scholarly journals Inhibition of Short Patch and Long Patch Base Excision Repair by an Oxidized Abasic Site

Biochemistry ◽  
2010 ◽  
Vol 49 (45) ◽  
pp. 9904-9910 ◽  
Author(s):  
Lirui Guan ◽  
Katarzyna Bebenek ◽  
Thomas A. Kunkel ◽  
Marc M. Greenberg
Keyword(s):  
Base Excision Repair ◽  
Excision Repair ◽  
Abasic Site ◽  
Oxidized Abasic Site ◽  
Base Excision

scholarly journals MSH2–MSH6 stimulates DNA polymerase η, suggesting a role for A:T mutations in antibody genes

2005 ◽  
Vol 201 (4) ◽  
pp. 637-645 ◽  
Author(s):  
Teresa M. Wilson ◽  
Alexandra Vaisman ◽  
Stella A. Martomo ◽  
Patsa Sullivan ◽  
Li Lan ◽  
...  
Keyword(s):  
Dna Polymerase ◽  
Base Excision Repair ◽  
Somatic Hypermutation ◽  
Excision Repair ◽  
Cytidine Deaminase ◽  
Abasic Site ◽  
Cell Extracts ◽  
Activation Induced Cytidine Deaminase ◽  
Base Excision

Activation-induced cytidine deaminase deaminates cytosine to uracil (dU) in DNA, which leads to mutations at C:G basepairs in immunoglobulin genes during somatic hypermutation. The mechanism that generates mutations at A:T basepairs, however, remains unclear. It appears to require the MSH2–MSH6 mismatch repair heterodimer and DNA polymerase (pol) η, as mutations of A:T are decreased in mice and humans lacking these proteins. Here, we demonstrate that these proteins interact physically and functionally. First, we show that MSH2–MSH6 binds to a U:G mismatch but not to other DNA intermediates produced during base excision repair of dUs, including an abasic site and a deoxyribose phosphate group. Second, MSH2 binds to pol η in solution, and endogenous MSH2 associates with the pol in cell extracts. Third, MSH2–MSH6 stimulates the catalytic activity of pol η in vitro. These observations suggest that the interaction between MSH2–MSH6 and DNA pol η stimulates synthesis of mutations at bases located downstream of the initial dU lesion, including A:T pairs.

scholarly journals R-loops promote trinucleotide repeat deletion through DNA base excision repair enzymatic activities

2020 ◽  
Vol 295 (40) ◽  
pp. 13902-13913
Author(s):  
Eduardo E. Laverde ◽  
Yanhao Lai ◽  
Fenfei Leng ◽  
Lata Balakrishnan ◽  
Catherine H. Freudenreich ◽  
...  
Keyword(s):  
Base Excision Repair ◽  
Trinucleotide Repeat ◽  
Excision Repair ◽  
Enzymatic Activities ◽  
Cag Repeat ◽  
Abasic Site ◽  
Dna Damage And Repair ◽  
Dna Base Excision Repair ◽  
Treatment And Prevention ◽  
Base Excision

Trinucleotide repeat (TNR) expansion and deletion are responsible for over 40 neurodegenerative diseases and associated with cancer. TNRs can undergo somatic instability that is mediated by DNA damage and repair and gene transcription. Recent studies have pointed toward a role for R-loops in causing TNR expansion and deletion, and it has been shown that base excision repair (BER) can result in CAG repeat deletion from R-loops in yeast. However, it remains unknown how BER in R-loops can mediate TNR instability. In this study, using biochemical approaches, we examined BER enzymatic activities and their influence on TNR R-loops. We found that AP endonuclease 1 incised an abasic site on the nontemplate strand of a TNR R-loop, creating a double-flap intermediate containing an RNA:DNA hybrid that subsequently inhibited polymerase β (pol β) synthesis of TNRs. This stimulated flap endonuclease 1 (FEN1) cleavage of TNRs engaged in an R-loop. Moreover, we showed that FEN1 also efficiently cleaved the RNA strand, facilitating pol β loop/hairpin bypass synthesis and the resolution of TNR R-loops through BER. Consequently, this resulted in fewer TNRs synthesized by pol β than those removed by FEN1, thereby leading to repeat deletion. Our results indicate that TNR R-loops preferentially lead to repeat deletion during BER by disrupting the balance between the addition and removal of TNRs. Our discoveries open a new avenue for the treatment and prevention of repeat expansion diseases and cancer.

scholarly journals Mammalian Abasic Site Base Excision Repair

1998 ◽  
Vol 273 (33) ◽  
pp. 21203-21209 ◽  
Author(s):  
Deepak K. Srivastava ◽  
Brian J. Vande Berg ◽  
Rajendra Prasad ◽  
James T. Molina ◽  
William A. Beard ◽  
...  
Keyword(s):  
Base Excision Repair ◽  
Excision Repair ◽  
Abasic Site ◽  
Base Excision

scholarly journals Role of polymerase β in complementing aprataxin deficiency during abasic-site base excision repair

2014 ◽  
Vol 21 (5) ◽  
pp. 497-499 ◽  
Author(s):  
Melike Çağlayan ◽  
Vinod K Batra ◽  
Akira Sassa ◽  
Rajendra Prasad ◽  
Samuel H Wilson
Keyword(s):  
Base Excision Repair ◽  
Excision Repair ◽  
Abasic Site ◽  
Base Excision

scholarly journals Removal of Oxidative DNA Damage via FEN1-Dependent Long-Patch Base Excision Repair in Human Cell Mitochondria

2008 ◽  
Vol 28 (16) ◽  
pp. 4975-4987 ◽  
Author(s):  
Pingfang Liu ◽  
Limin Qian ◽  
Jung-Suk Sung ◽  
Nadja C. de Souza-Pinto ◽  
Li Zheng ◽  
...  
Keyword(s):  
Dna Damage ◽  
Base Excision Repair ◽  
Oxidative Dna Damage ◽  
Excision Repair ◽  
Subcellular Fractionation ◽  
Major Type ◽  
Abasic Site ◽  
Intact Cells ◽  
Base Excision ◽  
Extent Of Damage

ABSTRACT Repair of oxidative DNA damage in mitochondria was thought limited to short-patch base excision repair (SP-BER) replacing a single nucleotide. However, certain oxidative lesions cannot be processed by SP-BER. Here we report that 2-deoxyribonolactone (dL), a major type of oxidized abasic site, inhibits replication by mitochondrial DNA (mtDNA) polymerase γ and interferes with SP-BER by covalently trapping polymerase γ during attempted dL excision. However, repair of dL was detected in human mitochondrial extracts, and we show that this repair is via long-patch BER (LP-BER) dependent on flap endonuclease 1 (FEN1), not previously known to be present in mitochondria. FEN1 was retained in protease-treated mitochondria and detected in mitochondrial nucleoids that contain known mitochondrial replication and transcription proteins. Results of immunofluorescence and subcellular fractionation studies were also consistent with the presence of FEN1 in the mitochondria of intact cells. Immunodepletion experiments showed that the LP-BER activity of mitochondrial extracts was strongly diminished in parallel with the removal of FEN1, although some activity remained, suggesting the presence of an additional flap-removing enzyme. Biological evidence for a FEN1 role in repairing mitochondrial oxidative DNA damage was provided by RNA interference experiments, with the extent of damage greater and the recovery slower in FEN1-depleted cells than in control cells. The mitochondrial LP-BER pathway likely plays important roles in repairing dL lesions and other oxidative lesions and perhaps in normal mtDNA replication.

scholarly journals Oxidative DNA damage is epigenetic by regulating gene transcription via base excision repair

2016 ◽  
Author(s):  
Aaron M. Fleming ◽  
Yun Ding ◽  
Cynthia J. Burrows
Keyword(s):  
Base Excision Repair ◽  
Oxidative Dna Damage ◽  
Excision Repair ◽  
Gene Activation ◽  
Gene Promoters ◽  
Abasic Site ◽  
Protein Activity ◽  
Modified Dna ◽  
G Quadruplex ◽  
Base Excision

AbstractReactive oxygen species (ROS) have emerged as important cellular signaling agents for survival. Herein, we demonstrate that ROS-mediated oxidation of DNA to yield 8-oxo-7,8-dihydroguanine (OG) in gene promoters is a signaling agent for gene activation. Enhanced gene expression occurs when OG is formed in guanine-rich, potential G-quadruplex sequences (PQS) in promoter coding strands to initiate base excision repair (BER) by 8-oxoguanine DNA glycosylase (OGG1) yielding an abasic site (AP). The AP enables melting of the duplex to unmask the PQS to adopt a G-quadruplex fold in which apurinic/apyrimidinic endonuclease 1 (APE1) binds, but inefficiently cleaves, the AP for activation of VEGF or NTHL1 genes. This concept allowed identification of 61 human DNA repair genes that might be activated by this mechanism. Identification of the oxidatively-modified DNA base OG as guiding protein activity on the genome and altering cellular phenotype ascribes an epigenetic role to OG.

scholarly journals ALKBH1 Is Dispensable for Abasic Site Cleavage during Base Excision Repair and Class Switch Recombination

PLoS ONE ◽  
2013 ◽  
Vol 8 (6) ◽  
pp. e67403 ◽  
Author(s):  
Tina A. Müller ◽  
Kefei Yu ◽  
Robert P. Hausinger ◽  
Katheryn Meek
Keyword(s):  
Base Excision Repair ◽  
Excision Repair ◽  
Class Switch Recombination ◽  
Abasic Site ◽  
Class Switch ◽  
Base Excision

scholarly journals HECTD1 promotes base excision repair in nucleosomes through chromatin remodelling

2019 ◽  
Vol 48 (3) ◽  
pp. 1301-1313 ◽  
Author(s):  
Laura Bennett ◽  
Eleanor C E T Madders ◽  
Jason L Parsons
Keyword(s):  
Dna Damage ◽  
Base Excision Repair ◽  
Genome Stability ◽  
Excision Repair ◽  
Chromatin Remodelling ◽  
Abasic Site ◽  
Cell Extracts ◽  
Base Excision ◽  
Cellular Dna

Abstract Base excision repair (BER) is the major cellular DNA repair pathway that recognises and excises damaged DNA bases to help maintain genome stability. Whilst the major enzymes and mechanisms co-ordinating BER are well known, the process of BER in chromatin where DNA is compacted with histones, remains unclear. Using reconstituted mononucleosomes containing a site-specific synthetic abasic site (tetrahydrofuran, THF), we demonstrate that the DNA damage is less efficiently incised by recombinant AP endonuclease 1 (APE1) when the DNA backbone is facing the histone core (THF-in) compared to that orientated away (THF-out). However, when utilizing HeLa whole cell extracts, the difference in incision of THF-in versus THF-out is less pronounced suggesting the presence of chromatin remodelling factors that stimulate THF accessibility to APE1. We subsequently purified an activity from HeLa cell extracts and identify this as the E3 ubiquitin ligase, HECTD1. We demonstrate that a recombinant truncated form of HECTD1 can stimulate incision of THF-in by APE1 in vitro by histone ubiquitylation, and that siRNA-mediated depletion of HECTD1 leads to deficiencies in DNA damage repair and decreased cell survival following x-ray irradiation, particularly in normal fibroblasts. Thus, we have now identified HECTD1 as an important factor in promoting BER in chromatin.

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