Functions of disordered regions in mammalian early base excision repair proteins

Abstract

Reactive oxygen species, generated endogenously and induced as a toxic response, produce several dozen oxidized or modified bases and/or single-strand breaks in mammalian and other genomes. These lesions are predominantly repaired via the conserved base excision repair (BER) pathway. BER is initiated with excision of oxidized or modified bases by DNA glycosylases leading to formation of abasic (AP) site or strand break at the lesion site. Structural analysis by experimental and modeling approaches shows the presence of a disordered segment commonly localized at the N- or C-terminus as a characteristic signature of mammalian DNA glycosylases which is absent in their bacterial prototypes. Recent studies on unstructured regions in DNA metabolizing proteins have indicated their essential role in interaction with other proteins and target DNA recognition. In this review, we have discussed the unique presence of disordered segments in human DNA glycosylases, and AP endonuclease involved in the processing of glycosylase products, and their critical role in regulating repair functions. These disordered segments also include sites for posttranslational modifications and nuclear localization signal. The teleological basis for their structural flexibility is discussed.

Fig. 1

Schematic representation of base excision (a) and single-strand break (b) repair steps in mammalian cells. Monofunctional DNA glycosylases (UDG, MPG) excise alkylated and modified bases from DNA to generate AP sites that are then cleaved by APE1. The 5′ blocking group at the break site is removed by Polβ to generate a single-nucleotide gap that is filled in by Polβ (and sealed by DNA ligase IIIα). Oxidized bases are excised by OGG1/NTH1 and NEILs which also cleave the DNA strand to generate 3′ blocking groups. DNA is directly cleaved by ROS/radiation and topoisomerases to generate 3′ or 5′ blocking groups (3′D* and 5′D*) which are removed by several end cleaning enzymes. Other details are described in the text

Fig. 2

Secondary structure prediction of hNEIL1 and its E. coli prototype endonuclease VIII (Nei) by PrDOS (a,c) and PONDR (b,d) softwares. The protein sequences were obtained from NCBI database. Sequences in red in PrDOS and a score of 0.5 and above in the PONDR plot indicate disordered structures. The disordered C-terminal segment (wiggled line) of hNEIL1 is absent in Nei

Fig. 3

PONDR plot of predicted secondary structures of hNTH1, hMYH, hAPE1 and their E. coli prototypes endonuclease III (Nth), MutY, Xth, respectively. Wiggled lines at the N-termini of human enzymes represent disordered segments

Fig. 4

PONDR plot of disordered conformation at the N-terminus of hTDG and UNG2. HNEIL2 has an internal disordered region

Fig. 5

PrDOS secondary structure prediction of hOGG1 and Polβ indicate short disordered segments (sequence in red) at both termini

Fig. 6

Schematic of multiple regulatory functions of disordered regions in early BER enzymes