DNA glycosylases search for and remove oxidized DNA bases

Abstract

The following mini review summarizes recent research from the Author’s laboratory as presented to the Environmental Mutagen Society in October 2012. It provides an overview of the DNA glycosylases that recognize oxidized DNA bases using the Fpg/Nei family of DNA glycosylases as models for how structure can inform function. For example, even though human NEIL1 and the plant and fungal orthologs lack the zinc finger shown to be required for binding, DNA crystal structures revealed a “zincless finger” with the same properties. Also the “lesion recognition loop” is not involved in lesion recognition rather stabilization of 8-oxoG in the active site pocket. Unlike the other Fpg/Nei family members, Neil3 lacks two of the three void-filling residues that stabilize the duplex and interact with the opposite strand which may account for its preference for lesions in single stranded DNA. We also showed, using single molecule approaches, that DNA glycosylases search for their substrates in a sea of undamaged DNA by using a wedge residue that is inserted into the DNA helix to probe for the presence of damage.

Tautomerization-dependent recognition and excision of oxidation damage in base-excision DNA repair

“…S2D). It was thought that NEIL1 lacked such a lesion recognition loop (5). Although the loop region between helices αG and αH is much shorter in NEIL1, our structures revealed that NEIL1 uses such a flexible loop to allow recognition of both THF and Tg.…”

“…Such oxidized DNA bases are primarily recognized and removed by the baseexcision repair (BER) pathway, which is initiated by a lesionspecific DNA glycosylase (1)(2)(3)(4). Based on sequence homology and structural motifs, glycosylases that cleave oxidation damage are grouped into two families: the helix-hairpin-helix (HhH) family and the Fpg/Nei family (5,6); the latter is named after the prototypical bacterial members formamidopyrimidine DNA glycosylase (Fpg) and endonuclease eight (Nei).…”

“…Recent studies have determined several complex structures of MvNei1 (mimivirus Nei1), a viral ortholog of human NEIL1 (33,34). However, MvNei1 and NEIL1 have apparent differences in their 3D structures and enzymatic properties (5). Hence, structures of human NEIL1 with bound substrates are…”

NEIL1 p.Gln282Stop variant is predominantly localized in the cytoplasm and exhibits reduced activity in suppressing mutations

“…However, this does not exclude the possibility of NEIL1 being a causative gene for such a cancer predisposition syndromes, because familial aggregation of cancers without identification of causative germline mutation is not uncommon; for example, approximately 30% of individuals diagnosed with colorectal cancer have a family history of the disease, however, only approximately 5% are found to carry germline mutations in genes responsible for known hereditary cancer syndromes (Stoffel and Kastrinos, 2014). Considering the role of NEIL1 in the repair of the genomic DNA (Wallace, 2013) as well as existence of MAP due to germline mutations of another DNA glycosylase, MUTYH (Shinmura et al, 2012;Mazzei et al, 2013;Cao et al, 2013), it is possible that in some part, familial clustering of cancer is attributable to germline variants of the NEIL1 gene. In addition, it is also possible that germline NEIL1 variants are low-risk alleles for cancers.…”

Unveiling the non-repair face of the Base Excision Repair pathway in RNA processing: A missing link between DNA repair and gene expression?

“…An additional family of DNA glycosylases, represented by the human NEIL1 and NEIL2 enzymes, is also able to operate a β,δ-elimination reaction, leaving a 3′-phosphate nick [2]. Higher eukaryotes are provided with a vast array of DNA glycosylases with a significant redundancy in their damage selectivity for this reason, single knockout of several DNA glycosylases is not lethal per se, although an accumulation of unrepaired DNA lesions occurs [3].…”