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Chapter 7 : Nucleotide Excision Repair

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Abstract:

Nucleotide excision repair (NER) is a multistep process that leads to the formation of gaps in the DNA duplex that must be filled by repair synthesis and covalently sealed by DNA ligase. This chapter discusses the NER in prokaryotes. In the bacterium , both specific recognition of base damage and incision of the affected DNA strand on either side of sites of base damage are effected by three proteins designated UvrA, UvrB, and UvrC (for “UV radiation”). These three proteins are not associated as a stable complex during NER but, rather, interact in a sequential fashion. Regardless, they are variously referred to in the literature as subunits of the or the , or as the . The chapter elaborates on NER in a number of selected prokaryotes other than and in the archaea. It concludes with a brief discussion of some of the commonly used experimental techniques for detecting and measuring biochemical events associated with NER, particularly since many of these techniques are frequently referred to in the literature. The chapter presents the essential principles of several of these techniques, with a special emphasis on those used for studies with intact bacterial cells.

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Nucleotide Excision Repair, p 227-266. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch7
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Figures

Image of Figure 7–1
Figure 7–1

NER-defective (uvr) strains of are abnormally sensitive to killing by a wide variety of DNA-damaging agents, including UV radiation, mitomycin C, nitrogen mustard, and MNNG.

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Nucleotide Excision Repair, p 227-266. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch7
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Image of Figure 7–2
Figure 7–2

UV-irradiated DNA is incised by extracts of cells which are proficient for NER (uvr) in the presence of ATP and Mg (left). Extracts of mutant cells fail to demonstrate the preferential incision of UV-irradiated DNA with or without ATP (center); however, mixtures of extracts from different mutant cells complement each other for nicking activity in the presence of ATP (right). Incision (nicking) of DNA was measured by the conversion of covalently closed circular (form I) DNA to relaxed circular or linear configurations.

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Nucleotide Excision Repair, p 227-266. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch7
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Image of Figure 7–3
Figure 7–3

Diagrammatic representation of functional motifs identified in the amino acid sequence of the UvrA protein (940 amino acids). The locations of the two Walker type A consensus sequences for nucleotide (ATP) binding are shown, as well as the two zinc fingers and the helix-turn-helix (H-T-H) motifs. (Adapted from reference .)

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Nucleotide Excision Repair, p 227-266. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch7
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Image of Figure 7–4
Figure 7–4

Nucleotide sequence of a DNA fragment containing the gene regulatory regions. The numbering of nucleotides is relative to a transcriptional start site designated S1. Pribnow boxes and —35 sequences for three promoters (P1, P2, and P3) are identified, as is a region protected from DNase I attack by the binding of LexA protein.

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Nucleotide Excision Repair, p 227-266. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch7
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Image of Figure 7–5
Figure 7–5

The UvrB protein has an amino acid sequence motif that resembles ones observed in the Ada protein (see chapter 5). Those in the Ada protein are sites of preferred proteolytic cleavage of the protein.

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Nucleotide Excision Repair, p 227-266. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch7
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Image of Figure 7–6
Figure 7–6

Amino acid sequence alignment of UvrB protein from (Tt) and (Ec). Identical amino acids are highlighted in gold boxes, and similar amino acids (R/K, D/E, S/T, L/I/V/F/Y/M) are boxed in grey. Secondary-structure elements are indicated in boxes above the sequences. Black-outlined boxes denote α-helices, and gold-outlined boxes denote β-sheets. These are numbered sequentially, and the first two letters denote the corresponding domain (see Fig. 7–7 ). Regions of the protein that are disordered in the crystal structure are identified by black overlines. DNA helicase consensus sequences are identified by black underlines and the roman numerals below these. (Adapted from reference .)

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Nucleotide Excision Repair, p 227-266. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch7
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Image of Figure 7–7
Figure 7–7

The crystal structures of (shown here) and UvrB proteins have similar overall architectures. Domain 1a (domain H1 in UvrB) and domain 3 (domain H2 in UvrB) have similar folds but are unrelated in amino acid sequence (see Fig. 7–6 ). Both domains consist of central β-sheets flanked by α-helices. ATP binds at the interface between domains 3 and 1a (dashed circle). This arrangement resembles the RecA-type ATPase domains found in other DNA helicases. Domain 1b (P1 in UvrB) is derived from protruding loops of domain 1a (H1 in UvrB) that comprise three “arms” that pack together in a module that appears to be flexibly linked to domain 1a (see Fig. 7–6 ).

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Nucleotide Excision Repair, p 227-266. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch7
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Image of Figure 7–8
Figure 7–8

The ATP-binding site of the UvrB protein is located at the bottom of the cleft between domains 1a (H1) and 3 (H2) (see Fig. 7–7 ). UvrB interacts with both the adenine and phosphate moieties of the bound ATP (shown in white). The ATP cofactor is specifically recognized through hydrogen-bonding interactions with N-6 and N-7 of adenine made by the side chain of Gln17, a conserved amino acid in the UvrB protein. A stacking interaction between Tyr11 and the adenine base further contributes to ATP binding in the active site. The beta and gamma phosphate oxygens of ATP are contacted by an Mg metal ion (grey sphere) that is in turn coordinated by two acidic residues (Asp338 and Glu339). This arrangement of charged residues and a bound metal is a common feature of ATPases and GTPases. Nearby basic residues (Arg540 and Arg543) may help position the gamma phosphate of ATP, and Lys45 could activate water for hydrolysis of the bound nucleotide.

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Nucleotide Excision Repair, p 227-266. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch7
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Image of Figure 7–9
Figure 7–9

Crystal structures of UvrB reveal a large connecting loop (shown in gold) between a β-strand and an α-helix of domain 1a located in a cleft between domains 1b and 3. The loop of UvrB is termed the β-hairpin and corresponds to the A1 finger of the UvrB structure.

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Nucleotide Excision Repair, p 227-266. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch7
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Image of Figure 7–10
Figure 7–10

The six helicase domains identified in UvrB protein are located in the cleft between domains 1a and 3, near the ATP binding site.

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Nucleotide Excision Repair, p 227-266. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch7
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Image of Figure 7–11
Figure 7–11

Model for the formation of a stable UvrB-damaged-DNA complex during NER in (A) A site of base damage on one DNA strand is represented diagrammatically. (B to D) The (UvrA)UvrB protein complex forms in solution (B and C) and initially binds to DNA at a site some distance from the damage (D). Promoters in genes might constitute preferential sites for the initial “docking” of such complexes. The (UvrA)UvrB complex tracks along the DNA using a DNA helicase activity (D). (E and F) When the site of base damage is encountered (E), UvrA protein dissociates from the complex, leaving a stable UvrB-DNA complex (F). This is associated with bending and kinking of the DNA.

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Nucleotide Excision Repair, p 227-266. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch7
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Image of Figure 7–12
Figure 7–12

Alignment of amino acid sequences of the β-hairpin (β -connecting loop) in UvrB proteins from a number of bacteria, showing the conserved nature of this region, especially the hydrophobic residues (gold). (Adapted from reference .)

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Nucleotide Excision Repair, p 227-266. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch7
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Image of Figure 7–13
Figure 7–13

Summary of different UvrB-DNA complexes generated during NER. The ATPase/ DNA helicase activity of the (UvrA)UvrB protein complex facilitates binding of the complex close to a site of base damage in DNA and translocation to the damaged site. ATP hydrolysis leads to the formation of a propreincision complex. Subsequent binding of ATP to the propreincision complex generates a preincision complex to which UvrC protein binds, leading to incision of the damaged DNA strand 3’ and 5’ to the damaged base(s). (Adapted from reference .)

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Nucleotide Excision Repair, p 227-266. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch7
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Image of Figure 7–14
Figure 7–14

Atomic force microscopy images of (UvrA)UvrB-DNA (grey arrows) and UvrB-DNA (white arrows) complexes on damaged DNA. (Adapted from reference .)

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Nucleotide Excision Repair, p 227-266. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch7
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Image of Figure 7–15
Figure 7–15

Bimodal damage-specific nicking of DNA containing a CPD by the UvrABC endonuclease. Following formation of a stable UvrB-damaged DNA complex (A and B; also see Fig. 7–11 ), UvrC protein binds at the site (C). Conformational changes then position the catalytically active UvrC subunit (intimately associated with UvrB protein) so as to incise the damaged DNA strand 4 nucleotides 3’ (D) and then 7 nucleotides 5’ (E) to the dimer.

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Nucleotide Excision Repair, p 227-266. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch7
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Image of Figure 7–16
Figure 7–16

Schematic box representation of UvrC protein showing regions of amino acid sequence homology to protein (residues 19 to 55) and an HhH domain (residues 555 to 610), as well as the coiled-coil domain (residues 201 to 240) required for interaction with UvrB protein. Amino acid residues D399, D438, D466, and H358 are in the active site for 5’ incision, and amino acid residue R42 is part of the active site for 3’ incision. (Adapted from reference .)

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Nucleotide Excision Repair, p 227-266. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch7
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Image of Figure 7–17
Figure 7–17

Alignment of the N-terminal region of the UvrC amino acid sequence with Cho proteins from (Eco), serovar Typhimurium (Sty), serovar Enteritidis (Sen), and (Kpn) and with a 24-kDa protein from (Mhy), a 43-kDa protein from (Cac), and a 69-kDa protein from (Mtu). Amino acid residues in the other orthologs that are identical or similar to those in UvrC protein are highlighted in gold boxes. The underlined sequence is the UvrB-binding domain of UvrC protein. (Adapted from reference .)

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Nucleotide Excision Repair, p 227-266. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch7
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Image of Figure 7–18
Figure 7–18

Incision of UV-irradiated supercoiled DNA by Uvr protein or by Cho protein from Supercoiled UV-irradiated plasmid DNA was incubated with the indicated proteins. The electrophoretic mobilities of unnicked supercoiled (Sc) and relaxed nicked (Rel) DNA are shown. Note that both Cho protein (lane 2) and UvrC protein (lane 3) cut the UV-irradiated DNA only in the presence of both UvrA and UvrB proteins. There is some background of nicked DNA in lanes 1, 4, and 5. (Adapted from reference .)

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Nucleotide Excision Repair, p 227-266. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch7
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Image of Figure 7–19
Figure 7–19

(A) Mutants defective in the gene show a reduced rate and extent of loss of thymine-containing pyrimidine dimers from DNA compared to a wild-type strain (uvr). (B) Such mutants are also abnormally sensitive to UV radiation, but not as sensitive as mutants defective in the gene.

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Nucleotide Excision Repair, p 227-266. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch7
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Image of Figure 7–20
Figure 7–20

Model for postincisional events during NER in (A and B) DNA helicase II (UvrD protein) is required for the release of an oligonucleotide fragment (excision) following bimodal incisions generated by the UvrABC endonuclease and for the displacement of UvrC protein. (C) UvrB protein remains bound to the gapped DNA during the excision reaction and is released during the repair synthesis reaction catalyzed by Pol I. DNA ligation completes the NER reaction.

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Nucleotide Excision Repair, p 227-266. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch7
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Image of Figure 7–21
Figure 7–21

Measurement of the sizes of repair patches generated during in vitro NER in The plasmid DNA substrate contains a single psoralen adduct bound to thymine in a defined position (circled T) within a PvuII (P) restriction fragment. This substrate is incubated in four separate reactions, with each reaction mixture containing the UvrABC endonuclease, Pol I, DNA ligase, and three unlabeled dNTPs with one labeled dNTP ([-yS]dNTP). In each reaction, the dNTPs and [γ-S]dNTP are varied. Following the reaction, the DNA is digested with PvuII. The resulting 322-bp DNA fragment is end labeled with polynucleotide kinase and heated in the presence of iodoethanol. This compound ethylates the phosphorothioate groups incorporated during repair synthesis, rendering them sensitive to hydrolysis at high temperature. The DNA fragment is then analyzed on a sequencing gel, generating a sequence ladder of the repair patch. The sequence of the repair patch can be unambiguously read, and its size can be accurately measured. (Adapted from reference .)

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Nucleotide Excision Repair, p 227-266. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch7
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Image of Figure 7–22
Figure 7–22

mutants is shown here) are abnormally sensitive to killing by UV radiation. However, they are not as sensitive as mutants.

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Nucleotide Excision Repair, p 227-266. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch7
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Image of Figure 7–23
Figure 7–23

Phenotypic complementation of the UV radiation sensitivity of an mutant by introduction of a plasmid carrying the cloned mfd gene. (Adapted from reference .)

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Nucleotide Excision Repair, p 227-266. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch7
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Image of Figure 7–24
Figure 7–24

Model for strand-specific NER in (A) RNA polymerase is shown transcribing a template DNA strand that contains base damage ahead of the transcription complex. (B to D) Stalling of RNA polymerase at the site of base damage in the transcribed strand (B) results in the binding of TRCF (C) and displacement of the polymerase and the truncated transcript, leaving TRCF bound at the site of damage (D). (E and F) TRCF binds to UvrA protein, resulting in the recruitment of the (UvrA)UvrB complex to the site of damage (E), where NER occurs (F). (Adapted from reference .)

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Nucleotide Excision Repair, p 227-266. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch7
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Image of Figure 7–25
Figure 7–25

Amino acid alignments of RecG and Mfd proteins from various prokaryotes. Only the most highly conserved residues are shown. (Adapted from reference .)

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Nucleotide Excision Repair, p 227-266. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch7
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Image of Figure 7–26
Figure 7–26

The presence of CPD (represented as T=T) in the DNA of UV-irradiated cells can be detected with the use of dimer-specific enzyme probes such as the or phage T4 PD-DNA glycosylase/AP lyases (see chapter 6). Radiolabeled DNA is extracted from cells and incubated with the enzyme. The enzyme catalyzes the formation of strand breaks at PD (enzyme sensitive) sites. DNA containing dimers (enzyme-sensitive sites) sediments more slowly in alkaline sucrose gradients than does DNA containing no (or fewer) dimers.

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Nucleotide Excision Repair, p 227-266. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch7
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Image of Figure 7–27
Figure 7–27

Schematic illustration of the detection of repair synthesis by buoyant density centrifugation of DNA containing 5-BrU. DNA is prelabeled with [C]thymidine to provide a uniform label. Following exposure to UV radiation (or some other form of DNA damage), repair synthesis during NER takes place in the presence of [H]BrU. DNA synthesized both by semiconservative (gold lines) and by nonsemiconservative (gold triangles) modes will thus be density labeled. To distinguish between these, the DNA is fragmented (by shearing) and sedimented to equilibrium density. Fragments of DNA containing strands that were synthesized semiconservatively will have a hybrid density detected by the position of the H radioactivity (left). Repair synthesis patches are too small to alter the density of the DNA, and hence the H radiolabel appears at the position of normal-density DNA (right).

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Nucleotide Excision Repair, p 227-266. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch7
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Image of Figure 7–28
Figure 7–28

Sedimentation patterns in alkaline sucrose of labeled DNA from normal human fibroblasts treated with UV radiation or left untreated and allowed to repair in the presence of 5-BrU before exposure to 313-nm photolysis. Photolysis of incorporated 5-BrU results in strand breakage of the DNA when sedimented in alkali No degradation of DNA is observed in the absence of photolytic irradiation The amount of 313-nm irradiation required to cause strand breakage at all sites of 5-BrU incorporation provides a means of estimating the size of the DNA synthesis (repair) patches.

Citation: Errol C, Graham C, Wolfram S, Richard D, Roger A, Tom E. 2006. Nucleotide Excision Repair, p 227-266. In DNA Repair and Mutagenesis, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816704.ch7
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References

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