Structural and functional determinants of the archaeal 8-oxoguanine-DNA glycosylase AGOG for DNA damage recognition and processing

Abstract

8-Oxoguanine (GO) is a major purine oxidation product in DNA. Because of its highly mutagenic properties, GO absolutely must be eliminated from DNA. To do this, aerobic and anaerobic organisms from the three kingdoms of life have evolved repair mechanisms to prevent its deleterious effect on genetic integrity. The major way to remove GO is the base excision repair pathway, usually initiated by a GO-DNA glycosylase. First identified in bacteria (Fpg) and eukaryotes (OGG1), GO-DNA glycosylases were more recently identified in archaea (OGG2 and AGOG). AGOG is the less documented enzyme and its mode of damage recognition and removing remains to be clarified at the molecular and atomic levels. This study presents a complete structural characterisation of apo AGOGs from Pyrococcus abyssi (Pab) and Thermococcus gammatolerans (Tga) and the first structure of Pab-AGOG bound to lesion-containing single- or double-stranded DNA. By combining X-ray structure analysis, site directed mutagenesis and biochemistry experiments, we identified key amino acid residues of AGOGs responsible for the specific recognition of the lesion and the base opposite the lesion and for catalysis. Moreover, a unique binding mode of GO, involving double base flipping, never observed for any other DNA glycosylases, is revealed. In addition to unravelling the properties of AGOGs, our study, through comparative biochemical and structural analysis, offers new insights into the evolutionary plasticity of DNA glycosylases across all three kingdoms of life.

Oxidative DNA damage on the VEGF G‐quadruplex forming promoter is repaired via long‐patch BER

“…As a bifunctional DNA glycosylase, OGG1 also has AP lyase activity, which creates a nick in the DNA by cleaving the phosphodiester bond 3′ of the AP site. Of note, OGG1 is thought to function primarily in a monofunctional mode in cellulo leaving strand cleavage to APE1 (Allgayer et al, 2016; Dalhus et al, 2011; Franck et al, 2022; Hill et al, 2001). OGG1 has demonstrated strong substrate specificity, with preference for 8oxoG:C base pairs in double‐stranded DNA as opposed to 8oxoG in single‐stranded DNA (Franck et al, 2022).…”

“…Of note, OGG1 is thought to function primarily in a monofunctional mode in cellulo leaving strand cleavage to APE1 (Allgayer et al, 2016; Dalhus et al, 2011; Franck et al, 2022; Hill et al, 2001). OGG1 has demonstrated strong substrate specificity, with preference for 8oxoG:C base pairs in double‐stranded DNA as opposed to 8oxoG in single‐stranded DNA (Franck et al, 2022). In the context of the VEGF G4 DNA sequence, weak OGG1 activity has been demonstrated on a single‐stranded G4 oligonucleotide containing five G‐runs but not on a VEGF G4 DNA sequence with only four runs (Fleming et al, 2015).…”

“…Prior studies utilizing single‐stranded DNA G4 substrates have consistently revealed a lack of and/or very weak OGG1 glycosylase activity toward G4 DNA containing 8oxoG (Ferino and Xodo, 2021; Zhou et al, 2015). Moreover, OGG1 has been shown not to have activity on non‐G4 single‐stranded DNA substrates as well (Franck et al, 2022). In addition, based on changes in FRET signals during stopped flow kinetic analysis it has been asserted that while OGG1 can bind single‐stranded G4 DNA, that it cannot form the appropriate contacts to induce 8oxoG eversion (Kuznetsova et al, 2020).…”

“…C base pairs in double-stranded DNA as opposed to 8oxoG in singlestranded DNA (Franck et al, 2022). In the context of the VEGF G4…”

“…Prior studies utilizing single-stranded DNA G4 substrates have consistently revealed a lack of and/or very weak OGG1 glycosylase activity toward G4 DNA containing 8oxoG (Ferino and Xodo, 2021;Zhou et al, 2015). Moreover, OGG1 has been shown not to have activity on non-G4 single-stranded DNA substrates as well (Franck et al, 2022). In addition, based on changes in FRET signals during…”