Nonenzymatic release of N7-methylguanine channels repair of abasic sites into an AP endonuclease-independent pathway in Arabidopsis

Abstract

SignificanceAbasic (apurinic/apyrimidinic, AP) sites in DNA result from spontaneous and repair-mediated base release. They may be processed by AP endonucleases or AP lyases, but the relative roles of both types of enzymes are poorly understood. Our study reveals that the model plant Arabidopsis uses an AP lyase-dependent pathway to repair AP sites generated by spontaneous loss of N7-methylguanine (N7-meG), a major lesion arising from DNA methylation damage. We further show that the main Arabidopsis AP endonuclease is active on AP sites generated by enzymatic excision of N7-meG, but not on those arising from N7-meG loss. Our findings identify an important role for AP lyase activity in plants and challenge the assumption that spontaneous and repair-generated AP sites have identical biochemical properties.

Nucleotide Metabolism in Plants

“…Also the degradation of cytokinins produces small amounts of adenine (Schmülling et al, 2003). Purine bases are released from nucleic acids by spontaneous depurination (Barbado et al, 2018), resulting in low amounts of adenine and guanine. The metabolic source of hypoxanthine is likely the spontaneous deamination of adenine in DNA, resulting in a hypoxanthine base, which is removed from the DNA by base excision repair (Karran and Lindahl, 1980).…”

DNA Base Excision Repair in Plants: An Unfolding Story With Familiar and Novel Characters

“…Unlike human APE1, ARP discriminates between AP sites generated by spontaneous base loss or by enzymatic excision. Thus, ARP cleaves AP sites generated by N7-meG excision but is unable to process AP sites originated due to spontaneous depurination of N7-meG, suggesting that these two types of AP sites possess different chemical or structural properties not yet identified (Barbado et al, 2018). In addition to AP endonuclease activity, AP endonucleases are endowed with phosphodiesterase and/or phosphatase activities involved in cleaning blocked DNA ends (see the section Cleaning of DNA Termini ).…”

“…Evidence of an important role of AP lyases in the processing of abasic sites has also been reported recently in plants. In Arabidopsis , spontaneous depurination of MMS-induced N7-meG generates AP sites that are not recognized by ARP (see above) and are exclusively repaired through an AP endonuclease-independent route initiated by the AP lyase activity of AtFPG (Barbado et al, 2018). AtFPG is the major, possibly the only, AP lyase activity detectable in Arabidopsis cell extracts (Barbado et al, 2018).…”

“…In Arabidopsis , spontaneous depurination of MMS-induced N7-meG generates AP sites that are not recognized by ARP (see above) and are exclusively repaired through an AP endonuclease-independent route initiated by the AP lyase activity of AtFPG (Barbado et al, 2018). AtFPG is the major, possibly the only, AP lyase activity detectable in Arabidopsis cell extracts (Barbado et al, 2018). AP site incision catalyzed by AtFPG generates a 3′-P end that is converted to 3′-OH by the DNA 3′-phosphatase ZDP (see the section Blocked 3′-Termini ) before repair is completed (Barbado et al, 2018).…”

Dowsing for salinity tolerance related genes in chickpea through genome wide association and in silico PCR analysis

“…The over-expression of AP has been thought to be responsible for enhancing osmotic stress tolerance in Medicago truncatula 148 . The AP lyase-dependent pathway to repair sites could generate new phenotypes and mutations 149 . Additionally, it was reported that in Arabidopsis, the DNA glycosylase/lyase has an active role in DNA demethylation of ROS1, which possesses several enzymatic activities 150 and some AP genes function downstream of ROS1 in a ZDP-independent branch of the active DNA demethylation pathway in Arabidopsis 151 .…”