The Human DNA glycosylases NEIL1 and NEIL3 Excise Psoralen-Induced DNA-DNA Cross-Links in a Four-Stranded DNA Structure

Abstract

Interstrand cross-links (ICLs) are highly cytotoxic DNA lesions that block DNA replication and transcription by preventing strand separation. Previously, we demonstrated that the bacterial and human DNA glycosylases Nei and NEIL1 excise unhooked psoralen-derived ICLs in three-stranded DNA via hydrolysis of the glycosidic bond between the crosslinked base and deoxyribose sugar. Furthermore, NEIL3 from Xenopus laevis has been shown to cleave psoralen- and abasic site-induced ICLs in Xenopus egg extracts. Here we report that human NEIL3 cleaves psoralen-induced DNA-DNA cross-links in three-stranded and four-stranded DNA substrates to generate unhooked DNA fragments containing either an abasic site or a psoralen-thymine monoadduct. Furthermore, while Nei and NEIL1 also cleave a psoralen-induced four-stranded DNA substrate to generate two unhooked DNA duplexes with a nick, NEIL3 targets both DNA strands in the ICL without generating single-strand breaks. The DNA substrate specificities of these Nei-like enzymes imply the occurrence of long uninterrupted three- and four-stranded crosslinked DNA-DNA structures that may originate in vivo from DNA replication fork bypass of an ICL. In conclusion, the Nei-like DNA glycosylases unhook psoralen-derived ICLs in various DNA structures via a genuine repair mechanism in which complex DNA lesions can be removed without generation of highly toxic double-strand breaks.

Base and nucleotide excision repair facilitate resolution of platinum drugs-induced transcription blockage

“…BER is well known to recognize subtle nucleobase modifications like oxidations. Some DNA glycosylases have also been implicated in repair of different types of DNA crosslinks ( 40–43 ). However, the observation that platinum drug-induced XRCC1 chromatin binding is dependent on OGG1 is striking, because this glycosylase is mainly known to have affinity for 8-oxoG oxidative lesions and not for DNA crosslinks ( 8 ).…”

“…However, BER involvement was confirmed by the fact that platinum drug-induced immobilization of XRCC1 was predominantly dependent on OGG1, a glycosylase exclusively implicated in BER ( 66 ). Some DNA glycosylases, like NEIL1 and NEIL3, have been shown to recognize and cleave psoralen-induced ICLs ( 40 , 42 , 43 ) and also the MPG glycosylase has been implicated in protection against ICL induction by various crosslinking agents ( 41 , 67 ). Possibly, OGG1 may also recognize platinum-induced DNA crosslinks and BER could protect against platinum drugs by recognizing and removing platinum-DNA lesions via OGG1.…”

The Biochemical Role of the Human NEIL1 and NEIL3 DNA Glycosylases on Model DNA Replication Forks

“…This result is especially striking for Tg, where virtually no incision activity was observed for the lesion in the dsDNA substrate. Both hNEIL1 and hNEIL3 DNA glycosylases present extremely weak cleavage activity on the relatively abundant cellular oxidized base 8-oxoG, despite high levels of DNA glycosylase/lyase activity on the further oxidation products of 8-oxoG, Sp and Gh [22,24]. Whilst hNEIL3 Fl appeared to display comparatively reduced DNA glycosylase activity in comparison to hNEIL1, this is likely due to issues associated with expression of fully active hNEIL3 FL in E. coli , due to incorrect folding of the protein and inefficient removal of the N-terminal methionine residue, even in the presence of the modified aminopeptidase [21].…”

“…However human NEIL1 (hNEIL1) has a general preference for oxidized bases (with the notable exception of 8-oxoguanine (8-oxoG)) in double-stranded (ds) DNA exhibiting a β,δ-lyase activity, while human NEIL3 (hNEIL3) has been shown to have a preference for single-stranded (ss) DNA, incising the DNA through a weak β-lyase activity [23]. Both hNEIL1 and hNEIL3 though have high levels of activity on the further oxidation products of 8-oxoG, spiroiminodyhidantoin (Sp) and guanidinohydantoin (Gh) [20,21,22,23,24]. hNEIL1 and the mouse ortholog of NEIL3 have also been demonstrated to excise Sp and Gh lesions in G-quadruplex structures with a preference for DNA in telomeric context, suggestive of structural preferences of the NEIL glycosylases [18,25,26].…”

“…hNEIL3 was demonstrated to co-precipitate with the replisome, while mitotic defects in the form of telomere bridges have been observed in NEIL3 -/- MEFs, hNEIL3 knockdown HCT116 colorectal cancer cells and DNA glycosylase null primary human D132V mutant fibroblasts [18,31]. More recently, hNEIL1 and hNEIL3 were found to process psoralen mono-adducts and interstrand DNA crosslinks (ICLs) in three and four-stranded DNA structures and unhooking ICLs at replication fork structures [24,32,33]. Therefore, cumulatively, this evidence advocates a role for hNEIL1 and hNEIL3 in DNA replication associated DNA repair and coordination, in actively dividing cells.…”