New Players in Recognition of Intact and Cleaved AP Sites: Implication in DNA Repair in Mammalian Cells

Ходырева, С. Н.; Lavrik, Olga I.

doi:10.5772/24591

Cited by 4 publications

(6 citation statements)

References 88 publications

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“…These results lead us to infer the presence of an intrinsic AP lyase activity in Bsu LigD that exerts its reaction through a β-elimination mechanism. In support of this, replacement of the AP site with tetrahydrofuran (THF), a stable AP analog resistant to the β-elimination reaction ( 24 , 28 ) inhibited the Bsu LigD activity (Figure 4 , right panel).…”

Section: Resultsmentioning

confidence: 78%

“…Although classically repair of AP sites has relied on the recognition and incision of the abasic site by the BER AP endonucleases and further release of the 5′-dRP moiety by the lyase activity of a specialized DNA polymerase, as the eukaryotic polymerases β ( 24 ), ι ( 25 ), λ ( 26 ) and θ ( 27 ), there is an increasing number of proteins provided with a 5′-dRP lyase activity that could participate in protecting cells against AP sites, a fact that could reflect the importance for processing such an abundant and deleterious DNA damage [reviewed in ( 28 )]. Thus, in addition to the DNA repair polymerases mentioned above, the Escherichia coli DNA polymerase I has been shown to have a dRP-lyase activity although its biological significance has not been established ( 29 ).…”

Section: Introductionmentioning

confidence: 99%

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Identification of a conserved 5′-dRP lyase activity in bacterial DNA repair ligase D and its potential role in base excision repair

et al. 2016

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Bacillus subtilis is one of the bacterial members provided with a nonhomologous end joining (NHEJ) system constituted by the DNA-binding Ku homodimer that recruits the ATP-dependent DNA Ligase D (BsuLigD) to the double-stranded DNA breaks (DSBs) ends. BsuLigD has inherent polymerization and ligase activities that allow it to fill the short gaps that can arise after realignment of the broken ends and to seal the resulting nicks, contributing to genome stability during the stationary phase and germination of spores. Here we show that BsuLigD also has an intrinsic 5′-2-deoxyribose-5-phosphate (dRP) lyase activity located at the N-terminal ligase domain that in coordination with the polymerization and ligase activities allows efficient repairing of 2′-deoxyuridine-containing DNA in an in vitro reconstituted Base Excision Repair (BER) reaction. The requirement of a polymerization, a dRP removal and a final sealing step in BER, together with the joint participation of BsuLigD with the spore specific AP endonuclease in conferring spore resistance to ultrahigh vacuum desiccation suggest that BsuLigD could actively participate in this pathway. We demonstrate the presence of the dRP lyase activity also in the homolog protein from the distantly related bacterium Pseudomonas aeruginosa, allowing us to expand our results to other bacterial LigDs.

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Section: Resultsmentioning

confidence: 78%

Section: Introductionmentioning

confidence: 99%

Identification of a conserved 5′-dRP lyase activity in bacterial DNA repair ligase D and its potential role in base excision repair

et al. 2016

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“…The aforementioned conclusion was supported by the inhibition of Bsu Ku activity when the AP site was replaced with tetrahydrofuran (THF), a stable AP analog resistant to the β-elimination reaction (Figure 1B ) ( 39 , 40 ). Additionally, it was analysed whether a covalent Bsu Ku–DNA complex could be trapped by chemical reduction as it occurs with other enzymes that proceed through a β-elimination mechanism ( 41 ).…”

Section: Resultsmentioning

confidence: 78%

“…These results are consistent with cleavage 3′ to the AP site in a metal-independent manner, leading us to infer the presence of an intrinsic AP-lyase activity in Bsu Ku, active also on AP-containing dsDNA substrates, although much less efficiently than on ssDNA molecules ( k obs = 5 × 10 −3 ± 5 × 10 −4 min −1 ) (see Supplementary Figure S1). Furthermore, the results suggest that Bsu Ku exerts its AP lyase activity through a β-elimination reaction since if it had been through a β,δ-mechanism the products released should have migrated even faster than those produced by h APE1 due to the presence of a 3′ phosphate group ( 39 ).…”

Section: Resultsmentioning

confidence: 99%

Efficient processing of abasic sites by bacterial nonhomologous end-joining Ku proteins

Ory

Zafra

Vega

2014

Nucleic Acids Research

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Intracellular reactive oxygen species as well as the exposure to harsh environmental conditions can cause, in the single chromosome of Bacillus subtilis spores, the formation of apurinic/apyrimidinic (AP) sites and strand breaks whose repair during outgrowth is crucial to guarantee cell viability. Whereas double-stranded breaks are mended by the nonhomologous end joining (NHEJ) system composed of an ATP-dependent DNA Ligase D (LigD) and the DNA-end-binding protein Ku, repair of AP sites would rely on an AP endonuclease or an AP-lyase, a polymerase and a ligase. Here we show that B. subtilis Ku (BsuKu), along with its pivotal role in allowing joining of two broken ends by B. subtilis LigD (BsuLigD), is endowed with an AP/deoxyribose 5′-phosphate (5′-dRP)-lyase activity that can act on ssDNA, nicked molecules and DNA molecules without ends, suggesting a potential role in BER during spore outgrowth. Coordination with BsuLigD makes possible the efficient joining of DNA ends with near terminal abasic sites. The role of this new enzymatic activity of Ku and its potential importance in the NHEJ pathway is discussed. The presence of an AP-lyase activity also in the homolog protein from the distantly related bacterium Pseudomonas aeruginosa allows us to expand our results to other bacterial Ku proteins.

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“…The studies showed that during the BER process in nuclei of mammalian cells AP endonuclease cleaves more than 95 % of emerging AP sites, but there is an alternative way with participation of bifunctional DNA glycosylases [86][87][88], this way is also typical for the mitochondrial BER system. Such bifunctional glycosylases as OGG1 and NTH1 after the cleavage of the N-glycosidic bond cut the AP site by β-elimination mechanism; as a result, a gap emerges with 3'-unsaturated phosphoaldehyde PUA and 5'-phosphate group at the ends.…”

Section: Base Excision Repair Bermentioning

confidence: 99%

Untitled

2016

Biopolym. Cell

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The role of mitochondria in cellular metabolism and functioning can hardly be overestimated. Mitochondria carry out many functions, and their main function is the production of ATP, the energetic "currency" of the cell. Mitochondria possess a small circular DNA, which codes for 13 proteins. Mitochondrial DNA, or mtDNA, as well as the nuclear one, is subjected to the influence of environmental and endogenous factors. This may lead to mtDNA damage. Here we review the data on mtDNA damage and repair mechanisms. The functioning of mitochondria directly depends on integrity of mtDNA, and therefore, on correct functioning of the mtDNA repair system. These systems differ from the repair systems of nuclear DNA and are in general understudied. The existence of excision nucleotides repair system correcting bulky lesions in mitochondria is still under question. Specific degradation of damaged mtDNA can probably serve as an alternative way to prevent the accumulation of bulky lesions. A search for new pathways of mtDNA repair is of considerable interest.

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New Players in Recognition of Intact and Cleaved AP Sites: Implication in DNA Repair in Mammalian Cells

Cited by 4 publications

References 88 publications

Identification of a conserved 5′-dRP lyase activity in bacterial DNA repair ligase D and its potential role in base excision repair

Identification of a conserved 5′-dRP lyase activity in bacterial DNA repair ligase D and its potential role in base excision repair

Efficient processing of abasic sites by bacterial nonhomologous end-joining Ku proteins

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