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

Abstract

Base excision repair (BER) is a critical genome defense pathway that deals with a broad range of non-voluminous DNA lesions induced by endogenous or exogenous genotoxic agents. BER is a complex process initiated by the excision of the damaged base, proceeds through a sequence of reactions that generate various DNA intermediates, and culminates with restoration of the original DNA structure. BER has been extensively studied in microbial and animal systems, but knowledge in plants has lagged behind until recently. Results obtained so far indicate that plants share many BER factors with other organisms, but also possess some unique features and combinations. Plant BER plays an important role in preserving genome integrity through removal of damaged bases. However, it performs additional important functions, such as the replacement of the naturally modified base 5-methylcytosine with cytosine in a plant-specific pathway for active DNA demethylation.

Structural Aspects of DNA Repair and Recombination in Crop Improvement

“…Base Excision Repair repairs DNA lesions resulting from oxidation, alkylation, or deamination of the nitrogenous base of DNA (Roldan-Arjona et al, 2019). The first step involves damage recognition and cleavage of N-glycosidic bond resulting in the generation of an abasic site (AP site) by DNA glycosylases.…”

“…Short patch BER inserts only one nucleotide, whereas long patch BER inserts multiple nucleotides resulting in a 5 flap structure, requiring further processing by flap endonuclease (FEN1) before ligation. The mechanism of BER in plants is almost identical to other organisms with specific differences (Manova and Gruszka, 2015;Roldan-Arjona et al, 2019). Among mammals, DNA polymerase β and DNA ligase III play a significant role in short patch BER (Kubota et al, 1996).…”

“…Monofunctional glycosylases cleave only N-glycosidic bonds resulting in an AP site. In contrast, bifunctional glycosylases cleave the N-glycosidic bond and phosphodiester bond (Roldan-Arjona et al, 2019). Bifunctional DNA glycosylases possess an AP lyase activity in addition to the DNA glycosylase activity.…”

“…The structure consists of N-terminal and C-terminal α-helical domains, connected by a type II β-hairpin ( Figure 3C). Various homologs of E. coli DNA glycosylases acting upon alkylated purines and oxidized bases are present in Arabidopsis (Bjelland et al, 1993;Labahn et al, 1996;Britt, 2002;Roldan-Arjona et al, 2019). Members of this family involved in excising oxidized bases have also been identified and characterized from Arabidopsis.…”

“…Plants exclusively contain 5-meC DNA glycosylases. They form a separate family of glycosylases (DEMETER-LIKE (DML) family) of HhH superfamily (Zhu, 2009;Brooks et al, 2013;Roldan-Arjona et al, 2019). DML family comprises of proteins like DME (DEMETER) (Choi et al, 2002), Ros1 (Repressor of silencing 1) (Gong et al, 2002), DML2 (DME-like 2), and DML3 (DME-like 3) (Ortega-Galisteo et al, 2008) from Arabidopsis.…”