Variation in base excision repair capacity

Abstract

The major DNA repair pathway for coping with spontaneous forms of DNA damage, such as natural hydrolytic products or oxidative lesions, is base excision repair (BER). In particular, BER processes mutagenic and cytotoxic DNA lesions such as non-bulky base modifications, abasic sites, and a range of chemically distinct single-strand breaks. Defects in BER have been linked to cancer predisposition, neurodegenerative disorders, and immunodeficiency. Recent data indicate a large degree of sequence variability in DNA repair genes and several studies have associated BER gene polymorphisms with disease risk, including cancer of several sites. The intent of this review is to describe the range of BER capacity among individuals and the functional consequences of BER genetic variants. We also discuss studies that associate BER deficiency with disease risk and the current state of BER capacity measurement assays. KeywordsDNA repair capacity; base excision; pathway assay; polymorphism; disease susceptibility Overview of Base Excision Repair: Connection to DiseaseBase excision repair (BER) is the major DNA repair pathway for most spontaneous, alkylative, and oxidative DNA lesions. The process (Figure 1), which aims to remove and replace a damaged nucleotide, is typically initiated by one of several substrate-selective DNA glycosylases, which recognize and excise a range of base modifications such as uracil, 8-oxoguanine (8-oxo-dG), and 3-methyladenine among others [1,2]. The resulting apurinic/ apyrimidinic (AP) site, which can also be formed at high frequency by spontaneous (i.e., non-enzymatic) hydrolysis of the N-glycosidic bond, is then incised by an AP endonuclease, APE1 (aka APEX1 or REF1) in mammals [3][4][5]. The 5'-deoxyribose phosphate strand break product is subsequently removed and the missing nucleotide gap is filled, two steps that are most frequently executed by DNA polymerase β (POLβ) in mammals [6]. The remaining nick is sealed by a DNA ligase, which in mammals is typically ligase 3α (LIG3α) in complex with x-ray cross-complementing protein 1 (XRCC1) [7]. If executed as shown in Figure 1, the process is termed short-patch BER, since it involves the incorporation of only a * To whom correspondence should be addressed: wilsonda@mail.nih.gov; Phone, Fax,.. Publisher's Disclaimer:This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. NIH Public Access NIH-PA Author ManuscriptNIH-PA Author Manuscript NIH-PA Author Manuscript single nucleotide. However, there are other sub-branches of BER -involving specialized single-strand break processing enzymes or the long-patch (2-13 nucleotides) proliferat...

Poly(ADP-ribose) Polymerase 1 (PARP-1) Binds to 8-Oxoguanine-DNA Glycosylase (OGG1)

“…This impairment in the recruitment and binding of BER proteins may then delay the DNA repair process or potentially lead to the accumulation of damaged DNA. Importantly, several of the OGG1 polymorphisms have been shown to have decreased catalytic activity, which may hinder the activation of PARP-1 and the early steps in the BER pathway (37,(51)(52)(53)(54). Indeed, both the R229Q and S326C have an impaired ability to activate PARP-1 compared with wild-type OGG1.…”

“…Indeed, both the R229Q and S326C have an impaired ability to activate PARP-1 compared with wild-type OGG1. This difference may be due to the fact that the S326C polymorphism exists as a dimer and has decreased enzymatic activity compared with wild-type and the R229Q polymorphism has decreased activity and is a thermolabile protein (37,(51)(52)(53)(54). Future work lies in further understanding the interplay between the OGG1 polymorphisms and PARP-1.…”

“…Several OGG1 polymorphisms have been reported and correlate with diseases including cancer and Alzheimer disease (25,26,50,51). Two frequently observed OGG1 polymorphisms include the R229Q and S326C mutations in the C terminus of OGG1 (17,52).…”

Multiplexed DNA repair assays for multiple lesions and multiple doses via transcription inhibition and transcriptional mutagenesis

“…Left unrepaired, these lesions have the potential to alter cellular function and compromise the health of the organism, leading to degenerative diseases, cancer, and premature aging (1)(2)(3)(4)(5). Consequently, interindividual variations in DNA repair capacity (DRC) are thought to contribute to the fact that people have different susceptibilities to these diseases (6)(7)(8)(9)(10). Furthermore, the efficacy of cancer chemotherapy with DNA-damaging agents depends on the DRC of the targeted cells (11).…”

Investigating the Cellular Localization of APE1.

“…Further site-directed mutagenesis studies on APEl active site using N68A, D70A, Y171F, D210N, F266A, D308A, and H309S confirmed that APEl shares the same active site for both abasic DNA incision activities and RNA cleaving activity (Kim et al 201 lb). However, these APEl mutants retained their ability to bind the RNA substrate, required 2'-OH on the sugar for cleavage, and did not require presence of a divalent ion unlike abasic DNA incision activity of APEl (Kim et al 2011). Therefore, it was postulated that although APEl shares the same active site, they may have different mechanisms for cleaving RNA, abasic ssRNA, and abasic DNA.…”