Kuhn, R. Francis, and L.P. Spear (1995) Cocaine sensitization in periadolescent and adult rats. J Pharmacol Exp Ther 275:345-357 Periadolescent rats have been reported to be affected differentially by catecholaminergic agents when compared with younger or adult animals. The present study evaluated the behavioral responsivity of periadolescent (34- to 39-day-old) and adult (60- to 70-day-old) Sprague-Dawley rats of both sexes to i.p. cocaine (Coc) administration (0, 10 or 20 mg/kg, once daily for 4 days). All animals received injections of both saline and Coc every day paired with a different context, with one-half of the animals receiving the drug in the home cage (Coc-Home) and the other half in the testing chamber (Coc-Test). Forty-eight hours after the last drug injection, all animals were challenged with 10 mg/kg i.p. of Coc, and their behavior in the test chamber was scored. As expected, acute Coc induced a prominent increase in a number of behaviors, and this response profile was less marked in periadolescent relative to adult animals. In contrast, Coc-Test animals of both ages showed a clear behavioral sensitization relative to the chronic saline group. No evidence of carry-over effects was found in Coc-Home animals. Females were in general more sensitive than males to acute Coc effects. The development of behavioral sensitization to Coc was a function of age-specific alterations in sensitivity to psychostimulants. Periadolescent rats of both sexes showed sensitization to the locomotor activating effects (matrix crossings) of Coc, whereas a consistent sensitization profile for both stereotyped head scanning and focused sniffing activities were found in adults but not in periadolescents. Chronic Coc reduced body weight and food consumption, particularly in adult males, whereas it did not affect periadolescent patterns. No evidence of sensitization to Coc was found in the hormonal parameters considered. Bass, T., L.E. White, R.D. Wood, A.L. Werner, and F.P. Schinco (1995) Rapid decompression of congenital hydrocephalus associated with parenchymal hemorrhage. J Neuroimaging 5:249-251 A newborn boy with congenital hydrocephalus was diagnosed with aqueductal stenosis using magnetic resonance imaging. Low-resistance ventriculoperitoneal shunt placement was followed by clinical deterioration. Repeat imaging studies revealed a collapsed cortical mantle with subdural hemorrhage. In addition to subdural blood, often associated with marked cerebral conformational changes, extensive intraparenchymal hemorrhage was seen. For extreme congenital hydrocephalus, ventriculoperitoneal shunts with greater resistance to flow than the currently used neonatal shunt devices may be indicated, to allow a more gradual ventricular decompression. Wood, R.D., V.A. Molina, J.M. Wagner, and L.P. Spear (1995) Play behavior and stress responsivity in periadolescent offspring exposed prenatally to cocaine. Pharmacol Biochem Behav 52:367-374 Play behavior and stress responsiveness were examined in offspring exposed gestationally to cocaine. The subjects were offspring of Sprague-Dawley rat dams given s.c. injections of 40 mg/kg/3 cc cocaine HC1 daily from gestational days 8-20 (C40), pair-fed dams injected daily with saline (PF), and untreated control dams (LC). Periadolescent (postnatal day (P) 30-36) male and female rats were assigned to either pretest Stress or No Stress conditions. Every other day Stress animals were exposed to a stressor (on P30--foot shock; P32--white noise; P34-- forced swim; P36--foot shock), with each stressor being administered 4 h prior to a play session. Immobility during one of the stressors, foot shock, was used to assess stress responsiveness. Play sessions consisted of pairing each experimental animal with a same-sex, nonexperimentally manipulated conspecific for 7 min. The results indicated that periadolescent offspring exposed gestationally to cocaine differed from controls in their stress responsivity, as evidenced by a failure to show increased immobility during the final foot shock session. Also, while cocaine-exposed juveniles did not differ from controls in their own play behavior, these offspring elicited less play solicitation from conspecifics, as evidenced by an increased latency to be pounced, and decreased frequency and duration of being pounced. These findings parallel earlier evidence for altered stress responsiveness in adult cocaine-exposed rats and also suggest that prenatal exposure to cocaine results in altered social cues. Davies, A.A., E.C. Friedberg, A.E. Tomkinson, R.D. Wood, and S.C. West (1995) Role of the Rad1 and Rad10 proteins in nucleotide excision repair and recombination. J Biol Chem 270:24638-24641 In Saccharomyces cerevisiae, the RAD1 and RAD10 genes are involved in DNA nucleotide excision repair (NER) and in a pathway of mitotic recombination that occurs between direct repeat DNA sequences. In this paper, we show that purified Rad1 and Rad10 interact with a synthetic bubble structure and incise the DNA at the 5'-side of the centrally unpaired region. When Rad1-Rad10 and purified XPG protein (the human homolog of yeast Rad2 protein) were co-incubated with the DNA substrate, we observed incisions at both ends of the bubble. This reaction mimics the dual incision step in nucleotide excision repair in vivo. In addition, the recent suggestion that Rad1 can act to resolve Holliday junctions (Habraken, Y., Sung, P., Prakash, L., and Prakash, S. (1994) Nature 371, 531-534), explaining the recombination defect observed in rad1 mutants, has been further investigated. However, using proteins purified in two different laboratories we were unable to show any interaction between Rad1 and synthetic Holliday junctions. The role that Rad1-Rad10 plays in recombination is likely to resemble its activity in NER by acting upon partially unpaired DNA intermediates such as those formed by recombination mechanisms involving single- strand DNA annealing.
Kearsey, J.M., M.K. Shivji, P.A. Hall, and R.D. Wood (1995) Does the p53 up-regulated Gadd45 protein have a role in excision repair? Science 270:1004-5; discu During nucleotide excision repair, damaged DNA is incised on both sides of a lesion and an oligomer containing the damage is excised and replaced by repair DNA synthesis. The latter step is accomplished in vitro by proteins that include the DNA polymerase accessory factor PCNA, which binds to DNA ends to initiate repair synthesis. An increased association of PCNA with nuclei occurs after UV irradiation of nonreplicating DNA in normal human fibroblasts, probably following incision of damaged DNA. This property was used to detect the catalysis of nucleotide excision repair incisions in damaged DNA in vivo, by immunostaining of quiescent human fibroblasts with the widely available PC10 antibody. We summarize here a comprehensive survey of PCNA immunostaining in repair-defective xeroderma pigmentosum (XP) cells in comparison to normal cells. XP-A and XP-G cells were completely defective in staining for PCNA 30 min after UV irradiation. This strongly suggests that XPA and XPG proteins are absolutely required in cells before any incisions can be formed in damaged DNA. XP-B, XP-C, XP- D, and XP-F cells showed an intermediate level of staining for PCNA after UV irradiation, indicative of partial incision capacity in those cells. UV-irradiated XP-E and XP-V cells showed normal PCNA immunostaining levels, consistent with evidence that the corresponding factors are not essential for the incision step of repair. The results provide further evidence for the involvement of PCNA in the repair process in vivo and give an alternative to traditional approaches for measurement of nucleotide excision repair capability. Aboussekhra, A., and R.D. Wood (1995) Detection of nucleotide excision repair incisions in human fibroblasts by immunostaining for PCNA. Exp Cell Res 221:326-332 During nucleotide excision repair, damaged DNA is incised on both sides of a lesion and an oligomer containing the damage is excised and replaced by repair DNA synthesis. The latter step is accomplished in vitro by proteins that include the DNA polymerase accessory factor PCNA, which binds to DNA ends to initiate repair synthesis. An increased association of PCNA with nuclei occurs after UV irradiation of nonreplicating DNA in normal human fibroblasts, probably following incision of damaged DNA. This property was used to detect the catalysis of nucleotide excision repair incisions in damaged DNA in vivo, by immunostaining of quiescent human fibroblasts with the widely available PC10 antibody. We summarize here a comprehensive survey of PCNA immunostaining in repair-defective xeroderma pigmentosum (XP) cells in comparison to normal cells. XP-A and XP-G cells were completely defective in staining for PCNA 30 min after UV irradiation. This strongly suggests that XPA and XPG proteins are absolutely required in cells before any incisions can be formed in damaged DNA. XP-B, XP-C, XP- D, and XP-F cells showed an intermediate level of staining for PCNA after UV irradiation, indicative of partial incision capacity in those cells. UV-irradiated XP-E and XP-V cells showed normal PCNA immunostaining levels, consistent with evidence that the corresponding factors are not essential for the incision step of repair. The results provide further evidence for the involvement of PCNA in the repair process in vivo and give an alternative to traditional approaches for measurement of nucleotide excision repair capability. Tanaka, K., and R.D. Wood (1994) Xeroderma pigmentosum and nucleotide excision repair of DNA. Trends Biochem Sci 19:83-86 Nucleotide excision repair is a versatile strategy for removing DNA damage from the genome. Tremendous progress in understanding this process has been made in the last few years, and the field continues to develop rapidly. Exciting connections have emerged between nucleotide excision repair, transcription, and DNA replication, but many mysteries remain concerning the biochemical details of the mechanism, the connection with several human inherited syndromes, and the role of DNA repair in preventing cancer. Aboussekhra, A., and R.D. Wood (1994) Repair of UV-damaged DNA by mammalian cells and Saccharomyces cerevisiae. Curr Opin Genet Dev 4:212-220 Cells use many strategies to repair genomic damage caused by environmental agents and arising from the natural instability of the polynucleotide structure. Nucleotide excision repair is the most versatile DNA repair pathway and is the main defense of mammalian cells against UV-induced DNA damage. Defects in proteins involved in this pathway can lead to inherited disorders (such as xeroderma pigmentosum, Cockayne's syndrome and trichothiodystrophy) that are associated with hypersensitivity to sunlight. Most of the proteins and genes involved in these syndromes have now been identified. Study of UV-sensitive yeast RAD mutants has greatly aided this process and has revealed strong conservation of the components of nucleotide excision repair in eukaryotes. It has recently become clear that some of the proteins involved in the DNA repair process have dual functions and also participate in basal transcription and DNA replication. Samec, S., T.A. Jones, J. Corlet, D. Scherly, D. Sheer, R.D. Wood, and S.G. Clarkson (1994) The human gene for xeroderma pigmentosum complementation group G (XPG) maps to 13q33 by fluorescence in situ hybridization. Genomics 21:283-285 Complementation group G of xeroderma pigmentosum (XP-G) is one of the most rare and phenotypically heterogeneous forms of this inherited disorder. XP-G patients vary from having a very mild defect in DNA repair to being severely affected, and a few cases are also associated with the neurological complications of Cockayne's syndrome. The XPG gene encodes an acidic protein with a predicted molecular mass of 133 kDa that confers normal UV resistance when expressed in XP-G cells. Here we report the isolation of full-length XPG as a soluble protein expressed from a recombinant baculovirus. The purified polypeptide corrects the DNA nucleotide excision repair defect of XP-G cell extracts in vitro, and it acts as a magnesium-dependent single-stranded DNA endonuclease. This is the first direct evidence for a human protein with properties that implicate it in the incision step of nucleotide excision repair. O'Donovan, A., D. Scherly, S.G. Clarkson, and R.D. Wood (1994) Isolation of active recombinant XPG protein, a human DNA repair endonuclease. J Biol Chem 269:15965-15968 Complementation group G of xeroderma pigmentosum (XP-G) is one of the most rare and phenotypically heterogeneous forms of this inherited disorder. XP-G patients vary from having a very mild defect in DNA repair to being severely affected, and a few cases are also associated with the neurological complications of Cockayne's syndrome. The XPG gene encodes an acidic protein with a predicted molecular mass of 133 kDa that confers normal UV resistance when expressed in XP-G cells. Here we report the isolation of full-length XPG as a soluble protein expressed from a recombinant baculovirus. The purified polypeptide corrects the DNA nucleotide excision repair defect of XP-G cell extracts in vitro, and it acts as a magnesium-dependent single-stranded DNA endonuclease. This is the first direct evidence for a human protein with properties that implicate it in the incision step of nucleotide excision repair.
Lehmann, A.R., D. Bootsma, S.G. Clarkson, J.E. Cleaver, P.J. McAlpine, K. Tanaka, L.H. Thompson, and R.D. Wood (1994) Nomenclature of human DNA repair genes. Mutat Res 315:41-42 The UV hypersensitivity of xeroderma pigmentosum (XP) complementation group A cells is restored to near-normal by transfection of the XPA gene located on human chromosome 9. However, it has been reported that a cosmid related to a cDNA on chromosome 8 is also able to partially correct the UV sensitivity of XP-A cells. We describe here an investigation of a representative cosmid transfectant, denoted 2-0-A2. Whole cell extracts prepared from 2-0-A2 cells carried out DNA repair synthesis in vitro that was in the normal range, consistent with their UV-resistant phenotype. Immunoblotting indicated that 2-0-A2 cells expressed full-length XPA protein. This was unexpected because the 2-0- A2 cell line was thought to have been isolated by transfection of a cell line derived from patient XP2OS, and a known homozygous mutation in XP2OS prevents expression of XPA gene product. This mutation creates an AlwNI restriction endonuclease cleavage site in XPA and was not present in 2-0-A2. These results prompted an RFLP analysis which revealed that the 2-0-A2 cell line was not derived from XP2OS but from another line that fails to express XPA protein, XP12BE. It appears that the significant UV-resistance and DNA repair capacity of 2-0-A2 can be ascribed to the re-expression of XPA in XP12BE, and it is unnecessary to postulate a second XP-A complementing gene to explain the results. Wood, R.D. (1994) Studying nucleotide excision repair of mammalian DNA in a cell-free system. Ann N Y Acad Sci 726:274-9; discus The UV hypersensitivity of xeroderma pigmentosum (XP) complementation group A cells is restored to near-normal by transfection of the XPA gene located on human chromosome 9. However, it has been reported that a cosmid related to a cDNA on chromosome 8 is also able to partially correct the UV sensitivity of XP-A cells. We describe here an investigation of a representative cosmid transfectant, denoted 2-0-A2. Whole cell extracts prepared from 2-0-A2 cells carried out DNA repair synthesis in vitro that was in the normal range, consistent with their UV-resistant phenotype. Immunoblotting indicated that 2-0-A2 cells expressed full-length XPA protein. This was unexpected because the 2-0- A2 cell line was thought to have been isolated by transfection of a cell line derived from patient XP2OS, and a known homozygous mutation in XP2OS prevents expression of XPA gene product. This mutation creates an AlwNI restriction endonuclease cleavage site in XPA and was not present in 2-0-A2. These results prompted an RFLP analysis which revealed that the 2-0-A2 cell line was not derived from XP2OS but from another line that fails to express XPA protein, XP12BE. It appears that the significant UV-resistance and DNA repair capacity of 2-0-A2 can be ascribed to the re-expression of XPA in XP12BE, and it is unnecessary to postulate a second XP-A complementing gene to explain the results. Jones, C.J., R.S. Lloyd, and R.D. Wood (1994) Analysis of cells harboring a putative DNA repair gene reveals a lack of evidence for a second independent xeroderma pigmentosum group A correcting gene. Mutat Res 324:159-164 The UV hypersensitivity of xeroderma pigmentosum (XP) complementation group A cells is restored to near-normal by transfection of the XPA gene located on human chromosome 9. However, it has been reported that a cosmid related to a cDNA on chromosome 8 is also able to partially correct the UV sensitivity of XP-A cells. We describe here an investigation of a representative cosmid transfectant, denoted 2-0-A2. Whole cell extracts prepared from 2-0-A2 cells carried out DNA repa |
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