scholarly journals (5′S) 5′,8-cyclo-2′-deoxyadenosine Cannot Stop BER. Clustered DNA Lesion Studies

2021 ◽  
Vol 22 (11) ◽  
pp. 5934
Author(s):  
Boleslaw T. Karwowski
Keyword(s):  
Excision Repair ◽  
Nuclear Extract ◽  
Dna Lesions ◽  
Nuclear Antigen ◽  
Damage Site ◽  
Dna Lesion ◽  
Nucleotide Excision ◽  
Chemical Factors ◽  
Base Excision ◽  
Living Organisms

As a result of external and endocellular physical-chemical factors, every day approximately ~105 DNA lesions might be formed in each human cell. During evolution, living organisms have developed numerous repair systems, of which Base Excision Repair (BER) is the most common. 5′,8-cyclo-2′-deoxyadenosine (cdA) is a tandem lesion that is removed by the Nucleotide Excision Repair (NER) mechanism. Previously, it was assumed that BER machinery was not able to remove (5′S)cdA from the genome. In this study; however, it has been demonstrated that, if (5′S)cdA is a part of a single-stranded clustered DNA lesion, it can be removed from ds-DNA by BER. The above is theoretically possible in two cases: (A) When, during repair, clustered lesions form Okazaki-like fragments; or (B) when the (5′S)cdA moiety is located in the oligonucleotide strand on the 3′-end side of the adjacent DNA damage site, but not when it appears at the opposite 5′-end side. To explain this phenomenon, pure enzymes involved in BER were used (polymerase β (Polβ), a Proliferating Cell Nuclear Antigen (PCNA), and the X-Ray Repair Cross-Complementing Protein 1 (XRCC1)), as well as the Nuclear Extract (NE) from xrs5 cells. It has been found that Polβ can effectively elongate the primer strand in the presence of XRCC1 or PCNA. Moreover, supplementation of the NE from xrs5 cells with Polβ (artificial Polβ overexpression) forced oligonucleotide repair via BER in all the discussed cases.

scholarly journals Nucleotide Excision Repair: From Molecular Defects to Neurological Abnormalities

2021 ◽  
Vol 22 (12) ◽  
pp. 6220
Author(s):  
Yuliya Krasikova ◽  
Nadejda Rechkunova ◽  
Olga Lavrik
Keyword(s):  
Mitochondrial Dysfunction ◽  
Nucleotide Excision Repair ◽  
Excision Repair ◽  
Genetic Disorders ◽  
Light Sensitivity ◽  
Dna Lesions ◽  
Specific Class ◽  
Dna Lesion ◽  
Nucleotide Excision ◽  
Low Efficiency

Nucleotide excision repair (NER) is the most versatile DNA repair pathway, which can remove diverse bulky DNA lesions destabilizing a DNA duplex. NER defects cause several autosomal recessive genetic disorders. Xeroderma pigmentosum (XP) is one of the NER-associated syndromes characterized by low efficiency of the removal of bulky DNA adducts generated by ultraviolet radiation. XP patients have extremely high ultraviolet-light sensitivity of sun-exposed tissues, often resulting in multiple skin and eye cancers. Some XP patients develop characteristic neurodegeneration that is believed to derive from their inability to repair neuronal DNA damaged by endogenous metabolites. A specific class of oxidatively induced DNA lesions, 8,5′-cyclopurine-2′-deoxynucleosides, is considered endogenous DNA lesions mainly responsible for neurological problems in XP. Growing evidence suggests that XP is accompanied by defective mitophagy, as in primary mitochondrial disorders. Moreover, NER pathway is absent in mitochondria, implying that the mitochondrial dysfunction is secondary to nuclear NER defects. In this review, we discuss the current understanding of the NER molecular mechanism and focuses on the NER linkage with the neurological degeneration in patients with XP. We also present recent research advances regarding NER involvement in oxidative DNA lesion repair. Finally, we highlight how mitochondrial dysfunction may be associated with XP.

scholarly journals Mechanism of DNA Lesion Homing and Recognition by the Uvr Nucleotide Excision Repair System

Research ◽  
2019 ◽  
Vol 2019 ◽  
pp. 1-11 ◽  
Author(s):  
Seung-Joo Lee ◽  
Rou-Jia Sung ◽  
Gregory L. Verdine
Keyword(s):  
Dna Repair ◽  
Nucleotide Excision Repair ◽  
Excision Repair ◽  
Dna Lesions ◽  
Repair System ◽  
Genome Maintenance ◽  
Dna Lesion ◽  
Nucleotide Excision ◽  
Biochemical Studies ◽  
Lesion Recognition

Nucleotide excision repair (NER) is an essential DNA repair system distinguished from other such systems by its extraordinary versatility. NER removes a wide variety of structurally dissimilar lesions having only their bulkiness in common. NER can also repair several less bulky nucleobase lesions, such as 8-oxoguanine. Thus, how a single DNA repair system distinguishes such a diverse array of structurally divergent lesions from undamaged DNA has been one of the great unsolved mysteries in the field of genome maintenance. Here we employ a synthetic crystallography approach to obtain crystal structures of the pivotal NER enzyme UvrB in complex with duplex DNA, trapped at the stage of lesion-recognition. These structures coupled with biochemical studies suggest that UvrB integrates the ATPase-dependent helicase/translocase and lesion-recognition activities. Our work also conclusively establishes the identity of the lesion-containing strand and provides a compelling insight to how UvrB recognizes a diverse array of DNA lesions.

scholarly journals Alkyltransferase-like protein clusters scan DNA rapidly over long distances and recruit NER to alkyl-DNA lesions

2020 ◽  
Vol 117 (17) ◽  
pp. 9318-9328
Author(s):  
Natascha Rill ◽  
Ann Mukhortava ◽  
Sonja Lorenz ◽  
Ingrid Tessmer
Keyword(s):  
Single Molecule ◽  
Molecular Level ◽  
Excision Repair ◽  
Therapeutic Benefit ◽  
Dna Lesions ◽  
Repair System ◽  
Cytotoxic Potential ◽  
Dna Lesion ◽  
Search Mechanism ◽  
Nucleotide Excision

Alkylation of guanine bases in DNA is detrimental to cells due to its high mutagenic and cytotoxic potential and is repaired by the alkyltransferase AGT. Additionally, alkyltransferase-like proteins (ATLs), which are structurally similar to AGTs, have been identified in many organisms. While ATLs are per se catalytically inactive, strong evidence has suggested that ATLs target alkyl lesions to the nucleotide excision repair system (NER). Using a combination of single-molecule and ensemble approaches, we show here recruitment of UvrA, the initiating enzyme of prokaryotic NER, to an alkyl lesion by ATL. We further characterize lesion recognition by ATL and directly visualize DNA lesion search by highly motile ATL and ATL–UvrA complexes on DNA at the molecular level. Based on the high similarity of ATLs and the DNA-interacting domain of AGTs, our results provide important insight in the lesion search mechanism, not only by ATL but also by AGT, thus opening opportunities for controlling the action of AGT for therapeutic benefit during chemotherapy.

scholarly journals Nucleotide excision repair of abasic DNA lesions

2019 ◽  
Vol 47 (16) ◽  
pp. 8537-8547 ◽  
Author(s):  
Nataliya Kitsera ◽  
Marta Rodriguez-Alvarez ◽  
Steffen Emmert ◽  
Thomas Carell ◽  
Andriy Khobta
Keyword(s):  
Nucleotide Excision Repair ◽  
Excision Repair ◽  
Dna Lesions ◽  
Transcription Rate ◽  
Repair Pathway ◽  
Nucleotide Excision ◽  
Repair Mechanisms ◽  
Nucleotide Excision Repair Pathway ◽  
Ap Sites ◽  
Base Excision

AbstractApurinic/apyrimidinic (AP) sites are a class of highly mutagenic and toxic DNA lesions arising in the genome from a number of exogenous and endogenous sources. Repair of AP lesions takes place predominantly by the base excision pathway (BER). However, among chemically heterogeneous AP lesions formed in DNA, some are resistant to the endonuclease APE1 and thus refractory to BER. Here, we employed two types of reporter constructs accommodating synthetic APE1-resistant AP lesions to investigate the auxiliary repair mechanisms in human cells. By combined analyses of recovery of the transcription rate and suppression of transcriptional mutagenesis at specifically positioned AP lesions, we demonstrate that nucleotide excision repair pathway (NER) efficiently removes BER-resistant AP lesions and significantly enhances the repair of APE1-sensitive ones. Our results further indicate that core NER components XPA and XPF are equally required and that both global genome (GG-NER) and transcription coupled (TC-NER) subpathways contribute to the repair.

scholarly journals Poly(ADP-ribose) polymerase 1 escorts XPC to UV-induced DNA lesions during nucleotide excision repair

2017 ◽  
Vol 114 (33) ◽  
pp. E6847-E6856 ◽  
Author(s):  
Mihaela Robu ◽  
Rashmi G. Shah ◽  
Nupur K. Purohit ◽  
Pengbo Zhou ◽  
Hanspeter Naegeli ◽  
...  
Keyword(s):  
Steady State ◽  
Nucleotide Excision Repair ◽  
Excision Repair ◽  
Dna Lesions ◽  
Stable Complex ◽  
Lesion Site ◽  
Genomic Context ◽  
Dna Lesion ◽  
Nucleotide Excision ◽  
Damaged Dna

Xeroderma pigmentosum C (XPC) protein initiates the global genomic subpathway of nucleotide excision repair (GG-NER) for removal of UV-induced direct photolesions from genomic DNA. The XPC has an inherent capacity to identify and stabilize at the DNA lesion sites, and this function is facilitated in the genomic context by UV-damaged DNA-binding protein 2 (DDB2), which is part of a multiprotein UV–DDB ubiquitin ligase complex. The nuclear enzyme poly(ADP-ribose) polymerase 1 (PARP1) has been shown to facilitate the lesion recognition step of GG-NER via its interaction with DDB2 at the lesion site. Here, we show that PARP1 plays an additional DDB2-independent direct role in recruitment and stabilization of XPC at the UV-induced DNA lesions to promote GG-NER. It forms a stable complex with XPC in the nucleoplasm under steady-state conditions before irradiation and rapidly escorts it to the damaged DNA after UV irradiation in a DDB2-independent manner. The catalytic activity of PARP1 is not required for the initial complex formation with XPC in the nucleoplasm but it enhances the recruitment of XPC to the DNA lesion site after irradiation. Using purified proteins, we also show that the PARP1–XPC complex facilitates the handover of XPC to the UV-lesion site in the presence of the UV–DDB ligase complex. Thus, the lesion search function of XPC in the genomic context is controlled by XPC itself, DDB2, and PARP1. Our results reveal a paradigm that the known interaction of many proteins with PARP1 under steady-state conditions could have functional significance for these proteins.

scholarly journals DICER- and MMSET-catalyzed H4K20me2 recruits the nucleotide excision repair factor XPA to DNA damage sites

2017 ◽  
Vol 217 (2) ◽  
pp. 527-540 ◽  
Author(s):  
Shalaka Chitale ◽  
Holger Richly
Keyword(s):  
Dna Damage ◽  
Dna Repair ◽  
Nucleotide Excision Repair ◽  
Excision Repair ◽  
Uv Light ◽  
Dna Lesions ◽  
Histone H4 ◽  
Damage Site ◽  
Nucleotide Excision ◽  
Lesion Recognition

Ultraviolet (UV) irradiation triggers the recruitment of DNA repair factors to the lesion sites and the deposition of histone marks as part of the DNA damage response. The major DNA repair pathway removing DNA lesions caused by exposure to UV light is nucleotide excision repair (NER). We have previously demonstrated that the endoribonuclease DICER facilitates chromatin decondensation during lesion recognition in the global-genomic branch of NER. Here, we report that DICER mediates the recruitment of the methyltransferase MMSET to the DNA damage site. We show that MMSET is required for efficient NER and that it catalyzes the dimethylation of histone H4 at lysine 20 (H4K20me2). H4K20me2 at DNA damage sites facilitates the recruitment of the NER factor XPA. Our work thus provides evidence for an H4K20me2-dependent mechanism of XPA recruitment during lesion recognition in the global-genomic branch of NER.

scholarly journals Yeast RAD26, a Homolog of the Human CSB Gene, Functions Independently of Nucleotide Excision Repair and Base Excision Repair in Promoting Transcription through Damaged Bases

2002 ◽  
Vol 22 (12) ◽  
pp. 4383-4389 ◽  
Author(s):  
Sung-Keun Lee ◽  
Sung-Lim Yu ◽  
Louise Prakash ◽  
Satya Prakash
Keyword(s):  
Rna Polymerase Ii ◽  
Nucleotide Excision Repair ◽  
Base Excision Repair ◽  
Excision Repair ◽  
Dna Lesions ◽  
Nucleotide Excision ◽  
Severe Reduction ◽  
Base Excision ◽  
Group B

ABSTRACT RAD26 in the yeast Saccharomyces cerevisiae is the counterpart of the human Cockayne syndrome group B (CSB) gene. Both RAD26 and CSB act in the preferential repair of UV lesions on the transcribed strand, and in this process, they function together with the components of nucleotide excision repair (NER). Here, we examine the role of RAD26 in the repair of DNA lesions induced upon treatment with the alkylating agent methyl methanesulfonate (MMS). MMS-induced DNA lesions include base damages such as 3-methyl adenine and 7-methyl guanine, and these lesions are removed in yeast by the alternate competing pathways of base excision repair (BER), which is initiated by the action of MAG1-encoded N-methyl purine DNA glycosylase, and NER. Interestingly, a synergistic increase in MMS sensitivity was observed in the rad26Δ strain upon inactivation of NER or BER, indicating that RAD26 promotes the survival of MMS-treated cells by a mechanism that acts independently of either of these repair pathways. The galactose-inducible transcription of the GAL2, GAL7, and GAL10 genes is reduced in MMS-treated rad26Δ cells and also in mag1Δ rad14Δ cells, whereas a very severe reduction in transcription occurs in MMS-treated mag1Δ rad14Δ rad26Δ cells. From these observations, we infer that RAD26 plays a role in promoting transcription by RNA polymerase II through damaged bases. The implications of these observations are discussed in this paper.

scholarly journals Nucleotide excision repair–initiating proteins bind to oxidative DNA lesions in vivo

2012 ◽  
Vol 199 (7) ◽  
pp. 1037-1046 ◽  
Author(s):  
Hervé Menoni ◽  
Jan H.J. Hoeijmakers ◽  
Wim Vermeulen
Keyword(s):  
Nucleotide Excision Repair ◽  
Oxidative Dna Damage ◽  
Excision Repair ◽  
Dna Lesions ◽  
Dna Damages ◽  
Nucleotide Excision ◽  
Repair Factor ◽  
Base Excision ◽  
Group B

Base excision repair (BER) is the main repair pathway to eliminate abundant oxidative DNA lesions such as 8-oxo-7,8-dihydroguanine. Recent data suggest that the key transcription-coupled nucleotide excision repair factor (TC-NER) Cockayne syndrome group B (CSB) and the global genome NER-initiating factor XPC are implicated in the protection of cells against oxidative DNA damages. Our novel live-cell imaging approach revealed a strong and very rapid recruitment of XPC and CSB to sites of oxidative DNA lesions in living cells. The absence of detectable accumulation of downstream NER factors at the site of local oxidative DNA damage provide the first in vivo indication of the involvement of CSB and XPC in the repair of oxidative DNA lesions independent of the remainder of the NER reaction. Interestingly, CSB exhibited different and transcription-dependent kinetics in the two compartments studied (nucleolus and nucleoplasm), suggesting a direct transcription-dependent involvement of CSB in the repair of oxidative lesions associated with different RNA polymerases but not involving other NER proteins.

scholarly journals Endonuclease IV Is the Main Base Excision Repair Enzyme Involved in DNA Damage Induced by UVA Radiation and Stannous Chloride

2010 ◽  
Vol 2010 ◽  
pp. 1-9 ◽  
Author(s):  
Ellen S. Motta ◽  
Paulo Thiago Souza-Santos ◽  
Tuany R. Cassiano ◽  
Flávio J. S. Dantas ◽  
Adriano Caldeira-de-Araujo ◽  
...  
Keyword(s):  
Stannous Chloride ◽  
Excision Repair ◽  
Dna Lesions ◽  
Dna Breaks ◽  
Strand Breaks ◽  
E Coli ◽  
Dna Lesion ◽  
Base Excision ◽  
Dna Strand ◽  
Uva Radiation

Stannous chloride (SnCl2) and UVA induce DNA lesions through ROS. The aim of this work was to study the toxicity induced by UVA preillumination, followed bySnCl2treatment.E. coliBER mutants were used to identify genes which could play a role in DNA lesion repair generated by these agents. The survival assays showed (i) Thenfomutant was the most sensitive toSnCl2; (ii) lethal synergistic effect was observed after UVA pre-illumination, plusSnCl2incubation, thenfomutant being the most sensitive; (iii) wild type andnfomutants, transformed with pBW21 plasmid (nfo+) had their survival increased following treatments. The alkaline agarose gel electrophoresis assays pointed that (i) UVA induced DNA breaks andfpgmutant was the most sensitive; (ii)SnCl2-induced DNA strand breaks were higher than those from UVA andnfomutant had the slowest repair kinetics; (iii)UVA+SnCl2promoted an increase in DNA breaks thanSnCl2and, again,nfomutant displayed the slowest repair kinetics. In summary, Nfo protectsE. colicells against damage induced bySnCl2andUVA+SnCl2.

scholarly journals Method for assessment of nucleotide excision repair system efficiency ex vivo

Acta Naturae ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 122-125
Author(s):  
Aleksei A. Popov ◽  
Konstantin E. Orishchenko ◽  
Konstantin N. Naumenko ◽  
Aleksei N. Evdokimov ◽  
Irina O. Petruseva ◽  
...  
Keyword(s):  
Nucleotide Excision Repair ◽  
Fluorescent Protein ◽  
Excision Repair ◽  
Ex Vivo ◽  
Gene Promoter ◽  
Dna Lesions ◽  
Repair System ◽  
Wide Range ◽  
Nucleotide Excision ◽  
Living Organisms

The nucleotide excision repair (NER) is one of the main repair systems present in the cells of living organisms. It is responsible for the removal of a wide range of bulky DNA lesions. We succeeded in developing a method for assessing the efficiency of NER in the cell (ex vivo), which is a method based on the recovery of TagRFP fluorescent protein production through repair of the damage that blocks the expression of the appropriate gene. Our constructed plasmids containing bulky nFlu or nAnt lesions near the tagrfp gene promoter were shown to undergo repair in eukaryotic cells (HEK 293T) and that they can be used to analyze the efficiency of NER ex vivo. A comparative analysis of the time dependence of fluorescent cells accumulation after transfection with nFlu- and nAnt-DNA revealed that there are differences in how efficient their repair by the NER system of HEK 293T cells can be. The method can be used to assess the cell repair status and the repair efficiency of different structural damages.

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