Nucleotide Excision Repair in Eukaryotes

doi:10.1128/9781555816704.ch8

Chapter 8 : Nucleotide Excision Repair in Eukaryotes

Authors: C. Friedberg Errol¹, C. Walker Graham², Siede Wolfram³, D. Wood Richard⁴, A. Schultz Roger⁵, Ellenberger Tom⁶

VIEW AFFILIATIONS HIDE AFFILIATIONS

Affiliations: 1: Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas; 2: Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts; 3: Department of Cell Biology and Genetics, University of North Texas Health Science Center, Fort Worth, Texas; 4: Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania; 5: Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas; 6: Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts

Content Type: Reference

Publication Year: 2006

Category: Microbial Genetics and Molecular Biology

Book DOI: 10.1128/9781555816704

Chapter DOI: 10.1128/9781555816704.ch8

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Preview this chapter:

Nucleotide Excision Repair in Eukaryotes, Page 1 of 2

< Previous page | Next page > /docserver/preview/fulltext/10.1128/9781555816704/9781555813192_Chap08-1.gif /docserver/preview/fulltext/10.1128/9781555816704/9781555813192_Chap08-2.gif

Abstract:

This chapter considers the cell biology and genetics of nucleotide excision repair (NER) in eukaryotes and some biochemical properties of NER gene products. It presents experimental demonstration of NER in eukaryotic cells, and rate of removal of cyclobutane pyrimidine dimmers (CPD) and (6-4) photoproducts in yeast cells and mammalian cells. The discovery that the hereditary disease xeroderma pigmentosum (XP) affects NER in human cells established a powerful genetic framework for exploring molecular aspects of the pathogenesis of this disease and the mechanism of NER in eukaryotes. It discusses the molecular cloning of individual yeast genes for NER as well as their mammalian orthologs and considers biochemical information gleaned from the characterization of individual genes and their gene products. The majority of the genes and proteins considered in this chapter are required for or involved in steps associated with base damage recognition and bimodal incision of damaged DNA during NER in eukaryotes.

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Nucleotide Excision Repair in Eukaryotes, p 267-315. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch8

Key Concept Ranking

Gene Expression and Regulation: 0.4872609
Nuclear Magnetic Resonance Spectroscopy: 0.40683663

0.4872609

Highlighted Text: Show | Hide

Full text loading...

Figures

Nucleotide Excision Repair in Eukaryotes

/content/10.1128/9781555816704.ch08.ch08fig01

Figure 8–1

Repair synthesis of DNA during NER can be visualized by autoradiography. Cultured human HeLa cells were either unirradiated (top) or exposed to UV irradiation at 10 J/m2 (bottom) and were then labeled for 2 h with [3H]thymidine. Following autoradiography, cells in the S phase of the cell cycle show intense labeling of their nuclei ( 63 ). The remaining unirradiated cells show very low background labeling except for the occasional cell just entering or leaving S phase (top). Non-S-phase cells exposed to irradiation (bottom) show many autoradiographic grains, reflecting repair synthesis (so-called unscheduled DNA synthesis). (Adapted from reference 63 with permission.)

10.1128/9781555816704/f0268-01_thmb.gif

10.1128/9781555816704/f0268-01.gif

Figure 8–1

/content/10.1128/9781555816704.ch08.ch08fig02

Figure 8–2

Complementation of the UV-radiation sensitivity of immortalized XP-A cells. Shown is the survival after UV radiation as measured by colony-forming ability in repair-proficient human fibroblasts WI38VA13 (black), parental XP-A cells (grey), and XPA gene transfectants (gold). (Adapted from reference 403 .)

10.1128/9781555816704/f0269-01_thmb.gif

10.1128/9781555816704/f0269-01.gif

Figure 8–2

/content/10.1128/9781555816704.ch08.ch08fig03

Figure 8–3

Ligation-mediated PCR to detect locations of CPD. (A and B) Duplex DNA containing a CPD (triangle) is cleaved with T4 denV enzyme and denatured (A), and a gene-specific primer P1 is annealed and extended with DNA polymerase to the end of the fragment (B). (C) Linker DNA (black rectangles) is ligated to the ends of the DNA. (D) PCR is then performed with a second gene-specific primer P2 and a primer annealing to the linker. (E) The DNA products are separated on a sequencing gel and transferred to a membrane. A strand generated with gene-specific primer P3 is used as a hybridization probe to detect the PCR products.

10.1128/9781555816704/f0271-01_thmb.gif

10.1128/9781555816704/f0271-01.gif

Figure 8–3

/content/10.1128/9781555816704.ch08.ch08fig04

Figure 8–4

Detection of CPD and (6–4)PP in UV-irradiated DNA at the trinucleotide sequence TC-X. CPD are converted into DSB with a 5’ phosphate group by cleavage with T4 denV and by photolyase treatment to create ligatable ends. The resulting DNA break positions can be detected by ligation-mediated PCR (see Fig. 8–3 ). (6–4)PP and their Dewar isomers are converted into strand breaks with 5’ phosphate groups by cleavage in hot alkaline buffer. Note than an amplification product derived from a (6–4)PP is 1 nucleotide shorter than the product derived from a CPD at the same dipyrimidine sequence. Only one strand of the DNA duplex is shown. (Adapted from reference 300 .)

10.1128/9781555816704/f0271-02_thmb.gif

10.1128/9781555816704/f0271-02.gif

Figure 8–4

/content/10.1128/9781555816704.ch08.ch08fig05

Figure 8–5

A procedure for the isolation and end labeling of restriction fragments containing a gene, illustrated here for an RsaI restriction fragment from the MFA2 gene. (Top) Probes 1 and 2 are complementary to 3’ ends of the transcribed strand (TS) and the nontranscribed strand (NTS), respectively, of the MFA2-containing RsaI fragment. Each probe has a hexa(dT) overhang, connected to six further bases with a biotinylated residue at the 5’ end. RsaI-restricted DNA is denatured and annealed to probe 1 or 2 to isolate the MFA2 TS or NTS. (Bottom) These annealed fragments are separated from genomic DNA by using streptavidin-coated magnetic beads which bind the biotin. The beads, and consequently the bound sequences, are retained in the tube by placing a magnet at the side of the tube, while nonbound genomic DNA is washed away. The MFA2 fragments are then end labeled by incorporating six radiolabeled dATP molecules opposite the hexa(dT) sequence with DNA polymerase. These labeled fragments are eluted from the beads. To detect UV radiation-induced CPD in a fragment (represented by a triangle on the TS in the figure), the DNA is incised with T4 denV enzyme and the fragments are separated according to size on a DNA sequencing gel (see Fig. 10–18 for an example). (Adapted from reference 407 .)

10.1128/9781555816704/f0272-01_thmb.gif

10.1128/9781555816704/f0272-01.gif

Figure 8–5

/content/10.1128/9781555816704.ch08.ch08fig06

Figure 8–6

Kinetics of the removal of (6–4)PP (A) and CPD (B) from the DNA of UV-irradiated CHO cells. (Adapted from reference 273 .)

10.1128/9781555816704/f0272-02_thmb.gif

10.1128/9781555816704/f0272-02.gif

Figure 8–6

Kinetics of the removal of (6–4)PP (A) and CPD (B) from the DNA of UV-irradiated CHO cells. (Adapted from reference 273 .)

/content/10.1128/9781555816704.ch08.ch08fig07

Figure 8–7

Defective incision of UV-irradiated DNA in a rad3 mutant of S. cerevisiae in vivo. After UV irradiation, the wild-type (RAD) strain (A) and a rad16 mutant strain (C) generate incisions in DNA that shift the sedimentation position of DNA toward the top of the alkaline sucrose gradients. These incisions persist at 36°C because of the presence of the temperature-sensitive cdc9 mutation that prevents completion of NER by preventing DNA ligation. At 25°C DNA ligase is active and NER can be completed. This allows the formation of higher-molecular-weight DNA in wild-type and rad16 cells, which sediments faster in the gradients. No strand breaks are detected in the DNA of the rad3 mutant (B), even at 36°C, indicating that this mutant is defective in the incision of UV-irradiated DNA ( 118 ).

10.1128/9781555816704/f0273-01_thmb.gif

10.1128/9781555816704/f0273-01.gif

Figure 8–7

/content/10.1128/9781555816704.ch08.ch08fig08

Figure 8–8

DNA damage-specific incision in UV-irradiated normal and XP fibroblasts. The figure shows the relative retention of DNA on filters as measured by the alkaline elution technique. Normal human fibroblasts generate transient strand breaks in their DNA during postirradiation incubation. This results in a reduced retention of the DNA on the filters following denaturation of the DNA in alkali because of the smaller size of the DNA fragments. The gradual return to higher-molecular-weight DNA associated with the completion of NER is reflected by increased filter retention. Incision of DNA in XP cells is reduced or absent as measured by this technique ( 109 ).

10.1128/9781555816704/f0273-02_thmb.gif

10.1128/9781555816704/f0273-02.gif

Figure 8–8

/content/10.1128/9781555816704.ch08.ch08fig09

Figure 8–9

Detection of NER incisions by the alkaline unwinding technique. Confluent monolayers of a human fibroblast cell line were exposed to incident UV-C radiation doses of 0, 5, 10, or 20 J/m2 and then incubated at 37°C for the times indicated. At each time point, cells were lysed and exposed to alkaline conditions (0.03 M NaOH, plus 0.15 NaCl at 0°C). NER incisions present in the cells at the time of lysis serve as sites of unwinding to form single-stranded DNA that is monitored to calculate the number of breaks. The number of breaks at any time reflects ongoing NER. (Adapted from reference 94 .)

10.1128/9781555816704/f0273-03_thmb.gif

10.1128/9781555816704/f0273-03.gif

Figure 8–9

/content/10.1128/9781555816704.ch08.ch08fig10

Figure 8–10

Comparison of the kinetics of repair synthesis in human fibroblasts and the loss of ESS in DNA sensitive to the T4 denV enzyme, which nicks at CPD in DNA. Cells for the repair synthesis assay were UV irradiated with a dose of 10 J/m2 and for the ESS assay with a dose of 5 J/m2.

10.1128/9781555816704/f0274-01_thmb.gif

10.1128/9781555816704/f0274-01.gif

Figure 8–10

/content/10.1128/9781555816704.ch08.ch08fig11

Figure 8–11

(A) Deletion of the RAD10 gene of S. cerevisiae results in more sensitivity to killing by UV radiation than that of a rad10-1 point mutant, to a level comparable to that sustained by a rad3 mutant ( 453 ). (B) Deletion of the RAD7 gene results in less sensitivity to killing by UV radiation than deletion of the RAD10 gene does ( 299 ). (Note the different UV dose scales in panels A and B.)

10.1128/9781555816704/f0277-02_thmb.gif

10.1128/9781555816704/f0277-02.gif

Figure 8–11

/content/10.1128/9781555816704.ch08.ch08fig12

Figure 8–12

A mutant strain of S. pombe with a deletion of the rad13+ gene (the S. pombe ortholog of S. cerevisiae RAD2) is only marginally sensitive to UV radiation compared with an NERdefective strain (compare the UV radiation dose to that in Fig. 8–11 ). A plasmid carrying the cloned rad13+ gene corrects the UV radiation sensitivity of the S. pombe rad13 mutant. (Adapted from reference 55 .)

10.1128/9781555816704/f0280-01_thmb.gif

10.1128/9781555816704/f0280-01.gif

Figure 8–12

/content/10.1128/9781555816704.ch08.ch08fig13

Figure 8–13

Functional domains of human XPA protein. NLS, nuclear localization signal. (Adapted from reference 197 .)

10.1128/9781555816704/f0282-01_thmb.gif

10.1128/9781555816704/f0282-01.gif

Figure 8–13

Functional domains of human XPA protein. NLS, nuclear localization signal. (Adapted from reference 197 .)

/content/10.1128/9781555816704.ch08.ch08fig14

Figure 8–14

Binding of human XPA protein to DNA with altered base pairing. XPA protein was incubated together with 19-mer DNA duplexes, and the protein-DNA interaction monitored by an electrophoretic mobility shift assay. One strand of each substrate was labeled with 32P at its 5’ end. The positions of bound XPA-DNA complexes (B) and free DNA fragments (F) are indicated in the autoradiographs shown. (A) DNA fragments modified by site-directed AAF or benzo[a]pyrene (B[a]P) carcinogen-DNA adducts. (B) DNA fragments contained a C4’-pivaloyl adduct (denoted by *) in the center. (Adapted from reference 53 .)

10.1128/9781555816704/f0282-02_thmb.gif

10.1128/9781555816704/f0282-02.gif

Figure 8–14

/content/10.1128/9781555816704.ch08.ch08fig15

Figure 8–15

Domain organization of single-strand-DNA-binding (SSB) proteins. (A) Domain organization of SSB proteins in eukaryotes, bacteria, and archaea. Eukaryotes have a heterotrinieric SSB protein (RPA) with six OB-folds (gold boxes), four of which participate in DNA binding (A, B, C, and D). The third DNA-binding domain (labeled C) of RPA1 has a zinc-binding domain insertion (yellow box). Bacteria have a homotetrameric SSB protein with a single OB-fold in each polypeptide. The C-terminal third of E. coli SSB is a highly flexible “tail” (grey box) with an acidic terminus (black) that does not participate in DNA binding but plays a role in protein-protein interactions. Crenarchaeal SSB has a similar organization. (B) The OB-fold ( 269 ) is a five-strand, barrel-shaped structure that binds to ssDNA. Two views of an OB-fold are shown here. Most SSBs contain one or several tandem OB-fold domains. A variant of the OB-fold binds to dsDNA and is found in DNA ligases (see Fig. 6–38). (Panel A adapted from reference 192 .)

10.1128/9781555816704/f0283-01_thmb.gif

10.1128/9781555816704/f0283-01.gif

Figure 8–15

/content/10.1128/9781555816704.ch08.ch08fig16

Figure 8–16

The crystal structure of two OB-fold domains from the large subunit (RPA1) of human RPA shows how basic residues from the strands and connecting loops of the OB barrel contact the DNA backbone and aromatic residues stack against the bases of ssDNA ( 33 ) (see also Fig. 8–15 ).

10.1128/9781555816704/f0284-01_thmb.gif

10.1128/9781555816704/f0284-01.gif

Figure 8–16

/content/10.1128/9781555816704.ch08.ch08fig17

Figure 8–17

Interaction domains in Rad1 and Rad10 proteins. The regions between amino acids 90 and 210 of S. cerevisiae Rad10 and amino acids 809 to 997 of Rad1 are required for specific interaction between the two polypeptides.

10.1128/9781555816704/f0285-01_thmb.gif

10.1128/9781555816704/f0285-01.gif

Figure 8–17

/content/10.1128/9781555816704.ch08.ch08fig18

Figure 8–18

Rad1-Rad10 endonuclease cleaves partially duplex molecules. A bubble substrate (left) was formed by annealing two 90-mer oligonucleotides. These were of complementary sequence except for the central 30 unpaired nucleotides, which had 30 T residues on one strand and 30 C residues on the other (as in Fig. 8–27 ). One strand was labeled with 32P on the 5’ end, as indicated by an asterisk. A mixture of Rad1 and Rad10 proteins was incubated with the bubble, and the products were separated on a denaturing polyacrylamide gel and subjected to autoradiography (right). Rad1-Rad10 cleaves the labeled strand on the 5’ side of the bubble at the position shown, whereas neither Rad1 nor Rad10 alone shows cleavage activity. (Adapted from reference 76 .)

10.1128/9781555816704/f0285-02_thmb.gif

10.1128/9781555816704/f0285-02.gif

Figure 8–18

/content/10.1128/9781555816704.ch08.ch08fig19

Figure 8–19

Structure-specific nuclease activity of ERCC1-XPF. A 46-mer stem-loop structure (top), labeled at the 5’ end with 32P, is incised by purified ERCC1-XPF protein at the positions shown by the arrows within the duplex near the 5’ junction with the loop. Cleavage sites were analyzed by electrophoresis on a denaturing gel (bottom). (Adapted from reference 205 .)

10.1128/9781555816704/f0286-01_thmb.gif

10.1128/9781555816704/f0286-01.gif

Figure 8–19

/content/10.1128/9781555816704.ch08.ch08fig20

Figure 8–20

Model for the role of Rad1-Rad10 endonuclease in recombinational repair by the single-strand annealing pathway. Following the introduction of a DSB between two homologous sequences, the broken DNA ends are resected by a 5’ → 3’ exonuclease. Complementary overlapping 3’ ends then anneal, and the structure-specific nuclease activity of Rad1-Rad10 trims off the 3’-ended unpaired single strands. The DNA is then repaired by resynthesis and ligation, resulting in a deletion product in which sequences between two direct repeats have been lost. (Adapted from reference 76 .)

10.1128/9781555816704/f0287-01_thmb.gif

10.1128/9781555816704/f0287-01.gif

Figure 8–20

/content/10.1128/9781555816704.ch08.ch08fig21

Figure 8–21

Domain structure of XPF and ERCC1. XPF consists of two conserved areas (grey) separated by a less highly conserved region in the middle. The N-terminal area includes homology to SF2-family helicase domains I to III and a predicted leucine zipper (L-zipper) region. In the C-terminal region there is an area of similarity to ERCC1. Part of this region is highly similar to a region near the C terminus of archaeal helicases. In ERCC1, the first ca. 100 amino acids are dispensable and the remainder of the protein (light gold) has similarity to XPF. Some known mutations in CHO ERCC1 mutant cells and human XPF mutant cells are indicated. (Adapted from reference 120 .)

10.1128/9781555816704/f0288-01_thmb.gif

10.1128/9781555816704/f0288-01.gif

Figure 8–21

/content/10.1128/9781555816704.ch08.ch08fig22

Figure 8–22

Structural organization of XPF-like nucleases. In euryarchaea (top), as exemplified by Pyrococcus Hef, the nuclease is formed by homodimerization of two molecules, each containing a helicase domain, a nuclease domain, and a domain with two HhH motifs. Independent dimerization occurs between the HhH domains (dark gold) and the nuclease domains (grey) of each monomer. In the crenarchaea (middle), as exemplified by the enzyme from Sulfolobus, the nuclease is a homodimer of a shorter protein containing only nuclease and HhH domains. This enzyme is assisted in anchoring to the DNA by crenarchaeal PCNA. The eukaryotic nuclease (bottom) is a heterodimer of two related subunits, as exemplified by human XPF-ERCC1. The larger XPF subunit contains the active nuclease domain but has disrupted helicase motifs and one disrupted C-terminal HhH domain. XPF is dimerized with a smaller ERCC1 subunit having two HhH domains and a disrupted nuclease domain. (Adapted from reference 283 .)

10.1128/9781555816704/f0289-01_thmb.gif

10.1128/9781555816704/f0289-01.gif

Figure 8–22

/content/10.1128/9781555816704.ch08.ch08fig23

Figure 8–23

Highly conserved residues in the nuclease domain of XPF and Mus81 homologs. The alignment shows amino acids 712 to 724 of human XPF (Hs XPF) with the homologous regions of the XPF orthologs from mouse (Mm), Drosophila (Dm), S. pombe (Sp), and S. cerevisiae (Sc). The middle group of aligned sequences consists of putative helicase/nucleases from the euryarchaea Archaeoglobus fulgidus (Af), Methanococcus jannaschii (Mj), Methanothermobacter thermoautotrophicus (Mt), Pyrococcus abyssi (Pa), and the crenarcheaon S. solfataricus (Ss). The bottom group of sequences consists of eukaryotic Mus81 homologs. Results of alanine substitution mutations for the residues indicated in gold are shown in Fig. 8–24 . (Adapted from reference 93 .)

10.1128/9781555816704/f0289-02_thmb.gif

10.1128/9781555816704/f0289-02.gif

Figure 8–23

/content/10.1128/9781555816704.ch08.ch08fig24

Figure 8–24

Nuclease activity of wild-type and mutant ERCC1-XPF. A stem-loop substrate labeled with 32P (as in Fig. 8–19 ) was incised by wild-type ERCC1-XPF (WT) or mutant ERCC1-XPF in the presence of 0.4 mM MnCl2 (A) or 2 mM MgCl2 (B). An autoradiograph is shown of the 46-mer substrate and 9- to 10-mer products separated on a denaturing polyacrylamide gel. Highly conserved Asp (D), Glu (E), Arg (R), and Lys (K) residues were changed to Ala (a) as indicated. Residues 714, 715, 716, and 720 (bold) are depicted in Fig. 8–23 . (Adapted from reference 93 .)

10.1128/9781555816704/f0290-01_thmb.gif

10.1128/9781555816704/f0290-01.gif

Figure 8–24

/content/10.1128/9781555816704.ch08.ch08fig25

Figure 8–25

Structure of a thermostable homodimer of an XPF/Mus81 family enzyme from A. pernix, bound to dsDNA. The DNA in the crystal structure (shown horizontally as a stick model representation) represents part of a 3’ flap substrate. A second DNA duplex is modelled as part of the same 3’ flap substrate and is shown vertically as a backbone ribbon. The archaeal enzyme has a catalytic nuclease domain and a DNA-binding domain separated by a flexible linker. The two subunits of the homodimer are shown in two shades of gold, with twofold axes of symmetry indicated by black rods in the figure. The DNA-binding and nuclease domains become coupled on binding a DNA substrate, and the DNA is likely to be bent as part of the recognition of a double-strand DNA-single strand DNA discontinuity. (Adapted from reference 278 a.)

10.1128/9781555816704/f0290-02_thmb.gif

10.1128/9781555816704/f0290-02.gif

Figure 8–25

/content/10.1128/9781555816704.ch08.ch08fig26

Figure 8–26

Proposed scheme for substrate recognition by dimeric nucleases such as the archaeal XPF/Mus81 homologs and the mammalian heterodimeric ERCC1-XPF nuclease, based on the crystal structure shown in Fig. 8–25 . In this scheme, one subunit (B) binds to the DNA substrate and presents it for cleavage by the catalytic subunit (A). For ERCC1-XPF, the catalytically inactive “nuclease” domain of the ERCC1 subunit could stabilize the fold of the XPF nuclease and/or interact with the DNA. The HhH domains of ERCC1 and XPF are a dimerization interface, and one or both HhH subunits might also bind to DNA, as seen in the crystal structure of the archaeal XPF/Mus81 homolog ( Fig. 8–25 ). Although some XPF/Mus81 homologs lack the N-terminal helicaselike domain of eukaryotic XPF ( Fig. 8–21 ), it is likely that this domain also participates in binding to DNA. The modified DNA strand labeled X that is subject to cleavage by the XPF/Mus81 nucleases may be present in a bubble substrate, a single-stranded 3’ flap, or one strand of a four-way (Holliday) junction. Different enzymes from the XPF/Mus81 family cleave these DNA structures with different efficiencies.

10.1128/9781555816704/f0291-01_thmb.gif

10.1128/9781555816704/f0291-01.gif

Figure 8–26

/content/10.1128/9781555816704.ch08.ch08fig27

Figure 8–27

XPG nuclease cleaves on the 3’ side of bubble structures. Two 90-mer oligonucleotides were annealed to form a bubble structure. There is 30 bp of paired DNA on each side of the bubble; the bubble itself arises because the central part of the structure comprises 30 T residues on one strand and 30 C residues on the other. The top strand was labeled with 32Patthe 5’ end and treated with XPG, generating a 60-mer, as shown in the autoradiograph of a denaturing polyacrylamide gel. Precise size markers were generated by Maxam-Gilbert DNA-sequencing reactions (T + C and G + A). For the lanes at the right, the bubble was treated with two concentrations of S1 nuclease to nick in the single-stranded area. (Adapted from reference 95 .)

10.1128/9781555816704/f0292-01_thmb.gif

10.1128/9781555816704/f0292-01.gif

Figure 8–27

/content/10.1128/9781555816704.ch08.ch08fig28

Figure 8–28

Highly conserved residues in the XPG and FEN1 nuclease family. The upper part of the figure represents the conserved N-terminal (N) and internal (I) regions of some members of the structure-specific nuclease family. The total number of amino acids in each protein is indicated. Within each region, some of the most highly conserved amino acid residues are indicated, with identical residues in grey. Human XPG nuclease is inactivated if either of the highly conserved residues Asp77 or Glu791 (gold) is changed to Ala. In XP patients XP124LO and XP125LO, the causative mutation is a change of the highly conserved Ala792 (gold) to Val. (Adapted from reference 68 .)

10.1128/9781555816704/f0293-01_thmb.gif

10.1128/9781555816704/f0293-01.gif

Figure 8–28

/content/10.1128/9781555816704.ch08.ch08fig29

Figure 8–29

Protein sequence similarity between yeast Rad4 and human and Drosophila XPC. The diagram shows protein sequence similarity between the S. cerevisiae Rad4 protein and its orthologs human XPC and Drosophila Mus210. The most highly conserved region of about 370 amino acid residues is in the C-terminal part of the proteins (indicated in gold). Less highly conserved regions are present in the N-terminal part of the proteins (grey). The percentages of amino acid sequence identity and similarity are shown for these regions.

10.1128/9781555816704/f0293-02_thmb.gif

10.1128/9781555816704/f0293-02.gif

Figure 8–29

/content/10.1128/9781555816704.ch08.ch08fig30

Figure 8–30

Human XPC protein is associated with RAD23 proteins and centrin 2. A protein complex purified from HeLa cells, containing XPC complementing activity, contains XPC protein tightly bound to RAD23B or RAD23A as well as to the small centrin 2 (CEN2) protein. Positions of migration of the proteins on a silver-stained gel are shown. The asterisks indicate products derived from proteolysis of the large XPC subunit. (Adapted from reference 9 .)

10.1128/9781555816704/f0294-01_thmb.gif

10.1128/9781555816704/f0294-01.gif

Figure 8–30

/content/10.1128/9781555816704.ch08.ch08fig31

Figure 8–31

Functional domains in two human homologs of S. cerevisiae Rad23, RAD23A and RAD23B. The proteins have 58% identity and 67% similarity. The ubiquitin-like (UbL) and ubiquitin-associated (UbA) domains are shown, as well as a region that binds XPC protein (XPC-BD). The 398-amino-acid (aa) S. cerevisiae Rad23 protein has a similar domain organization and an overall 30% identity and 42% similarity to human RAD23B.

10.1128/9781555816704/f0294-02_thmb.gif

10.1128/9781555816704/f0294-02.gif

Figure 8–31

/content/10.1128/9781555816704.ch08.ch08fig32

Figure 8–32

Preferential binding of XPC-RAD23B protein to UVirradiated DNA. 32P-labeled 136-bp duplex DNA (1 ng) was unirradiated or UV irradiated with the indicated doses and incubated with XPC-RAD23B protein and 100 ng nonspecific poly(dI-dC) competitor DNA. (Adapted from reference 27 .)

10.1128/9781555816704/f0295-01_thmb.gif

10.1128/9781555816704/f0295-01.gif

Figure 8–32

/content/10.1128/9781555816704.ch08.ch08fig33

Figure 8–33

Binding of XPC-RAD23B to DNA containing small bubbles. The figure shows an autoradiograph of the products of a gel mobility shift assay using human XPC-RAD23B protein and 32P-labeled probes (about 55 bp long) containing duplex DNA, a region of three unpaired bases, or a region of five unpaired bases. (Adapted from reference 385 .)

10.1128/9781555816704/f0296-01_thmb.gif

10.1128/9781555816704/f0296-01.gif

Figure 8–33

/content/10.1128/9781555816704.ch08.ch08fig34

Figure 8–34

Partial amino acid sequence alignment of proteins sharing helicase consensus motifs. Two of the seven well-conserved helicase motifs ( Fig. 8–37 ), designated I and II, are shown here. Motif I, also known as a Walker type A sequence, contains a GK(T/S) sequence that is important in binding ATP. Motif II contains a DExH sequence important in binding a divalent cation, usually Mg2+ S. cerev., S. cerevisiae; Drosoph., Drosophila.

10.1128/9781555816704/f0296-02_thmb.gif

10.1128/9781555816704/f0296-02.gif

Figure 8–34

/content/10.1128/9781555816704.ch08.ch08fig35

Figure 8–35

(A) Rad3 DNA helicase activity can be demonstrated by measuring the displacement of a radiolabeled oligonucleotide annealed to complementary circular ssDNA. (B and C) Rad3 protein displaces such oligonucleotides with a strict 5’ → 3’ polarity with respect to the strand to which it is bound (the single-stranded circle) and with a pronounced pH dependence. Panel B represents an autoradiograph following gel electrophoresis, showing the displacement of the radiolabeled oligonucleotide. In lane 1, no Rad3 protein was added. Lanes 5 to 8 represent reactions at pH 5.3, 5.6, 5.9 and 6.2, respectively. Lane 2 is a control in which the substrate was heat denatured. The pH profile is shown graphically in panel C. The ATPase activity of Rad3 has the same pH requirements. (Adapted from reference 389 .)

10.1128/9781555816704/f0297-01_thmb.gif

10.1128/9781555816704/f0297-01.gif

Figure 8–35

/content/10.1128/9781555816704.ch08.ch08fig36

Figure 8–36

Yeast strains with mutations in the RAD3 gene that encode polypeptides carrying amino acid substitutions in conserved helicase motifs are defective in NER, as evidenced by a marked sensitivity to killing by UV radiation ( 376 ). The rad3-20 mutant allele encodes a polypeptide in which Gly47 in the highly conserved GKT helicase motif (see Fig. 8–34 ) is replaced with Asp; the rad3-21 allele encodes a polypeptide in which Lys48 in the GKT helicase motif is replaced with Glu; the rad3-1 allele encodes a polypeptide in which Glu236 in the DExH helicase motif II (see Fig. 8–34 ) is replaced with Lys, and the rad3-24 allele encodes a polypeptide in which Gly604 (helicase motif VI [ Fig. 8–37 ]) is replaced with Arg. (Adapted from reference 376 .)

10.1128/9781555816704/f0297-02_thmb.gif

10.1128/9781555816704/f0297-02.gif

Figure 8–36

/content/10.1128/9781555816704.ch08.ch08fig37

Figure 8–37

The predicted Rad16 polypeptide of S. cerevisiae contains consensus helicase family motifs (I to VI). These show extensive amino acid sequence identity to other members of the Swi/Snf family of proteins shown here. Amino acids shown in gold are identical in all or nearly all 10 polypeptides. Among the remaining amino acids, most of the differences reflect conservative substitutions. The conserved motifs are not contiguous in any of the proteins but are separated by protein sequences of different lengths (not shown here).

10.1128/9781555816704/f0300-01_thmb.gif

10.1128/9781555816704/f0300-01.gif

Figure 8–37

/content/10.1128/9781555816704.ch08.ch08fig38

Figure 8–38

Electrophoretic mobility shift measurements using a radiolabeled, UV-irradiated oligonucleotide and extracts from human cells. Extracts from repair-proficient cells and cells representing different XP complementation groups cause a shift of the mobility of the DNA in the gel. Only XP complementation group E cells lack activity for a major binding factor, designated DDB. (Adapted from reference 59 .)

10.1128/9781555816704/f0301-01_thmb.gif

10.1128/9781555816704/f0301-01.gif

Figure 8–38

/content/10.1128/9781555816704.ch08.ch08fig39

Figure 8–39

DDB1 as an intrinsic component of an E3 ubiquitin ligase with a wide range of substrates. DDB1 associates with other E3 ubiquitin ligase components including the cullin CUL4A and the ring finger protein RBX1 (which associates with an E2 enzyme in the ubiquitin pathway). Different partners can interact with DDB1, each of which is a “substrate adaptor” for a target of ubiquitination. The variable partners of DDB1 include DDB2 (with targets affecting the NER pathway), CSA (with partners affecting TC-NER), and V proteins of paramyxoviruses (with STAT targets affecting the interferon signaling pathway). (Provided by V. RapicOtrin and A.S. Levine.)

10.1128/9781555816704/f0303-01_thmb.gif

10.1128/9781555816704/f0303-01.gif

Figure 8–39

References

/content/book/10.1128/9781555816704.ch08

1. Aboussekhra, A.,, M. Biggerstaff,, M. K. K. Shivji,, J. A. Vilpo,, V. Moncollin,, V. N. Podust,, M. Protic,, U. Hübscher,, J.-M. Egly, and, R. D. Wood. 1995. Mammalian DNA nucleotide excision repair reconstituted with purified protein components. Cell 80 :859– 868.

2. Aboussekhra, A., and, F. Thoma. 1998. Nucleotide excision repair and photolyase preferentially repair the nontranscribed strand of RNA polymerase III-transcribed genes in Saccharomyces cerevisiae. Genes Dev. 12 :411– 421.

3. Adamczewski, J. P.,, M. Rossignol,, J. P. Tassan,, E. A. Nigg,, V. Moncollin, and, J. M. Egly. 1996. MAT1, cdk7 and cyclin H form a kinase complex which is UV light-sensitive upon association with TFIIH. EMBO J. 15 :1877– 1884.

4. Adimoolam, S.,, C. X. Lin, and, J. M. Ford. 2001. The p53-regulated cyclin-dependent kinase inhibitor, p21 (cip1, waf1, sdi1), is not required for global genomic and transcription-coupled nucleotide excision repair of UV-induced DNA photoproducts. J. Biol. Chem. 276 :25813– 25822.

5. Ahnstr1öm, G., 1989. Inhibition of DNA strand break rejoining in ultraviolet irradiated human cells: comparison of aphidicolin and cytosine arabinoside. Biochim. Biophys. Acta 1007 :357– 358.

6. Alapetite, C.,, T. Wachter,, E. Sage, and, E. Moustachi. 1996. Use of the alkaline comet assay to detect DNA-repair deficiencies in human fibroblasts exposed to UVC, UVB, UVA and gamma-rays. Int. J. Radiat. Biol. 69 :359– 369.

7. Al-Khodairy, F.,, E. Fotou,, K. S. Sheldrick,, D. J. Griffiths,, A. R. Lehmann, and, A. M. Carr. 1994. Identification and characterization of new elements involved in checkpoint and feedback controls in fission yeast. Mol. Biol. Cell 5 :147– 160.

8. Araj, H., and, P. D. Smith. 1996. Positional cloning of the Drosophila melanogaster mei-9 gene, the putative homolog of the Saccharomyces cerevisiae RAD1 gene. Mutat. Res. 364 :209– 215.

9. Araki, M.,, C. Masutani,, M. Takemura,, A. Uchida,, K. Sugasawa,, J. Kondoh,, Y. Ohkuma, and, F. Hanaoka. 2001. Centrosome protein centrin 2/caltractin 1 is part of the xeroderma pigmentosum group C complex that initiates global genome nucleotide excision repair. J. Biol. Chem. 276 :18665– 18672.

10. Araújo, 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 pre-assembled repairosome. Mol. Cell. Biol. 21 :2281– 2291.

11. Araújo, S. J.,, F. Tirode,, F. Coin,, H. Pospiech,, J. E. Syväoja,, M. Stucki,, U. Hübscher,, 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.

12. Aravind, L.,, D. R. Walker, and, E. V. Koonin. 1999. Conserved domains in DNA repair proteins and evolution of repair systems. Nucleic Acids Res. 27 :1223– 1242.

13. Asahina, H.,, I. Kuraoka,, M. Shirakawa,, E. H. Morita,, N. Miura,, I. Miyamoto,, E. Ohtsuka,, Y. Okada, and, K. Tanaka. 1994. The XPA protein is a zinc metalloprotein with an ability to recognize various kinds of DNA-damage. Mutat. Res. 315 :229– 237.

14. Bailis, A. M.,, L. Arthur, and, R. Rothstein. 1992. Genome rearrangement in top3 mutants of Saccharomyces cerevisiae requires a functional rad1 excision repair gene. Mol. Cell. Biol. 12 :4988– 4993.

15. Bailis, A. M.,, S. Maines, and, M. T. Negritto. 1995. The essential helicase gene RAD3 suppresses short-sequence recombination in Saccharomyces cerevisiae. Mol. Cell. Biol. 15 :3998– 4008.

16. Bailis, A. M., and, R. Rothstein. 1990. A defect in mismatch repair in Saccharomyces cerevisiae stimulates ectopic recombination between homologous genes by an excision repair dependent process. Genetics 126 :535– 547.

17. Bailly, V.,, C. H. Sommers,, P. Sung,, L. Prakash, and, S. Prakash. 1992. Specific complex-formation between proteins encoded by the yeast DNA-repair and recombination genes RAD1 and RAD10. Proc. Natl. Acad. Sci. USA 89 :8273– 8277.

18. Bang, D. d.,, R. Verhage,, N. Goosen,, J. Brouwer, and, P. van de Putte. 1992. Molecular cloning of RAD16, a gene involved in differential repair in Saccharomyces cerevisiae. Nucleic Acids Res. 20 :3925– 3931.

19. Bankmann, M.,, L. Prakash, and, S. Prakash. 1992. Yeast RAD14 and human xeroderma pigmentosum group A DNA repair genes encode homologous proteins. Nature 355 :555– 558.

20. Bardwell, A. J.,, L. Bardwell,, N. Iyer,, J. Q. Svejstrup,, W. J. Feaver,, R. D. Kornberg, and, E. C. Friedberg. 1994. Yeast nucleotide excision-repair proteins Rad2 and Rad4 interact with RNA-polymerase-II basal transcription factor-b (TFIIH). Mol. Cell. Biol. 14 :3569– 3576.

21. Bardwell, A. J.,, L. Bardwell,, D. K. Johnson, and, E. C. Friedberg. 1993. Yeast DNA recombination and repair proteins Rad1 and Rad10 constitute a complex in vivo mediated by localized hydrophobic domains. Mol. Microbiol. 8 :1177– 1188.

22. Bardwell, A. J.,, L. Bardwell,, A. E. Tomkinson, and, E. C. Fried-berg. 1994. Specific cleavage of model recombination and repair intermediates by the yeast Rad1-Rad10 DNA endonuclease. Science 265 :2082– 2085.

23. Bardwell, L.,, A. J. Bardwell,, W. J. Feaver,, J. Q. Svejstrup,, R. D. Kornberg, and, E. C. Friedberg. 1994. Yeast RAD3 protein binds directly to both Ssl2 and Ssl1 proteins–implications for the structure and function of transcription/repair factor-b. Proc. Natl. Acad. Sci. USA 91 :3926– 3930.

24. Bardwell, L.,, A. J. Cooper, and, E. C. Friedberg. 1992. Stable and specific association between the yeast recombination and DNA repair protein Rad1 and protein Rad10 in vitro. Mol. Cell. Biol. 12 :3041– 3049.

25. Barker, D. G.,, A. L. Johnson, and, L. H. Johnston. 1985. An improved assay for DNA ligase reveals temperature-sensitive activity in CDC9 mutants of S. cerevisiae. Mol. Gen. Genet. 200 :458– 462.

26. Batel, R.,, M. Fafandjel,, B. Blumbach,, H. C. Schroder,, H. M. Hassanein,, I. M. Muller, and, W. E. Muller. 1998. Expression of the human XPB/ERCC-3 excision repair gene-homolog in the sponge Geodia cydonium after exposure to ultraviolet radiation. Mutat. Res. 409 :123– 133.

27. Batty, D. P.,, V. R. Otrin,, A. S. Levine, and, R. D. Wood. 2000. Stable binding of human XPC-hHR23B complex to irradiated DNA confers strong discrimination for damaged sites. J. Mol. Biol. 300 :275– 290.

28. Bennetzen, J. L., and, B. D. Hall. 1982. Codon selection in yeast. J. Mol. Biol. 257 :3026– 3031.

29. Biggerstaff, M.,, D. E. Szymkowski, and, R. D. Wood. 1993. Co-correction of the ERCC1, ERCC4 and xeroderma pigmentosum group F DNA repair defects in vitro. EMBO J. 12 :3685– 3692.

30. Birnboim, H. C., and, A. Nasim. 1975. Excision of pyrimidine dimers by several UV-sensitive mutants of S. pombe. Mol. Gen. Genet. 136: 1– 8.

31. Bochkarev, A., and, E. Bochkareva. 2004. From RPA to BRCA2: lessons from single-stranded DNA binding by the OB-fold. Curr. Opin. Struct. Biol. 14 :36– 42.

32. Bochkarev, A.,, E. Bochkareva,, L. Frappier, and, A. M. Edwards. 1999. The crystal structure of the complex of replication protein A subunits RPA32 and RPA14 reveals a mechanism for single-stranded DNA binding. EMBO J. 18 :4498– 4504.

33. Bochkarev, A.,, R. A. Pfuetzner,, A. M. Edwards, and, L. Frappier. 1997. Structure of the single-stranded-DNA-binding domain of replication protein A bound to DNA. Nature 385 :176– 181.

34. Bochkareva, E.,, L. Frappier,, A. Edwards, and, A. Bochkarev. 1998. The RPA32 subunit of human replication protein A contains a single-stranded DNA-binding domain. J. Biol. Chem. 273 :3932– 3936.

35. Bootsma, D.,, M. P. Mulder,, J. A. Cohen, and, F. Pot. 1970. Different inherited levels of DNA repair replication in xeroderma pigmentosum cell strains after exposure to ultraviolet irradiation. Mutat. Res. 9 :507– 516.

36. Botta, E.,, T. Nardo,, B. C. Broughton,, S. Marinoni,, A. R. Lehmann, and, M. Stefanini. 1998. Analysis of mutations in the XPD gene in Italian patients with trichothiodystrophy–site of mutation correlates with repair deficiency, but gene dosage appears to determine clinical severity. Am. J. Hum. Genet. 63 :1036– 1048.

37. Boyd, J. B.,, J. M. Mason,, A. H. Yamamoto,, R. K. Brodberg,, S. S. Banga, and, K. Sakaguchi. 1987. A genetic and molecular analysis of DNA repair in Drosophila. J. Cell Sci. Suppl. 6 :39– 60.

38. Brand, M.,, J. G. Moggs,, M. Oulad-Abdelghani,, F. Lejeune,, F. J. Dilworth,, J. Stevenin,, G. Almouzni, and, L. Tora. 2001. UV-damaged DNA-binding protein in the TFTC complex links DNA damage recognition to nucleosome acetylation. EMBO J. 20 :3187– 3196.

39. Brill, S. J., and, S. Bastin-Shanower. 1998. Identification and characterization of the fourth single-stranded-DNA binding domain of replication protein A. Mol. Cell. Biol. 18 :7225– 7234.

40. Britt, A., and, C. Z. Jiang. 1999. Generation, identification, and characterization of repair-defective mutants of Arabidopsis. Methods Mol. Biol. 113 :31– 40.

41. Britt, A. B., 1996. DNA damage and repair in plants. Annu. Rev. Plant Physiol. 47 :75– 100.

42. Britt, A. B., 1998. DNA repair in higher plants, p. 577– 595. In J. A. Nickoloff and, M. F. Hoekstra (ed.), DNA Damage and Repair, vol. I. DNA Repair in Prokaryotes and Lower Eukaryotes. Humana Press, Totowa, N.J.

43. Britt, A. B., 1999. Molecular genetics of DNA repair in higher plants. Trends Plant Sci. 4 :20– 25.

44. Britt, A. B.,, J. J. Chen,, D. Wykoff, and, D. Mitchell. 1993. A UV-sensitive mutant of Arabidopsis defective in the repair of pyrimidine-pyrimidinone (6–4) dimers. Science 261 :1571– 1574.

45. Bronner, C. E.,, D. L. Welker, and, R. A. Deering. 1992. Mutations affecting sensitivity of the cellular slime mold Dictyostelium discoideum to DNA-damaging agents. Mutat. Res. 274 :187– 200.

46. Brookman, K. W.,, J. E. Lamerdin,, M. P. Thelen,, M. Hwang,, J. T. Reardon,, A. Sancar,, Z. Q. Zhou,, C. A. Walter,, C. N. Parris, and, L. H. Thompson. 1996. ERCC4 (XPF) encodes a human nucleotide excision repair protein with eukaryotic recombination homologs. Mol. Cell. Biol. 16 :6553– 6562.

47. Broughton, B. C.,, M. Berneburg,, H. Fawcett,, E. M. Taylor,, C. F. Arlett,, T. Nardo,, M. Stefanini,, E. Menefee,, V. H. Price,, S. Queille,, A. Sarasin,, E. Bohnert,, J. Krutmann,, R. Davidson,, K. H. Kraemer, and, A. R. Lehmann. 2001. Two individuals with features of both xeroderma pigmentosum and trichothiodystrophy highlight the complexity of the clinical outcomes of mutations in the XPD gene. Hum. Mol. Genet. 10 :2539– 2547.

48. Buchko, G. W.,, S. S. Ni,, B. D. Thrall, and, M. A. Kennedy. 1998. Structural features of the minimal DNA-binding domain (M98-F219) of human nucleotide excision-repair protein XPA. Nucleic Acids Res. 26 :2779– 2788.

49. Burns, J. L.,, S. N. Guzder,, P. Sung,, S. Prakash, and, L. Prakash. 1996. An affinity of human replication protein-A for ultraviolet-damaged DNA–implications for damage recognition in nucleotide excision-repair. J. Biol. Chem. 271 :11607– 11610.

50. Busch, D.,, J. Cleaver, and, D. Glaser. 1980. Large-scale isolation of UV-sensitive clones of CHO cells. Somatic Cell Genet. 6 :407– 418.

51. Busch, D.,, C. Greiner,, K. Lewis,, R. Ford,, G. Adair, and, L. Thompson. 1989. Summary of complementation groups of UV-sensitive CHO cell mutants isolated by large scale screening. Mutagenesis 4 :349– 354.

52. Busch, D.,, C. Greiner,, K. L. Rosenfeld,, R. Ford,, J. Dewit,, J. H. J. Hoeijmakers, and, L. H. Thompson. 1994. Complementation group assignments of moderately UV-sensitive CHO mutants isolated by large-scale screening (FAECB). Mutagenesis 9 :301– 306.

53. Buschta-Hedayat, N.,, T. Buterin,, M. T. Hess,, M. Missura, and, H. Naegeli. 1999. Recognition of nonhybridizing base pairs during nucleotide excision repair of DNA. Proc. Natl. Acad. Sci. USA 96 :6090– 6095.

54. Carr, A.,, H. Schmidt,, S. Kirchhoff,, W. Muriel,, K. Sheldrick,, D. Griffiths,, C. Basmacioglu,, S. Subramani,, M. Clegg, and, A. Nasim. 1994. The rad16 gene of Schizosaccharomyces pombe: a homolog of the RAD1 gene of Saccharomyces cerevisiae. Mol. Cell. Biol. 14 :2029– 2040.

55. Carr, A. M.,, K. S. Sheldrick,, J. M. Murray,, R. Al-Harithy,, F. Z. Watts, and, A. R. Lehmann. 1993. Evolutionary conservation of excision repair in Schizosaccharomyces pombe: evidence for a family of sequences related to the Saccharomyces cerevisiae RAD2 gene. Nucleic Acids Res. 21 :1345– 1349.

56. Cenkci, B.,, J. L. Petersen, and, G. D. Small. 2003. REX1, a novel gene required for DNA repair. J. Biol. Chem. 278 :22574– 22577.

57. Ceska, T.,, J. Sayers,, G. Stier, and, D. Suck. 1996. A helical arch allowing single-stranded-DNA to thread through T5 5’-exonuclease. Nature 382 :90– 93.

58. Chen, X.,, Y. Zhang,, L. Douglas, and, P. Zhou. 2001. UV-damaged DNA binding proteins are targets of Cul4A-mediated ubiquitination and degradation. J. Biol. Chem. 276 :48175– 48182.

59. Chu, G., and, E. Chang. 1988. Xeroderma pigmentosum group E cells lack a nuclear factor that binds to damaged DNA. Science 242 :564– 567.

60. Clarkson, J. M.,, D. L. Mitchell, and, G. M. Adair. 1983. The use of an immunological probe to measure the kinetics of DNA repair in normal and UV-sensitive mammalian cell lines. Mutat. Res. 112 :287– 299.

61. Clarkson, S. G., 2003. The XPG story. Biochimie 85 :1113– 1121.

62. Cleaver, J. E., 1968. Defective repair replication of DNA in xeroderma pigmentosum. Nature 218 :652– 656.

63. Cleaver, J. E., and, G. H. Thomas. 1981. Measurement of unscheduled DNA synthesis by autoradiography, p. 277– 287. In E. C. Fried-berg and, P. C. Hanawalt (ed.), DNA Repair. A Laboratory Manual of Research Procedures. Marcel Dekker, Inc. New York, N.Y.

64. Cloud, K.,, B. Shen,, G. Strniste, and, M. Park. 1995. XPG protein has structure-specific endonuclease activity. Mutat. Res. 347 :55– 60.

65. Clugston, C. K.,, K. McLaughlin,, M. K. Kenny, and, R. Brown. 1992. Binding of human single-stranded-DNA binding-protein to DNA damaged by the anticancer drug cis-diamminedichloroplatinum(II). Cancer Res. 52 :6375– 6379.

66. Collins, A. R., 1993. Mutant rodent cell-lines sensitive to ultraviolet-light, ionizing-radiation and cross-linking agents: a comprehensive survey of genetic and biochemical characteristics. Mutat. Res. 293 :99– 118.

67. Collins, A. R. S., and, R. T. Johnson. 1981. Use of metabolic inhibitors in repair studies, p. 314– 360. In E. C. Friedberg and, P. C. Hanawalt (ed.), DNA Repair. A Laboratory Manual of Research Procedures. Marcel Dekker, Inc. New York, N.Y.

68. 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.

69. Cooper, A. J., and, R. Waters. 1987. A complex pattern of sensitivity to simple monofunctional alkylating agents exists amongst the mutants of Saccharomyces cerevisiae. Mol. Gen. Genet. 209 :142– 148.

70. Couto, L. B., and, E. C. Friedberg. 1989. Nucleotide sequence of the wild type RAD4 gene of Saccharomyces cerevisiae and characterization of mutant rad4 alleles. J. Bacteriol. 171 :1862– 1869.

71. Coverley, D.,, M. K. Kenny,, D. P. Lane, and, R. D. Wood. 1992. A role for the human single-stranded DNA binding protein HSSB/RPA in an early stage of nucleotide excision repair. Nucleic Acids Res. 20 :3873– 3880.

72. Coverley, D.,, M. K. Kenny,, M. Munn,, W. D. Rupp,, D. P. Lane, and, R. D. Wood. 1991. Requirement for the replication protein SSB in human DNA excision repair. Nature 349 :538– 541.

73. Cox, B. S., and, J. M. Parry. 1968. The isolation, genetics and survival characteristics of ultraviolet light-sensitive mutants in yeast. Mutat. Res. 6 :37– 55.

74. Dai, S. M.,, H. H. Chen,, C. Chang,, A. D. Riggs, and, S. D. Flanagan. 2000. Ligation-mediated PCR for quantitative in vivo footprinting. Nat. Biotechnol. 18 :1108– 1111.

75. Datta, A.,, S. Bagchi,, A. Nag,, P. Shiyanov,, G. R. Adami,, T. Yoon, and, P. Raychaudhuri. 2001. The p48 subunit of the damaged-DNA binding protein DDB associates with the CBP/p300 family of histone acetyltransferase. Mutat. Res. 486 :89– 97.

76. 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.

77. de Boer, J.,, I. Donker,, J. de Wit,, J. H. J. Hoeijmakers, and, G. Weeda. 1998. Disruption of the mouse xeroderma pigmentosum group D DNA repair basal transcription gene results in preimplantation lethality. Cancer Res. 58 :89– 94.

78. de Jonge, A. J. R.,, W. Vermeulen,, W. Keijzer,, J. H. J. Hoeijmakers, and, D. Bootsma. 1985. Microinjection of Micrococcus luteus UVendonuclease restores UV-induced unscheduled DNA synthesis in cells of 9 xeroderma pigmentosum complementation groups. Mutat. Res. 150 :99– 105.

79. de Jonge, A. J. R.,, W. Vermeulen,, B. Klein, and, J. H. J. Hoeijmakers. 1983. Microinjection of human cell extracts corrects xeroderma pigmentosum defect. EMBO J. 2 :637– 641.

80. de Laat, W. L.,, E. Appeldoorn,, N. G. J. Jaspers, and, J. H. J. Hoeijmakers. 1998. DNA structural elements required for ERCC1-XPF endonuclease activity. J. Biol. Chem. 273 :7835– 7842.

81. de Laat, W. L.,, E. Appeldoorn,, K. Sugasawa,, E. Weterings,, N. G. J. Jaspers, and, J. H. J. Hoeijmakers. 1998. DNA-binding polarity of human replication protein A positions nucleases in nucleotide excision repair. Genes Dev. 12 :2598– 2609.

82. de Laat, W. L.,, A. M. Sijbers,, H. Odijk,, N. G. J. Jaspers, and, J. H. J. Hoeijmakers. 1998. Mapping of interaction domains between human repair proteins ERCC1 and XPF. Nucleic Acids Res. 26 :4146– 4152.

83. Devault, A.,, A. M. Martinez,, D. Fesquet,, J. C. Labbe,, N. Morin,, J. P. Tassan,, E. A. Nigg,, J. C. Cavadore, and, M. Doree. 1995. MAT1 (’menage a trois’), a new RING finger protein subunit stabilizing cyclin H-cdk7 complexes in starfish and Xenopus CAK. EMBO J. 14 :5027– 5036.

84. de Weerd-Kastelein, E. A.,, W. Keijzer, and, D. Bootsma. 1972. Genetic heterogeneity of xeroderma pigmentosum demonstrated by somatic cell hybridization. Nat. New Biol. 238 :80– 83.

85. Djordjevic, B., and, L. J. Tolmach. 1967. Responses of synchronous populations of HeLa cells to ultraviolet irradiation at selected stages of the generation cycle. Radiat. Res. 32 :327– 346.

86. Dohmen, R. J.,, P. Wu, and, A. Varshavsky. 1994. Heat-inducible degron: a method for constructing temperature-sensitive mutants. Science 263 :1273– 1276.

87. Drapkin, R.,, J. T. Reardon,, A. Ansari,, J. C. Huang,, L. Zawel,, K. J. Ahn,, A. Sancar, and, D. Reinberg. 1994. Dual role of TFIIH in DNA excision repair and in transcription by RNA polymerase II. Nature 368 :769– 772.

88. Dualan, R.,, T. Brody,, S. Keeney,, A. F. Nichols,, A. Admon, and, S. Linn. 1995. Chromosomal localization and cDNA cloning of the genes ( DDB1 and DDB2) for the p127 and p48 subunits of a human damage-specific DNA-binding protein. Genomics 29 :62– 69.

89. Dusenbery, R. L., and, P. D. Smith. 1996. Cellular responses to DNA damage in Drosophila melanogaster. Mutat. Res. 364 :133– 145.

90. Eggset, G.,, G. Volden, and, H. Krokan. 1987. Characterization of antibodies specific for UV-damaged DNA by ELISA. Photochem. Photobiol. 45 :485– 491.

91. Ehmann, U. K., and, E. C. Friedberg. 1980. An investigation of the effect of radioactive labeling of DNA on excision repair in UV-irradiated human fibroblasts. Biophys. J. 31 :285– 291.

92. Elsasser, S.,, R. R. Gali,, M. Schwickart,, C. N. Larsen,, D. S. Leggett,, B. Muller,, M. T. Feng,, F. Tubing,, G. A. Dittmar, and, D. Finley. 2002. Proteasome subunit Rpn1 binds ubiquitin-like protein domains. Nat. Cell Biol. 4 :725– 730.

93. Enzlin, J. H., and, O. D. Schärer. 2002. The active site of the DNA repair endonuclease XPF-ERCC1 forms a highly conserved nuclease motif. EMBO J. 21 :2045– 2053.

94. Erixon, K., and, G. Ahnstrom. 1979. Single-strand breaks in DNA during repair of UV-induced damage in normal human and xeroderma pigmentosum cells as determined by alkaline DNA unwinding and hydroxylapatite chromatography: effects of hydroxyurea, 5-fluorodeoxyuridine and 1-fS-D-arabinofuranosylcytosme on the kinetics of repair. Mutat. Res. 59 :257– 271.

95. 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.

96. 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.

97. Fairman, M. P., and, B. Stillman. 1988. Cellular factors required for multiple stages of SV40 DNA replication in vitro. EMBO J. 7 :1211– 1218.

98. Feaver, W. J.,, N. L. Henry,, Z. G. Wang,, X. H. Wu,, J. Q. Svejstrup,, D. A. Bushnell,, E. C. Friedberg, and, R. D. Kornberg. 1997. Genes for Tfb2, Tfb3, and Tfb4 subunits of yeast transcription/repair factor IIH: homology to human cyclin-dependent kinase activating kinase and IIH subunits. J. Biol. Chem. 272 :19319– 19327.

99. Feaver, W. J.,, W. Huang, and, E. C. Friedberg. 1999. The TFB4 subunit of yeast TFIIH is required for both nucleotide excision repair and RNA polymerase II transcription. J. Biol. Chem. 274 :29564– 29567.

100. Feaver, W. J.,, W. Huang,, O. Gileadi,, L. Myers,, C. M. Gustafsson,, R. D. Kornberg, and, E. C. Friedberg. 2000. Subunit interactions in yeast transcription/repair factor TFIIH. Requirement for Tfb3 subunit in nucleotide excision repair. J. Biol. Chem. 275 :5941– 5946.

101. Feaver, W. J.,, J. Q. Svejstrup,, L. Bardwell,, A. J. Bardwell,, S. Bu-ratowski,, K. D. Gulyas,, T. F. Donahue,, E. C. Friedberg, and, R. D. Kornberg. 1993. Dual roles of a multiprotein complex from Saccharomyces cerevisiae in transcription and DNA repair. Cell 75 :1379– 1387.

102. Feldberg, R. S., and, L. Grossman. 1976. A DNA binding protein from human placenta specific for ultraviolet damaged DNA. Biochemistry 15 :2402– 2408.

103. Fisher, R. P.,, P. Jin,, H. M. Chamberlin, and, D. O. Morgan. 1995. Alternative mechanisms of CAK assembly require an assembly factor or an activating kinase. Cell 83 :47– 57.

104. Fishman-Lobell, J., and, J. E. Haber. 1992. Removal of nonhomologous DNA ends in double-strand break recombination: the role of the yeast ultraviolet repair gene RAD1. Science 258 :480– 484.

105. Fleer, R.,, C. M. Nicolet,, G. A. Pure, and, E. C. Friedberg. 1987. RAD4 gene of S. cerevisiae: molecular cloning and partial characterization of a gene that is inactivated in E. coli. Mol. Cell. Biol. 7 :1180– 1192.

106. Fleer, R.,, W. Siede, and, E. C. Friedberg. 1987. Mutational inactivation of the Saccharomyces cerevisiae RAD4 gene in Escherichia coli. J. Bacteriol. 169 :4884– 4892.

107. Flejter, W. L.,, L. D. McDaniel,, D. Johns,, E. C. Friedberg, and, R. A. Schultz. 1992. Correction of xeroderma pigmentosum complementation group D mutant cell phenotypes by chromosome and gene transfer: involvement of the human ERCC2 DNA repair gene. Proc. Natl. Acad. Sci. USA 89 :261– 265.

108. Ford, J. M.,, E. L. Baron, and, P. C. Hanawalt. 1998. Human fibroblasts expressing the human-papillomavirus E6 gene are deficient in global genomic nucleotide excision repair and sensitive to ultraviolet irradiation. Cancer Res. 58 :599– 603.

109. Fornace, A. J.,, K. W. Kohn, and, H. E. Kann. 1976. DNA single-strand breaks during repair of UV damage in human fibroblasts and abnormalities of repair in xeroderma pigmentosum. Proc. Natl. Acad. Sci. USA 73 :39– 43.

110. Frederick, G. D.,, R. H. Amirkhan,, R. A. Schultz, and, E. C. Friedberg. 1994. Structural and mutational analysis of the xeroderma pigmentosum group D ( XPD) gene. Hum. Mol. Genet. 3 :1783– 1788.

111. Friedberg, E. C., 1988. Deoxyribonucleic acid repair in the yeast Saccharomyces cerevisae. Microbiol. Rev. 52 :70– 102.

112. Friedberg, E. C., 1997. Correcting the Blueprint of Life: an Historical Account of the Discovery of DNA Repair Mechanisms. Cold Spring Harbor Laboratory Press, Plainview, N.Y.

113. Friedberg, E. C., and, P. C. Hanawalt (ed.) 1981. DNA Repair: a Laboratory Manual of Research Procedures, vol., 1, part B. Marcel Dekker, Inc., New York, N.Y.

114. Friedberg, E. C., and, P. C. Hanawalt (ed.), 1981. DNA Repair: a Laboratory Manual of Research Procedures, vol. 1, part A. Marcel Dekker, Inc., New York, N.Y.

115. Friedberg, E. C., and, P. C. Hanawalt (ed.), 1983. DNA Repair: a Laboratory Manual of Research Procedures, vol. 2. Marcel Dekker, Inc., New York, N.Y.

116. Friedberg, E. C., and, P. C. Hanawalt (ed.) 1988. DNA Repair. a Laboratory Manual of Research Procedures, vol., 3. Marcel Dekker, Inc., New York, N.Y.

117. Friedberg, E. C.,, W. Siede, and, A. J. Cooper. 1991. Cellular responses to DNA damage in yeast, p. 147– 192. In J. R. Broach,, J. R. Pringle, and, E. W. Jones (ed.), The Molecular and Cellular Biology ofthe Yeast Saccharomyces. Genome Dynamics, Protein Synthesis, and Energetics. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.

118. Friedberg, E. C.,, G. C. Walker, and, W. Siede. 1995. DNA Repair and Mutagenesis. ASM Press, Washington, D.C.

119. Fujiwara, Y.,, C. Masutani,, T. Mizukoshi,, J. Kondo,, F. Hanaoka, and, S. Iwai. 1999. Characterization of DNA recognition by the human UVdamaged DNA-binding protein. J. Biol. Chem. 274 :20027– 20033.

120. 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.

121. Gao, S. W.,, R. Drouin, and, G. P. Holmquist. 1994. DNA repair rates mapped along the human PGK1 gene at nucleotide resolution. Science 263 :1438– 1440.

122. Gedik, C. M., and, A. R. Collins. 1990. Comparison of effects of fostriecin, novobiocin, and camptothecin, inhibitors of DNA topoisomerases, on DNA replication and repair in human cells. Nucleic Acids Res. 18 :1007– 1013.

123. Giannelli, F.,, S. A. Pawsey, and, J. A. Avery. 1982. Differences in patterns of complementation of the more common groups of xeroderma pigmentosum: possible implications. Cell 29 :451– 458.

124. Gietz, R. D., and, S. Prakash. 1988. Cloning and nucleotide sequence analysis of the Saccharomyces cerevisiae RAD4 gene required for excision repair of UV damaged DNA. Gene 74 :535– 541.

125. Giglia-Mari, G.,, F. Coin,, J. A. Ranish,, D. Hoogstraten,, A. Theil,, N. Wijgers,, N. G. Jaspers,, A. Raams,, M. Argentini,, P. J. van der Spek,, E. Botta,, M. Stefanini,, J. M. Egly,, R. Aebersold,, J. H. Hoeijmakers, and, W. Vermeulen. 2004. A new, tenth subunit of TFIIH is responsible for the DNA repair syndrome trichothiodystrophy group A. Nat. Genet. 36 :714– 719.

126. Gileadi, O.,, W. J. Feaver, and, R. D. Kornberg. 1992. Cloning of a subunit of yeast RNA polymerase II transcription factor b and CTD kinase. Science 257 :1389– 1392.

127. Green, M. H. L.,, J. E. Lowe,, S. A. Harcourt,, P. Akinluyi,, T. Rowe,, J. Cole,, A. V. Anstey, and, C. F. Arlett. 1992. UV-C sensitivity of unstimulated and stimulated human lymphocytes from normal and xeroderma pigmentosum donors in the comet assay: a potential diagnostic technique. Mutat. Res. 273 :137– 144.

128. Grimaldi, K. A.,, S. R. McAdam, and, J. A. Hartley. 1999. PCRbased assays for strand-specific measurement of DNA damage and repair. II. Single-strand ligation-PCR. Methods Mol. Biol. 113 :241– 255.

129. Grimaldi, K. A.,, C. J. McGurk,, P. J. McHugh, and, J. A. Hartley. 2002. PCR-based methods for detecting DNA damage and its repair at the subgene and single nucleotide levels in cells. Mol. Biotechnol. 20 :181– 196.

130. Groisman, R.,, J. Polanowska,, I. Kuraoka,, J. Sawada,, M. Saijo,, R. Drapkin,, A. F. Kisselev,, K. Tanaka, and, Y. Nakatani. 2003. The ubiquitin ligase activity in the DDB2 and CSA complexes is differentially regulated by the COP9 signalosome in response to DNA damage. Cell 113 :357– 367.

131. Guillet, M., and, S. Boiteux. 2002. Endogenous DNA abasic sites cause cell death in the absence of Apn1, Apn2 and Rad1/Rad10 in Saccharomyces cerevisiae. EMBO J. 21 :2833– 2841.

132. Gulyas, K., and, T. Donahue. 1992. SSL2, a suppressor of a stem-loop mutation in the his4 leader encodes the yeast homolog of human ERCC3. Cell 69 :1031– 1042.

133. Guzder, S. N.,, Y. Habraken,, P. Sung,, L. Prakash, and, S. Prakash. 1995. Reconstitution of yeast nucleotide excision repair with purified Rad proteins, replication protein-A, and transcription factor TFIIH. J. Biol. Chem. 270 :12973– 12976.

134. Guzder, S. N.,, H. F. Qiu,, C. H. Sommers,, P. Sung,, L. Prakash, and, S. Prakash. 1994. DNA repair gene RAD3 of Saccharomyces cerevisiae is essential for transcription by RNA polymerase II. Nature 367 :91– 94.

135. Guzder, S. N.,, P. Sung,, V. Bailly,, L. Prakash, and, S. Prakash. 1994. Rad25 is a DNA helicase required for DNA repair and RNA-polymerase-II transcription. Nature 369 :578– 581.

136. Guzder, S. N.,, P. Sung,, L. Prakash, and, S. Prakash. 1993. Yeast DNA repair gene RAD14 encodes a zinc metalloprotein with affinity for ultraviolet-damaged DNA. Proc. Natl. Acad. Sci. USA 90 :5433– 5437.

137. Guzder, S. N.,, P. Sung,, L. Prakash, and, S. Prakash. 1997. Yeast Rad7-Rad16 complex, specific for the nucleotide excision-repair of the non-transcribed DNA strand, is an ATP-dependent DNA-damage sensor. J. Biol. Chem. 272 :21665– 21668.

138. Guzder, S. N.,, P. Sung,, L. Prakash, and, S. Prakash. 1998. Affinity of yeast nucleotide excision repair factor 2, consisting of the Rad4 and Rad23 proteins, for ultraviolet damaged DNA. J. Biol. Chem. 273 :31541– 31546.

139. Guzder, S. N.,, P. Sung,, L. Prakash, and, S. Prakash. 1998. The DNA-dependent ATPase activity of yeast nucleotide excision repair factor-4 and its role in DNA-damage recognition. J. Biol. Chem. 273 :6292– 6296.

140. Habraken, Y.,, P. Sung,, L. Prakash, and, S. Prakash. 1993. Yeast excision repair gene RAD2 encodes a single-stranded DNA endonuclease. Nature 366 :365– 368.

141. Habraken, Y.,, P. Sung,, L. Prakash, and, S. Prakash. 1994. A conserved 5’ to 3’ exonuclease activity in the yeast and human nucleotide excision repair proteins Rad2 and XPG. J. Biol. Chem. 269 :31342– 31345.

142. Habraken, Y.,, P. Sung,, L. Prakash, and, S. Prakash. 1995. Structure-specific nuclease activity in yeast nucleotide excision-repair protein Rad2. J. Biol. Chem. 270 :30194– 30198.

143. Hanawalt, P. C.,, P. K. Cooper, and, C. A. Smith. 1981. Repair replication schemes in bacteria and human cells. Prog. Nucleic Acid Res. Mol. Biol. 26 :181– 196.

144. Hanawalt, P. C.,, P. K. Cooper,, A. K. Ganesan, and, C. A. Smith. 1979. DNA repair in bacteria and mammalian cells. Annu. Rev. Biochem. 48 :783– 836.

145. Harosh, I.,, L. Naumovski, and, E. C. Friedberg. 1989. Purification and characterization of Rad3 ATPase/DNA helicase from Saccharomyces cerevisiae. J. Biol. Chem. 264 :532–539.

146. Harrington, J. J., and, M. R. Lieber. 1994. Functional domains within FEN-1 and Rad2 define a family of structure-specific endonucleases: implications for nucleotide excision repair. Genes Dev. 8 :1344– 1355.

147. Hartman, P. S., and, G. A. Nelson. 1998. Processing of DNA Damage in the nematode Caenorhabditis elegans, p. 557– 576. In J. A. Nickoloff and, M. F. Hoekstra (ed.), DNA Damage and Repair, vol. I. DNA Repair in Prokaryotes and Lower Eukaryotes. Humana Press, Totowa, N.J.

148. Hartwell, L., 1971. Genetic control of the cell division cycle in yeast. II Genes controlling DNA replication and its initiation. J. Mol. Biol. 59 :183– 194.

149. Hartwell, L. H., 1973. Three additional genes required for deoxyribonucleic acid synthesis in Saccharomyces cerevisiae. J. Bacteriol. 115 :996– 974.

150. Hatakeyama, S.,, Y. Ito,, A. Shimane,, C. Ishii, and, H. Inoue. 1998. Cloning and characterization of the yeast RAD1 homolog gene (mus-38) from Neurospora crassa: evidence for involvement in nucleotide excision repair. Curr. Genet. 33 :276– 283.

151. Hayes, S.,, P. Shiyanov,, X. Q. Chen, and, P. Raychaudhuri. 1998. DDB, a putative DNA repair protein, can function as a transcriptional partner of E2F1. Mol. Cell. Biol. 18 :240– 249.

152. He, Z.,, L. A. Henricksen,, M. S. Wold, and, C. J. Ingles. 1995. RPA involvement in the damage-recognition and incision steps of nucleotide excision repair. Nature 374 :566– 569.

153. He, Z. G.,, J. M. S. Wong,, H. S. Maniar,, S. J. Brill, and, C. J. Ingles. 1996. Assessing the requirements for nucleotide excision repair proteins of Saccharomyces cerevisiae in an in vitro system. J. Biol. Chem. 271 :28243– 28249.

154. Henderson, D. S. (ed.)., 1999. DNA Repair Protocols: Eukaryotic Systems. Humana Press: Totowa, N.J.

155. Henderson, D. S., 1999. Isolating DNA repair mutants of Drosophila melanogaster, p. 17– 30. In D. S. Henderson (ed.), DNA Repair Protocols: Eukaryotic Systems. Humana Press, Totowa, N.J.

156. Henning, K. A.,, C. Peterson,, R. Legerski, and, E. C. Friedberg. 1994. Cloning the Drosophila homolog of the xeroderma pigmentosum complementation group C gene reveals homology between the predicted human and Drosophila polypeptides and that encoded by the yeast RAD4 gene. Nucleic Acids Res. 22 :257– 261.

157. Hey, T.,, G. Lipps,, K. Sugasawa,, S. Iwai,, F. Hanaoka, and, G. Krauss. 2002. The XPC-HR23B complex displays high affinity and specificity for damaged DNA in a true-equilibrium fluorescence assay. Biochemistry 41 :6583– 6587.

158. Higgins, D. R.,, L. Prakash,, P. Reynolds, and, S. Prakash. 1984. Isolation and characterization of the RAD2 gene of Saccharomyces cerevisiae. Gene 30 :121– 128.

159. Higgins, D. R.,, S. Prakash,, P. Reynolds, and, L. Prakash. 1983. Molecular cloning and characterization of the RAD1 gene of S. cerevisiae. Gene 26 :119– 126.

160. Hirschfeld, S.,, A. S. Levine,, K. Ozato, and, M. Protic. 1990. A constitutive damage-specific DNA-binding protein is synthesized at higher levels in UV-irradiated primate cells. Mol. Cell. Biol. 10 :2041– 2048.

161. Ho, Y.,, A. Gruhler,, A. Heilbut,, G. D. Bader,, L. Moore,, S. L. Adams,, A. Millar,, P. Taylor,, K. Bennett,, K. Boutilier,, L. Yang,, C. Wolting,, I. Donaldson,, S. Schandorff,, J. Shewnarane,, M. Vo,, J. Taggart,, M. Goudreault,, B. Muskat,, C. Alfarano, et al., 2002. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415 :180– 183.

162. Hoeijmakers, J. H. J., 1993. Nucleotide excision repair. 1. From Escherichia coli to yeast. Trends Genet. 9 :173– 177.

163. Hoeijmakers, J. H. J., 1993. Nucleotide excision repair. 2. From yeast to mammals. Trends Genet. 9 :211– 217.

164. Hoeijmakers, J. H. J., and, D. Bootsma. 1990. Molecular genetics of eukaryotic DNA excision repair. Cancer Cells Mon. Rev. 2 :311– 320.

165. Hoeijmakers, J. H. J.,, A. P. M. Eker,, R. D. Wood, and, P. Robins. 1990. Use of in vivo and in vitro assays for the characterization of mammalian excision repair and isolation of repair proteins. Mutat. Res. 236 :223– 238.

166. Hoekema, A.,, R. A. Kastelein,, M. Vasser, and, H. A. de Boer. 1987. Codon replacement in the PGKI gene of Saccharomyces cerevisiae: experimental approach to study the role of biased codon usage in gene expression. Mol. Cell. Biol. 7 :2914– 2924.

167. Hohl, M.,, F. Thorel,, S. G. Clarkson, and, O. D. Scharer. 2003. Structural determinants for substrate binding and catalysis by the structure-specific endonuclease XPG. J. Biol. Chem. 278 :19500– 19508.

168. Hosfield, D. J.,, C. D. Mol,, B. H. Shen, and, J. A. Tainer. 1998. Structure of the DNA repair and replication endonuclease and exonuclease FEN-1: coupling DNA and PCNA binding to FEN-1 activity. Cell 95 :135– 146.

169. Houle, J. F., and, E. C. Friedberg. 1999. The Drosophila ortholog of the human XPG gene. Gene 234 :353– 360.

170. Houtsmuller, A. B.,, S. Rademakers,, A. L. Nigg,, D. Hoogstraten,, J. H. J. Hoeijmakers, and, W. Vermeulen. 1999. Action of DNA repair endonuclease ERCC1/XPF in living cells. Science 284 :958– 961.

171. Hsia, K. T.,, M. R. Millar,, S. King,, J. Selfridge,, N. J. Redhead,, D. W. Melton, and, P. T. Saunders. 2003. DNA repair gene Ercc1 is essential for normal spermatogenesis and oogenesis and for functional integrity of germ cell DNA in the mouse. Development 130 :369– 378.

172. Huang, W. Y.,, W. J. Feaver,, A. E. Tomkinson, and, E. C. Fried-berg. 1998. The N-degron protein degradation strategy for investigating the function of essential genes: requirement for replication protein-A and proliferating cell nuclear antigen proteins for nucleotide excision repair in yeast extracts. Mutat. Res. 408 :183– 194.

173. Hwang, B. J., and, G. Chu. 1993. Purification and characterization of a human protein that binds to damaged DNA. Biochemistry 32 :1657– 1666.

174. Hwang, B. J.,, J. M. Ford,, P. C. Hanawalt, and, G. Chu. 1999. Expression of the p48 xeroderma pigmentosum gene is p53-dependent and is involved in global genomic repair. Proc. Natl. Acad. Sci. USA 96 :424– 428.

175. Hwang, B. J.,, S. Toering,, U. Francke, and, G. Chu. 1998. p48 activates a UV-damaged-DNA binding-factor and is defective in xeroderma pigmentosum group-E cells that lack binding activity. Mol. Cell. Biol. 18 :4391– 4399.

176. Iakoucheva, L. M.,, A. L. Kimzey,, C. D. Masselon,, R. D. Smith,, A. K. Dunker, and, E. J. Ackerman. 2001. Aberrant mobility phenomena of the DNA repair protein XPA. Protein Sci. 10 :1353– 1362.

177. Ikegami, T.,, I. Kuraoka,, M. Saijo,, N. Kodo,, Y. Kyoguko,, K. Morikawa,, K. Tanaka, and, M. Shirakawa. 1998. Solution structure of the DNA- and RPA-binding domain of the human repair factor XPA. Nat. Struct. Biol. 5 :701– 706.

178. Itoh, T.,, S. Linn,, T. Ono, and, M. Yamaizumi. 2000. Reinvestigation of the classification of five cell strains of xeroderma pigmentosum group E with reclassification of three of them. J. Investig. Dermatol. 114 :1022– 1029.

179. Ivanov, E. L., and, J. E. Haber. 1995. RAD1 and RAD10, but not other excision repair genes, are required for double-strand break-induced recombination in Saccharomyces cerevisiae. Mol. Cell. Biol. 15 :2245– 2251.

180. Jansen, L. E. T.,, R. A. Verhage, and, J. A. Brouwer. 1998. Preferential binding of yeast Rad4-Rad23 complex to damaged DNA. J. Biol. Chem. 273 :33111– 33114.

181. Jiang, C. Z.,, C. N. Yen,, K. Cronin,, D. Mitchell, and, A. B. Britt. 1997. UV and gamma-radiation-sensitive mutants of Arabidopsis thaliana. Genetics 147 :1401– 1409.

182. Johnston, L. H., and, K. A. Nasmyth. 1978. Saccharomyces cerevisiae cell cycle mutant cdc9 is defective in DNA ligase. Nature 274 :891– 893.

183. Jones, C. J., and, R. D. Wood. 1993. Preferential binding of the xeroderma pigmentosum group A complementing protein to damaged DNA. Biochemistry 32 :12096– 12104.

184. Jong, A. Y.,, C. L. Kuo, and, J. L. Campbell. 1984. The CDC8 gene of yeast encodes thymidylate kinase. J. Biol. Chem. 259 :11052– 11059.

185. Kadkhodayan, S.,, E. P. Salazar,, M. J. Ramsey,, K. Takayama,, M. Z. Zdzienicka,, J. D. Tucker, and, C. A. Weber. 1997. Molecular analysis of ERCC2 mutations in the repair-deficient hamster mutants UVL-1 and V-H1. Mutat. Res. 385 :47– 57.

186. Kafer, E., and, G. S. May. 1998. Toward repair pathways in Aspergillus nidulans, p. 477– 502. In J. A. Nickoloff and, M. F. Hoekstra (ed.), DNA Damage and Repair, vol. I. DNA Repair in Prokaryotes and Lower Eukaryotes. Humana Press, Totowa, N.J.

187. Kantor, G. J., and, R. B. Setlow. 1981. Rate and extent of DNA repair in nondividing human deploid fibroblasts. Cancer Res. 41 :819– 825.

188. Keeney, S.,, G. J. Chang, and, S. Linn. 1993. Characterization of a human DNA-damage binding protein implicated in xeroderma pigmentosum E. J. Biol. Chem. 268 :21293– 21300.

189. Keeney, S.,, A. P. M. Eker,, T. Brody,, W. Vermeulen,, D. Bootsma,, J. H. J. Hoeijmakers, and, S. Linn. 1994. Correction of the DNA repair defect in xeroderma pigmentosum group E by injection of a DNA damage binding protein. Proc. Natl. Acad. Sci. USA 91 :4053– 4056.

190. Keijzer, W.,, A. Verkerk, and, D. Bootsma. 1982. Phenotypic correction of the defect in xeroderma pigmentosum after fusion with isolated cytoplasts. Exp. Cell Res. 140 :119– 125.

191. Kenny, M. K.,, U. Schlegel,, H. Furneaux, and, J. Hurwitz. 1990. The role of human single-stranded DNA binding protein and its individual subunits in simian virus 40 DNA replication. J. Biol. Chem. 265 :7693– 7700.

192. Kerr, I. D.,, R. I. Wadsworth,, L. Cubeddu,, W. Blankenfeldt,, J. H. Naismith, and, M. F. White. 2003. Insights into ssDNA recognition by the OB fold from a structural and thermodynamic study of Sulfolobus SSB protein. EMBO J. 22 :2561– 2570.

193. Kimura, S.,, Y. Tahira,, T. Ishibashi,, Y. Mori,, T. Mori,, J. Hashimoto, and, K. Sakaguchi. 2004. DNA repair in higher plants; photoreactivation is the major DNA repair pathway in non-proliferating cells while excision repair (nucleotide excision repair and base excision repair) is active in proliferating cells. Nucleic Acids Res. 32 :2760– 2767.

194. Klein, H., 1988. Different types of recombination events are controlled by the RAD1 and RAD52 genes of Saccharomyces cerevisiae. Genetics 120 :367– 377.

195. Knauf, J. A.,, S. H. Pendergrass,, B. L. Marrone,, G. F. Strniste,, M. A. MacInnes, and, M. S. Park. 1996. Multiple nuclear localization signals in XPG nuclease. Mutat. Res. 363 :67– 75.

196. Kobayashi, T.,, I. Kuraoka,, M. Saijo,, Y. Nakatsu,, A. Tanaka,, Y. Someda,, S. Fukuro, and, K. Tanaka. 1997. Mutations in the XPD gene leading to xeroderma pigmentosum symptoms. Hum. Mutat. 9 :322– 331.

197. Kobayashi, T.,, S. Takeuchi,, M. Saijo,, Y. Nakatsu,, H. Morioka,, E. Otsuka,, M. Wakasugi,, O. Nikaido, and, K. Tanaka. 1998. Mutational analysis of a function of xeroderma pigmentosum group-A (XPA) protein in strand-specific DNA repair. Nucleic Acids Res. 26 :4662– 4668.

198. Kohn, K. W.,, R. A. G. Ewig,, L. C. Erickson, and, L. A. Zwelling. 1981. Measurement of strand breaks and cross-links by alkaline elution, p. 379– 401. In E. C. Friedberg and, P. C. Hanawalt (ed.), DNA Repair: a Laboratory Manual of Research Procedures. Marcel Dekker, Inc., New York, N.Y.

199. Koken, M. H. M.,, C. Vreeken,, S. A. M. Bol,, N. C. Cheng,, I. Jaspers-Dekker,, J. H. J. Hoeijmakers,, J. C. J. Eeken,, G. Weeda, and, A. Pastink. 1992. Cloning and characterization of the Drosophila homolog of the xeroderma pigmentosum complementation group B correcting gene, ERCC3. Nucleic Acids Res. 20 :5541– 5548.

200. Komori, K.,, R. Fujikane,, H. Shinagawa, and, Y. Ishino. 2002. Novel endonuclease in Archaea cleaving DNA with various branched structure. Genes Genet. Syst. 77 :227– 241.

201. Komori, K.,, M. Hidaka,, T. Horiuchi,, R. Fujikane,, H. Shinagawa, and, Y. Ishino. 2004. Cooperation of the N-terminal helicase and Cterminal endonuclease activities of archaeal Hef protein in processing stalled replication fork. J. Biol. Chem. 279 :53175– 53185.

202. Kraemer, K. H.,, E. A. De Weerd-Kastelein,, J. H. Robbins,, W. Keijzer,, S. F.