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Domain 4:

Synthesis and Processing of Macromolecules

Direct DNA Lesion Reversal and Excision Repair in

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  • Authors: Sophie Couvé1, Alexander A. Ishchenko2, Olga S. Fedorova3, Erlan M. Ramanculov4, Jacques Laval5, and Murat Saparbaev6
  • Editor: Susan T. Lovett7
  • VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: Groupe «Réparation de l’ADN», Université Paris-Sud, CNRS UMR8200 and Génétique Oncologique EPHE, INSERM U753; 2: Groupe «Réparation de l’ADN», Université Paris-Sud, CNRS UMR8200; 3: Institut de Cancérologie Gustave Roussy, F-94805 Villejuif Cedex, France; Laboratory of Biopolymer Modification, Institute of Chemical Biology and Fundamental Medicine, University of Novosibirsk, 630090 Novosibirsk, Russian Federation; 4: National Center for Biotechnology of the Republic of Kazakhstan, Astana, Kazakhstan; 5: Groupe «Réparation de l’ADN», Université Paris-Sud, CNRS UMR8200; 6: Groupe «Réparation de l’ADN», Université Paris-Sud, CNRS UMR8200; 7: Brandeis University, Waltham, MA
  • Received 01 January 2012 Accepted 27 March 2012 Published 19 February 2013
  • Address correspondence to Murat Saparbaev smurat@igr.fr
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  • Abstract:

    Cellular DNA is constantly challenged by various endogenous and exogenous genotoxic factors that inevitably lead to DNA damage: structural and chemical modifications of primary DNA sequence. These DNA lesions are either cytotoxic, because they block DNA replication and transcription, or mutagenic due to the miscoding nature of the DNA modifications, or both, and are believed to contribute to cell lethality and mutagenesis. Studies on DNA repair in spearheaded formulation of principal strategies to counteract DNA damage and mutagenesis, such as: direct lesion reversal, DNA excision repair, mismatch and recombinational repair and genotoxic stress signalling pathways. These DNA repair pathways are universal among cellular organisms. Mechanistic principles used for each repair strategies are fundamentally different. Direct lesion reversal removes DNA damage without need for excision and de novo DNA synthesis, whereas DNA excision repair that includes pathways such as base excision, nucleotide excision, alternative excision and mismatch repair, proceeds through phosphodiester bond breakage, de novo DNA synthesis and ligation. Cell signalling systems, such as adaptive and oxidative stress responses, although not DNA repair pathways are nevertheless essential to counteract DNA damage and mutagenesis. The present review focuses on the nature of DNA damage, direct lesion reversal, DNA excision repair pathways and adaptive and oxidative stress responses in .

  • Citation: Couvé S, Ishchenko A, Fedorova O, Ramanculov E, Laval J, Saparbaev M. 2013. Direct DNA Lesion Reversal and Excision Repair in , EcoSal Plus 2013; doi:10.1128/ecosalplus.7.2.4

Key Concept Ranking

Bacteria and Archaea
0.57992107
DNA Synthesis
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DNA Polymerase I
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DNA Polymerase III
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/content/journal/ecosalplus/10.1128/ecosalplus.7.2.4
2013-02-19
2017-08-21

Abstract:

Cellular DNA is constantly challenged by various endogenous and exogenous genotoxic factors that inevitably lead to DNA damage: structural and chemical modifications of primary DNA sequence. These DNA lesions are either cytotoxic, because they block DNA replication and transcription, or mutagenic due to the miscoding nature of the DNA modifications, or both, and are believed to contribute to cell lethality and mutagenesis. Studies on DNA repair in spearheaded formulation of principal strategies to counteract DNA damage and mutagenesis, such as: direct lesion reversal, DNA excision repair, mismatch and recombinational repair and genotoxic stress signalling pathways. These DNA repair pathways are universal among cellular organisms. Mechanistic principles used for each repair strategies are fundamentally different. Direct lesion reversal removes DNA damage without need for excision and de novo DNA synthesis, whereas DNA excision repair that includes pathways such as base excision, nucleotide excision, alternative excision and mismatch repair, proceeds through phosphodiester bond breakage, de novo DNA synthesis and ligation. Cell signalling systems, such as adaptive and oxidative stress responses, although not DNA repair pathways are nevertheless essential to counteract DNA damage and mutagenesis. The present review focuses on the nature of DNA damage, direct lesion reversal, DNA excision repair pathways and adaptive and oxidative stress responses in .

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Figure 1

Citation: Couvé S, Ishchenko A, Fedorova O, Ramanculov E, Laval J, Saparbaev M. 2013. Direct DNA Lesion Reversal and Excision Repair in , EcoSal Plus 2013; doi:10.1128/ecosalplus.7.2.4
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Figure 2

(A) A monofunctional uracil-DNA glycosylase, UNG, generates the AP site, which is cleaved by exonuclease III (XthA), the major AP endonuclease, to generate a single-stranded nick with a 5′-deoxyribosephosphate group. This group is removed by DNA polymerase I through strand-displacement DNA synthesis coupled with a flap-structure endonuclease activity. (B) When bifunctional thymine glycol-DNA glycosylase Nth excises an oxidized base, it concomitantly performs β-elimination to generate a single-stranded nick with a 3′-α,β-unsaturated aldehyde. Xth removes the 3′-blocking group, generating a single nucleotide gap with a 3′-OH group that primes DNA repair synthesis by DNA polymerase I. Finally, the single-strand nick is sealed by DNA ligase to restore genetic integrity.

Citation: Couvé S, Ishchenko A, Fedorova O, Ramanculov E, Laval J, Saparbaev M. 2013. Direct DNA Lesion Reversal and Excision Repair in , EcoSal Plus 2013; doi:10.1128/ecosalplus.7.2.4
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Figure 3

(A) Fpg–8oxoG-DNA interactions (adapted from reference 233 ). (B) T4 endonuclease V–thymine dimer-DNA interactions (adapted from reference 237 ). (C) Endonuclease IV–AP site-DNA interactions (adapted from reference 238 ). (D) Endonuclease V–hypoxanthine-DNA interactions (adapted from reference 239 ).

Citation: Couvé S, Ishchenko A, Fedorova O, Ramanculov E, Laval J, Saparbaev M. 2013. Direct DNA Lesion Reversal and Excision Repair in , EcoSal Plus 2013; doi:10.1128/ecosalplus.7.2.4
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Figure 4

First, solution studies suggest that two monomers of UvrA (A) form a dimer in an ATP-dependent manner with four potential ATP-binding sites that may hydrolyze ATP and GTP. Then two UvrB (B) molecules bind to this UvrA dimer (for clarity, only one UvrB subunit is shown), and UvrAB interacts with DNA through the DNA-binding properties of UvrA. The cryptic ATP-binding site on UvrB becomes activated during the formation of the UvrAB complex responsible for damage search and recognition along DNA. Different models for the mechanism of damage recognition are proposed: the helicase-scanning model ( 349 , 350 , 351 ), the damage-processing model ( 352 ), and the padlock model ( 353 ). This complex binds to and wraps the DNA around one of the UvrB subunits and then waits for the arrival of the UvrC protein, responsible for both the 3′ and 5′ incision reactions of the damaged strand. After incision, UvrC dissociates, and UvrD (DNA helicase II), in concerted action with DNA polymerase I, releases the lesion-containing 12-base oligonucleotide, as well as the bound Uvr proteins. The resulting gap is filled in by DNA polymerase I, while the nick is sealed by DNA ligase.

Citation: Couvé S, Ishchenko A, Fedorova O, Ramanculov E, Laval J, Saparbaev M. 2013. Direct DNA Lesion Reversal and Excision Repair in , EcoSal Plus 2013; doi:10.1128/ecosalplus.7.2.4
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Figure 5

(A) Schematic illustration of the nucleotide incision repair (NIR) pathway for oxidative DNA base damage in . Nfo cleaves the phosphodiester bond 5′ to the lesion (DHU, 5,6-dihydrouracil) generated from oxidation of cytosine. Following the incision of DHU-containing DNA, DNA polymerase I initiates DNA repair synthesis coupled to removal of the remaining dangling DHU base. Finally, DNA ligase seals the single-strand nick and restores duplex integrity. (B) Endonuclease V-dependent repair is initiated by cleavage at the second phosphodiester bond 3′ to the lesion (Hx, hypoxanthine) generated from deamination of adenine. After Nfi-catalyzed cleavage, DNA polymerase I removes deoxyinosine and deoxyadenosine residues by its 3′-5′ exonuclease activity and then it fills in the gap, while DNA ligase seals the phosphodiester backbone.

Citation: Couvé S, Ishchenko A, Fedorova O, Ramanculov E, Laval J, Saparbaev M. 2013. Direct DNA Lesion Reversal and Excision Repair in , EcoSal Plus 2013; doi:10.1128/ecosalplus.7.2.4
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Figure 6

The Ada protein is represented in a dumbbell-shape structure to show N-terminal and C-terminal domains containing active cysteine residues (see the text for details). The Ada regulon contains the gene and also , , and genes shown as boxes. DNA is alkylated at the phosphate linkages (P-O-CH) and position of guanine (G-O-CH). The Ada protein demethylates Sp diastereoisomers of methylphosphotriesters in the sugar phosphate backbone by transferring the methyl groups to the N-terminal cysteine (Cys-38) and methylated bases by transferring the methyl groups to the C-terminal cysteine (Cys-321). The alkylation of Cys-38 converts Ada protein to a transcriptional activator that binds to the promoters of the Ada regulon, leading in enhanced transcription. The increased levels of Ada, AlkA, AlkB, and AidB proteins promote enhanced repair of alkylation damage in DNA (adapted from reference 470 ).

Citation: Couvé S, Ishchenko A, Fedorova O, Ramanculov E, Laval J, Saparbaev M. 2013. Direct DNA Lesion Reversal and Excision Repair in , EcoSal Plus 2013; doi:10.1128/ecosalplus.7.2.4
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Tables

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Table 1

genes involved in DNA repair

Citation: Couvé S, Ishchenko A, Fedorova O, Ramanculov E, Laval J, Saparbaev M. 2013. Direct DNA Lesion Reversal and Excision Repair in , EcoSal Plus 2013; doi:10.1128/ecosalplus.7.2.4

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