RNA editing changes the lesion specificity for the DNA repair enzyme NEIL1

Yeo, Jongchan; Goodman, Rena A.; Schirle, N.T.; David, Sheila S.; Beal, Peter A.

doi:10.1073/pnas.1009231107

Cited by 146 publications

(205 citation statements)

References 41 publications

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“…Lys242 is the form of NEIL1 encoded in the genome; RNA editing of NEIL1 pre-mRNA results in the edited Arg242 form, which was the NEIL1 protein studied in the sections above. The unedited Lys242 form was reported to be active toward Tg as well; in fact, the Tg excision activity of this form is ∼30-fold faster (30). We also confirmed that the Lys242 form cleaves Tg much faster than the Arg242 form ( Table 2).…”

Section: Computational Simulations Suggest That Tautomerization Promotessupporting

confidence: 74%

“…Whether or not NEIL1 also promotes tautomeric shifts of these substrates for efficient recognition and catalysis remains an open question at the moment. An ∼30-to 50-fold rate difference in Tg excision is observed between NEIL1 Arg242 and Lys242; yet unlike Tg, reaction rates are comparable for the two NEIL1 variants for both Gh and Sp (30). Therefore, it appears from this biochemical evidence that amino acid residues at position 242 may have different effects on the apparent reaction rates for different NEIL1 substrates.…”

Section: Discussionmentioning

confidence: 72%

“…When left unrepaired, Tg severely blocks replicative polymerases in continued DNA synthesis and elicits cytotoxic lethal consequences (29). Interestingly, Tg can be differentially processed by two naturally existing NEIL1 forms: one with a Lys at position 242, which is encoded in the genome, and the other with an Arg242 residue, due to RNA editing of NEIL1 pre-mRNA; the former removes Tg from duplex DNA ∼30 times faster than the latter (30). Subsequent binding analysis using synthetic Tg analogs shows that binding affinities are similar for the two NEIL1 forms, hinting that the editing effect is beyond substrate affinity (31).…”

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confidence: 99%

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

Zhu

Zhang

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

119

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NEIL1 (Nei-like 1) is a DNA repair glycosylase guarding the mammalian genome against oxidized DNA bases. As the first enzymes in the base-excision repair pathway, glycosylases must recognize the cognate substrates and catalyze their excision. Here we present crystal structures of human NEIL1 bound to a range of duplex DNA. Together with computational and biochemical analyses, our results suggest that NEIL1 promotes tautomerization of thymine glycol (Tg)-a preferred substrate-for optimal binding in its active site. Moreover, this tautomerization event also facilitates NEIL1-catalyzed Tg excision. To our knowledge, the present example represents the first documented case of enzymepromoted tautomerization for efficient substrate recognition and catalysis in an enzyme-catalyzed reaction.base-excision repair | substrate recognition | enzyme catalysis | glycosylase | QM/MM D NA oxidation damage can be induced by both endogenous and environmental reactive oxygen species. Such oxidized DNA bases are primarily recognized and removed by the baseexcision repair (BER) pathway, which is initiated by a lesionspecific DNA glycosylase (1-4). 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).NEIL1 (Nei-like 1) is one such Fpg/Nei family glycosylase that guards the mammalian genome against oxidation damage (7-10). NEIL1 is bifunctional in that it catalyzes both the hydrolysis of the N-glycosylic bond linking a base to a deoxyribose (glycosylase activity) and the subsequent cleavage of the DNA 3′ to the newly created apurinic/apyrimidinic site (lyase activity) (7-10). The N terminus contains the glycosylase domain of NEIL1, and the C terminus is intrinsically disordered (8,11). Whereas the C terminus is dispensable for both glycosylase and lyase activities in vitro, it interacts with many proteins in vivo and is required for efficient DNA repair activity inside the cells (12, 13). NEIL1 is also unique among the three human NEIL proteins in that it is increased in an S-phase-specific manner and carries out prereplicative repair of oxidized bases in the human genome (8,12). Moreover, increasing literature has further emphasized the importance of NEIL1's cellular repair activity, as NEIL1 deficiency has led to multiple abnormalities and is associated with severe human diseases, including cancer (14-19). Additionally, emerging evidence has also implicated a role of NEIL1 in active DNA demethylation (20)(21)(22).NEIL1 is capable of removing a wide array of oxidized pyrimidines and purines; representative substrates of extensive investigations include thymine glycol (Tg), 5-hydroxyuracil (5-OHU), 5-hydroxycytosine (5-OHC), dihydrothymine (DHT), and dihydrouracil (DHU), as well as the formamidopyridines (FapyA and FapyG), spiroiminodihydantoin (Sp), and guanidinohydanto...

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Section: Computational Simulations Suggest That Tautomerization Promotessupporting

confidence: 74%

Section: Discussionmentioning

confidence: 72%

mentioning

confidence: 99%

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

Zhu

Zhang

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

119

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“…In addition, mRNAs encoding the DNA repair enzyme NEIL1 can be edited at a lysine codon to produce an arginine (Li et al, 2009). This edit redirects NEIL1 from removing thymine glycol in dsDNA to the repair of guanidinohydantoin lesions (Onizuka et al, 2012;Yeo et al, 2010). It is intriguing to think that editing might influence DNA repair in a manner that is consistent with environmental insults.…”

Section: Editing Precisely Regulates Protein Functionmentioning

confidence: 99%

The emerging role of RNA editing in plasticity

Rosenthal¹

2015

Journal of Experimental Biology

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All true metazoans modify their RNAs by converting specific adenosine residues to inosine. Because inosine binds to cytosine, it is a biological mimic for guanosine. This subtle change, termed RNA editing, can have diverse effects on various RNA-mediated cellular pathways, including RNA interference, innate immunity, retrotransposon defense and messenger RNA recoding. Because RNA editing can be regulated, it is an ideal tool for increasing genetic diversity, adaptation and environmental acclimation. This review will cover the following themes related to RNA editing: (1) how it is used to modify different cellular RNAs, (2) how frequently it is used by different organisms to recode mRNA, (3) how specific recoding events regulate protein function, (4) how it is used in adaptation and (5) emerging evidence that it can be used for acclimation. Organismal biologists with an interest in adaptation and acclimation, but with little knowledge of RNA editing, are the intended audience.

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“…To determine whether our selected ribozyme framework could be applied to any editing site, we performed a cleavage assay against an mRNA fragment of the human DNA repair enzyme Nei endonuclease VIII-like 1 (NEIL1), which contains a K/R site that is an A-to-I editing site in the coding region ( Fig. 5A; Yeo et al 2010). Accordingly, for unedited-specific cleavage, the HHR was designed to hybridize with NEIL1 RNA in the stem I and III region, and the catalytic core and loop II sequences were used in HR-F39 (HRF39-NEIL1) (Fig.…”

Section: Resultsmentioning

confidence: 99%

Improved design of hammerhead ribozyme for selective digestion of target RNA through recognition of site-specific adenosine-to-inosine RNA editing

Fukuda

Kurihara

Yamaguchi

et al. 2014

RNA

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Adenosine-to-inosine (A-to-I) RNA editing is an endogenous regulatory mechanism involved in various biological processes. Site-specific, editing-state-dependent degradation of target RNA may be a powerful tool both for analyzing the mechanism of RNA editing and for regulating biological processes. Previously, we designed an artificial hammerhead ribozyme (HHR) for selective, site-specific RNA cleavage dependent on the A-to-I RNA editing state. In the present work, we developed an improved strategy for constructing a trans-acting HHR that specifically cleaves target editing sites in the adenosine but not the inosine state. Specificity for unedited sites was achieved by utilizing a sequence encoding the intrinsic cleavage specificity of a natural HHR. We used in vitro selection methods in an HHR library to select for an extended HHR containing a tertiary stabilization motif that facilitates HHR folding into an active conformation. By using this method, we successfully constructed highly active HHRs with unedited-specific cleavage. Moreover, using HHR cleavage followed by direct sequencing, we demonstrated that this ribozyme could cleave serotonin 2C receptor (HTR2C) mRNA extracted from mouse brain, depending on the site-specific editing state. This unedited-specific cleavage also enabled us to analyze the effect of editing state at the E and C sites on editing at other sites by using direct sequencing for the simultaneous quantification of the editing ratio at multiple sites. Our approach has the potential to elucidate the mechanism underlying the interdependencies of different editing states in substrate RNA with multiple editing sites.

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RNA editing changes the lesion specificity for the DNA repair enzyme NEIL1

Cited by 146 publications

References 41 publications

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

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

The emerging role of RNA editing in plasticity

Improved design of hammerhead ribozyme for selective digestion of target RNA through recognition of site-specific adenosine-to-inosine RNA editing

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