Functional importance and divergence of plant apurinic/apyrimidinic endonucleases in somatic and meiotic DNA repair

Abstract

Apurinic/apyrimidinic (AP) sites are one of the most abundant DNA lesions and are mainly repaired by AP endonucleases (APEs). While most eukaryotic genomes encode two APEs, plants usually possess three APEs, namely APE1L, APE2, and ARP. To date, the biological relevance and functional divergence of plant APEs are unclear. Here, we show that the three plant APEs have ancient origins, with the APE1L clade being plant-specific. In Arabidopsis thaliana, simultaneously mutating APE1L and APE2, but not ARP alone or in combination with either APE1L or APE2, results in clear developmental defects linked to genotoxic stress. Genetic analyses indicated that the three plant APEs have different substrate preferences in vivo. ARP is mainly responsible for AP site repair, while APE1L and APE2 prefer to repair 3’ blocked single-stranded DNA breaks. We further determined that APEs play an important role in DNA repair and the maintenance of genomic integrity in meiotic cells. The ape1l ape2 double mutant exhibited a greatly enhanced frequency of SPO11-1-dependent and -independent double-strand DNA breaks. The DNA damage response was activated in ape1l ape2 to trigger pollen abortion. Our findings suggest functional divergence of plant APEs and reveal important roles of plant APEs during vegetative and reproductive development.

The Arabidopsis DNA glycosylase MBD4L repairs the nuclear genome in vivo

“…In addition to hypersensitivity to 5‐FU, mbd4l and arp mutants share other phenotypes. Under control conditions, both mutants grow normally and lack dead cells at root tips (Figures 2 and 3; Figures S2 and S4; Li et al., 2023). However, mbd4l (Figure 5), but not arp , has increased expression of DDR genes whereas, interestingly, these genes are also induced in the ape1 / ape2 double mutant (Li et al., 2023).…”

“…Under control conditions, both mutants grow normally and lack dead cells at root tips (Figures 2 and 3; Figures S2 and S4; Li et al, 2023). However, mbd4l (Figure 5), but not arp, has increased expression of DDR genes whereas, interestingly, these genes are also induced in the ape1/ape2 double mutant (Li et al, 2023). Partial but not complete overlap of the mbd4l and arp phenotypes is consistent with the different subcellular localization of these enzymes, as MBD4L is exclusively nuclear, and ARP acts in both the nucleus (C ordoba-Cañero et al, 2011) and the chloroplast (Gutman & Niyogi, 2009).…”

Transcriptome analysis provides insight into the regulatory mechanisms underlying pollen germination recovery at normal high ambient temperature in wild banana (Musa itinerans)

“…For flowering plants, the DNA base excision repair process can facilitate DNA demethylation ( Gehring et al., 2009 ). APEs are involved in DNA damage repair during pollen meiosis, and double mutations in APE1L and APE2 can lead to increased chromosome fragmentation during pollen meiosis and ultimately pollen abortion, suggesting that DNA repair is important for pollen fertility ( Li et al., 2023 ). These results suggest that DNA methylation and repair support the maintenance of fertility.…”

The chromatin remodeler ERCC6 and the histone chaperone NAP1 are involved in apurinic/apyrimidinic endonuclease-mediated DNA repair

“…In Arabidopsis ( Arabidopsis thaliana ), Uracil N-glycosylase (UNG) encodes the primary UDG activity, and ung null mutant exhibits remarkable tolerance to 5-FU treatment along with increased uracil accumulation in DNA ( Cordoba-Canero et al 2010 ). Meanwhile, APE-redox protein (ARP) serves as the predominant enzyme responsible for cleaving AP sites in plants, despite the existence of its two sequence-related homologues known as AP endonuclease 1-like (APE1L) and APE2 ( Cordoba-Canero et al 2009 , 2011 ; Li et al 2023 ). Although displaying no phenotypic defects under normal growth conditions, the ARP-depleting mutant shows hypersensitivity to 5-FU, indicative of the critical role of ARP in resolving AP lesions, the intermediates generated by the monofunctional UNG ( Cordoba-Canero et al 2011 ).…”