scholarly journals Repair of Oxidized Bases in the Extremely Radiation-Resistant Bacterium Deinococcus radiodurans

1999 ◽  
Vol 181 (1) ◽  
pp. 262-269 ◽  
Author(s):  
Cécile Bauche ◽  
Jacques Laval
Keyword(s):  
Deinococcus Radiodurans ◽  
Excision Repair ◽  
Dna Glycosylase ◽  
Repair System ◽  
Thymine Glycol ◽  
Dna Damaging Agents ◽  
Repair Mechanisms ◽  
Radiation Resistant ◽  
Base Excision ◽  
Base Excision Repair System

ABSTRACT Deinococcus radiodurans is able to resist and survive extreme DNA damage induced by ionizing radiation and many other DNA-damaging agents. It is believed that it possesses highly efficient DNA repair mechanisms. To characterize the repair pathway of oxidized purines in this bacteria, we have purified, from crude extracts, proteins that recognize these oxidized bases. We report here thatD. radiodurans possesses two proteins excising the oxidized purines (formamidopyrimidine and 8-oxoguanine) by a DNA glycosylase–a purinic/apyrimidine lyase mechanism. Moreover, one of those proteins is endowed with a thymine glycol DNA glycosylase activity. One of these proteins could be the homolog of the Escherichia coli Fpg enzyme, which confirms the existence of a base excision repair system in this bacteria.

Self-Resistance to an Antitumor Antibiotic: A DNA Glycosylase Triggers the Base-Excision Repair System in Yatakemycin Biosynthesis

2012 ◽  
Vol 124 (42) ◽  
pp. 10684-10688
Author(s):  
Hui Xu ◽  
Wei Huang ◽  
Qing-Li He ◽  
Zhi-Xiong Zhao ◽  
Feng Zhang ◽  
...  
Keyword(s):  
Base Excision Repair ◽  
Excision Repair ◽  
Dna Glycosylase ◽  
Repair System ◽  
Antitumor Antibiotic ◽  
Base Excision ◽  
Base Excision Repair System

scholarly journals Molecular Mechanisms of the Whole DNA Repair System: A Comparison of Bacterial and Eukaryotic Systems

2010 ◽  
Vol 2010 ◽  
pp. 1-32 ◽  
Author(s):  
Rihito Morita ◽  
Shuhei Nakane ◽  
Atsuhiro Shimada ◽  
Masao Inoue ◽  
Hitoshi Iino ◽  
...  
Keyword(s):  
Dna Repair ◽  
Molecular Mechanisms ◽  
Excision Repair ◽  
Thermus Thermophilus ◽  
Repair System ◽  
System A ◽  
Recombination Repair ◽  
Repair Mechanisms ◽  
Repair Pathways ◽  
Base Excision

DNA is subjected to many endogenous and exogenous damages. All organisms have developed a complex network of DNA repair mechanisms. A variety of different DNA repair pathways have been reported: direct reversal, base excision repair, nucleotide excision repair, mismatch repair, and recombination repair pathways. Recent studies of the fundamental mechanisms for DNA repair processes have revealed a complexity beyond that initially expected, with inter- and intrapathway complementation as well as functional interactions between proteins involved in repair pathways. In this paper we give a broad overview of the whole DNA repair system and focus on the molecular basis of the repair machineries, particularly inThermus thermophilusHB8.

scholarly journals SMUG2 DNA glycosylase from Pedobacter heparinus as a new subfamily of the UDG superfamily

2017 ◽  
Vol 474 (6) ◽  
pp. 923-938 ◽  
Author(s):  
Panjiao Pang ◽  
Ye Yang ◽  
Jing Li ◽  
Zhong Wang ◽  
Weiguo Cao ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Excision Repair ◽  
Phylogenetic Analyses ◽  
Dna Glycosylase ◽  
Amino Acid Residues ◽  
Uracil Dna Glycosylase ◽  
Important Amino Acid ◽  
Repair Mechanisms ◽  
Ap Sites ◽  
Base Excision

Base deamination is a common type of DNA damage that occurs in all organisms. DNA repair mechanisms are essential to maintain genome integrity, in which the base excision repair (BER) pathway plays a major role in the removal of base damage. In the BER pathway, the uracil DNA glycosylase superfamily is responsible for excising the deaminated bases from DNA and generates apurinic/apyrimidinic (AP) sites. Using bioinformatics tools, we identified a family 3 SMUG1-like DNA glycoyslase from Pedobacter heparinus (named Phe SMUG2), which displays catalytic activities towards DNA containing uracil or hypoxanthine/xanthine. Phylogenetic analyses show that SMUG2 enzymes are closely related to family 3 SMUG1s but belong to a distinct branch of the family. The high-resolution crystal structure of the apoenzyme reveals that the general fold of Phe SMUG2 resembles SMUG1s, yet with several distinct local structural differences. Mutational studies, coupled with structural modeling, identified several important amino acid residues for glycosylase activity. Substitution of G65 with a tyrosine results in loss of all glycosylase activity. The crystal structure of the G65Y mutant suggests a potential misalignment at the active site due to the mutation. The relationship between the new subfamily and other families in the UDG superfamily is discussed. The present study provides new mechanistic insight into the molecular mechanism of the UDG superfamily.

scholarly journals When UDG and hAPE1 Meet Cyclopurines. How (5′R) and (5′S) 5′,8-Cyclo-2′-deoxyadenosine and 5′,8-Cyclo-2′-deoxyguanosine Affect UDG and hAPE1 Activity?

Molecules ◽  
2021 ◽  
Vol 26 (17) ◽  
pp. 5177
Author(s):  
Michał Szewczuk ◽  
Karolina Boguszewska ◽  
Julia Kaźmierczak-Barańska ◽  
Bolesław T. Karwowski
Keyword(s):  
Base Excision Repair ◽  
Excision Repair ◽  
Dna Lesions ◽  
Repair System ◽  
Cellular Mechanisms ◽  
Uracil Dna Glycosylase ◽  
Base Excision ◽  
Base Excision Repair System ◽  
Synthetic Oligonucleotides ◽  
Ap Site

Ionizing radiation is a factor that seriously damages cellular mechanisms/macromolecules, e.g., by inducing damage in the human genome, such as 5′,8-cyclo-2′-deoxypurines (cdPus). CdPus may become a component of clustered DNA lesions (CDL), which are notably unfavorable for the base excision repair system (BER). In this study, the influence of 5′S and 5′R diastereomers of 5′,8-cyclo-2′-deoxyadenosine (cdA) and 5′,8-cyclo-2′-deoxyguanosine (cdG) on the uracil-DNA glycosylase (UDG) and human AP site endonuclease 1 (hAPE1) activity has been taken under consideration. Synthetic oligonucleotides containing 2′-deoxyuridine (dU) and cdPu were used as a model of single-stranded CDL. The activity of the UDG and hAPE1 enzymes decreased in the presence of RcdG compared to ScdG. Contrary to the above, ScdA reduced enzyme activity more than RcdA. The presented results show the influence of cdPus lesions located within CDL on the activity of the initial stages of BER dependently on their position toward dU. Numerous studies have shown the biological importance of cdPus (e.g., as a risk of carcinogenesis). Due to that, it is important to understand how to recognize and eliminate this type of DNA damage from the genome.

scholarly journals The Influence of (5′R)- and (5′S)-5′,8-Cyclo-2′-Deoxyadenosine on UDG and hAPE1 Activity. Tandem Lesions are the Base Excision Repair System’s Nightmare

Cells ◽  
2019 ◽  
Vol 8 (11) ◽  
pp. 1303 ◽  
Author(s):  
Karwowski
Keyword(s):  
Dna Damage ◽  
Base Excision Repair ◽  
Excision Repair ◽  
Repair Process ◽  
Dna Lesions ◽  
Repair System ◽  
Base Excision ◽  
Base Excision Repair System ◽  
Tandem Lesions ◽  
Ap Site

DNA lesions are formed continuously in each living cell as a result of environmental factors, ionisation radiation, metabolic processes, etc. Most lesions are removed from the genome by the base excision repair system (BER). The activation of the BER protein cascade starts with DNA damage recognition by glycosylases. Uracil-DNA glycosylase (UDG) is one of the most evolutionary preserved glycosylases which remove the frequently occurring 2′-deoxyuridine from single (ss) and double-stranded (ds) oligonucleotides. Conversely, the unique tandem lesions (5′R)- and (5′S)-5′,8-cyclo-2′-deoxyadenosine (cdA) are not suitable substrates for BER machinery and are released from the genome by the nucleotide excision repair (NER) system. However, the cyclopurines appearing in a clustered DNA damage structure can influence the BER process of other lesions like dU. In this article, UDG inhibition by 5′S- and 5′R-cdA is shown and discussed in an experimental and theoretical manner. This phenomenon was observed when a tandem lesion appears in single or double-stranded oligonucleotides next to dU, on its 3′-end side. The cdA shift to the 5′-end side of dU in ss-DNA stops this effect in both cdA diastereomers. Surprisingly, in the case of ds-DNA, 5′S-cdA completely blocks uracil excision by UDG. Conversely, 5′R-cdA allows glycosylase for uracil removal, but the subsequently formed apurinic/apyrimidinic (AP) site is not suitable for human AP-site endonuclease 1 (hAPE1) activity. In conclusion, the appearance of the discussed tandem lesion in the structure of single or double-stranded DNA can stop the entire base repair process at its beginning, which due to UDG and hAPE1 inhibition can lead to mutagenesis. On the other hand, the presented results can cast some light on the UDG or hAPE1 inhibitors being used as a potential treatment.

The Influence of Hepatitis C Virus Therapy on the DNA Base Excision Repair System of Peripheral Blood Mononuclear Cells

2017 ◽  
Vol 36 (7) ◽  
pp. 535-540 ◽  
Author(s):  
Piotr Czarny ◽  
Anna Merecz-Sadowska ◽  
Kinga Majchrzak ◽  
Maciej Jabłkowski ◽  
Janusz Szemraj ◽  
...  
Keyword(s):  
Base Excision Repair ◽  
Mononuclear Cells ◽  
Excision Repair ◽  
Repair System ◽  
Peripheral Blood Mononuclear ◽  
Dna Base Excision Repair ◽  
Dna Base ◽  
Blood Mononuclear Cells ◽  
Base Excision ◽  
Base Excision Repair System

DNA base excision repair potentiates the protective effect of Salmonella Pathogenicity Island 2 within macrophages

Microbiology ◽  
2005 ◽  
Vol 151 (2) ◽  
pp. 557-567 ◽  
Author(s):  
Akamol E. Suvarnapunya ◽  
Murry A. Stein
Keyword(s):  
Base Excision Repair ◽  
Excision Repair ◽  
Pathogenicity Island ◽  
Discrete Systems ◽  
Dna Lesions ◽  
Repair System ◽  
Dna Base Excision Repair ◽  
Base Excision ◽  
Base Excision Repair System ◽  
Reactive Oxidants

Reactive oxidants are a primary weapon of the macrophage antibacterial arsenal. The ability of virulent Salmonella to repair oxidative DNA lesions via the base-excision repair system (BER) enables its survival and replication within the macrophage, but is not required for extracellular growth. Salmonella also inhibits the targeting of oxidant generators to the Salmonella-containing vacuole (SCV) via Salmonella Pathogenicity Island 2 (SPI2). Accordingly, the relative contributions of these two discrete systems to Salmonella resistance to both oxidative mutagenesis and lethality within RAW 264.7 macrophages were investigated. A mutant unable to initiate BER was constructed by deleting all three BER bifunctional glycosylases (Δfpg/nth/nei), and was significantly impaired for early intramacrophage survival. Mutations in various SPI2 effector (sifA and sseEFG) and structural (ssaV) genes were then analysed in the BER mutant background. Loss of SPI2 function alone appeared to increase macrophage-induced mutation. Statistical analyses of the reduced intramacrophage survival of SPI2 mutants and the corresponding SPI2/BER mutants indicated a synergistic interaction between BER and SPI2, suggesting that SPI2 promotes intramacrophage survival by protecting Salmonella DNA from exposure to macrophage oxidants. Furthermore, this protection may involve the SseF and SseG effectors. In contrast, the SifA effector did not seem to play a major role in oxidant protection. It is speculated that Salmonella initially stalls oxidative killing by preserving its genomic integrity through the function of BER, until it can upregulate SPI2 to limit its exposure to macrophage oxidants.

scholarly journals Gene-Targeted Mice Lacking the Trex1 (DNase III) 3′→5′ DNA Exonuclease Develop Inflammatory Myocarditis

2004 ◽  
Vol 24 (15) ◽  
pp. 6719-6727 ◽  
Author(s):  
Masashi Morita ◽  
Gordon Stamp ◽  
Peter Robins ◽  
Anna Dulic ◽  
Ian Rosewell ◽  
...  
Keyword(s):  
Nuclear Dna ◽  
Excision Repair ◽  
Spontaneous Mutation ◽  
Repair System ◽  
Dna Base Excision Repair ◽  
Dna Base ◽  
Base Excision ◽  
Base Excision Repair System

ABSTRACT TREX1, originally designated DNase III, was isolated as a major nuclear DNA-specific 3′→5′ exonuclease that is widely distributed in both proliferating and nonproliferating mammalian tissues. The cognate cDNA shows homology to the editing subunit of the Escherichia coli replicative DNA polymerase III holoenzyme and encodes an exonuclease which was able to serve a DNA-editing function in vitro, promoting rejoining of a 3′ mismatched residue in a reconstituted DNA base excision repair system. Here we report the generation of gene-targeted Trex1−/− mice. The null mice are viable and do not show the increase in spontaneous mutation frequency or cancer incidence that would be predicted if Trex1 served an obligatory role of editing mismatched 3′ termini generated during DNA repair or DNA replication in vivo. Unexpectedly, Trex1−/− mice exhibit a dramatically reduced survival and develop inflammatory myocarditis leading to progressive, often dilated, cardiomyopathy and circulatory failure.

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