Function and molecular mechanisms of APE2 in genome and epigenome integrity

Abstract

APE2 is a rising vital player in the maintenance of genome and epigenome integrity. In the past several years, a series of studies have shown the critical roles and functions of APE2. We seek to provide the first comprehensive review on several aspects of APE2 in genome and epigenome integrity. We first summarize the distinct functional domains or motifs within APE2 including EEP (endonuclease/exonuclease/phosphatase) domain, PIP box and Zf-GRF motifs from eight species (i.e., Homo sapiens, Mus musculus, Xenopus laevis, Ciona intestinalis, Arabidopsis thaliana, Schizosaccharomyces pombe, Saccharomyces cerevisiae, and Trypanosoma cruzi). Then we analyze various APE2 nuclease activities and associated DNA substrates, including AP endonuclease, 3'-phosphodiesterase, 3'-phosphatase, and 3'-5' exonuclease activities. We also examine several APE2 interaction proteins, including PCNA, Chk1, APE1, Myh1, and homologous recombination (HR) factors such as Rad51, Rad52, BRCA1, BRCA2, and BARD1. Furthermore, we provide insights into the roles of APE2 in various DNA repair pathways (base excision repair, single-strand break repair, and double-strand break repair), DNA damage response (DDR) pathways (ATR-Chk1 and p53-dependent), immunoglobulin class switch recombination and somatic hypermutation, as well as active DNA demethylation. Lastly, we summarize critical functions of APE2 in growth, development, and diseases. In this review, we provide the first comprehensive perspective which dissects all aspects of the multiple-function protein APE2 in genome and epigenome integrity.

Keywords: APE2; ATR-Chk1 pathway; DNA demethylation; DNA repair; Genome and epigenome integrity; Immune response.

Fig. 1.. Comparison of APE2 and its functional domains in eight different species.

(A) Schematic diagram shows structures of APE2/APN2 family proteins (Homo sapiens (HsAPE2, NP_055296.2), Mus musculus (MmAPEX2, Q68G58.1), Xenopus laevis (XlAPE2, AAH77433.1), Ciona intestinalis (CiAPEX2, ENSCINP00000010808.2), Arabidopsis thaliana (AtAPN2, NP_001328802), Schizosaccharomyces pombe (SpAPN2, AAR83752.1), Saccharomyces cerevisiae (ScAPN2, NP_009534.1), and Trypanosoma cruzi (TcAPE2, AGT41677.1). The functional domains (MLS, mitochondria localization sequence; EEP exonuclease/endonuclease/phosphatase; PIP, PCNA-interacting protein box; Zf-GRF, zinc finger motif containing conserved GRxF) and their associated amino acid locations are indicated by numbers below each protein map. (B) Phylogenetic analysis of the APE2 superfamily from Clustal Omega. The numbers after each of the eight species represents branch length of different APE2. Branch lengths are calculated from the multiple sequence alignment using Clustal Omega software and are proportional to the number of mutations from each of the sequences examined. (C-D) Alignment of amino acid sequences of PIP box or Zf-GRF motifs of APE2 in different species using Clustal Omega. *, identical residues; :, highly conserved residues; ., moderately conserved residues.

Fig. 2.. APE2 enzymatic activities and associated DNA substrates.

(A) A summary of APE2’s AP endonuclease, 3'-phosphodiesterase, 3'-phosphatase, and 3'-5' exonuclease activities from different species. “ND” indicates not determined. (B-H) Various different substrates of APE2 enzymatic activities. (B) AP endonuclease substrates; (C) 3'-phosphodiesterase and phosphatase substrates; (D) Exonuclease substrates; (E) dsDNA with different length of 5' overhang; (F) Nick or gap structure; (G) 2,3-cyclic phosphate and monophosphate; (H) 3'-recessed junction with mismatch pairs or opposite to 8-oxoG.

Fig. 3.. Current knowledge of the known APE2 interaction proteins and phenotypes of its various mutants.

(A) APE2 interaction proteins and their binding domains or sites within APE2. The residues of human APE2 that have been mutated and characterized in panel (B) are also labeled. (B) Summary of phenotypes from various APE2 mutants from different species and the homologous residues to HsAPE2 in these mutants.

Fig. 4.. A diagram of the known and predicted APE2 functions and our understanding of its biological significance.

(top) APE2 functions in DNA repair, DNA damage response, immune response, and epigenetic regulation in nucleus and possible DNA repair in mitochondrion. It is not clear whether APE2 communicates with each other between nucleus and mitochondrion. “?” indicates the undefined or controversial role of APE2. (bottom) An overview of the current significance that APE2 has concerning health and diseases.

Fig. 5.. Molecular mechanisms of APE2 in DNA repair and DDR pathways.

(A) Base excision repair (BER) pathway. APE2 may contribute to the generation of SSB from AP site via its endonuclease activity or the end processing of SSB with heterogenous termini after bifunctional DNA glycosylases via its 3'-phosphodiesterase or 3'-phosphatase activities. (B) SSB repair and ATR-Chk1 DDR pathways. APE2 promotes the continuation of 3'-5' SSB end resection via its exonuclease activity to generate longer ssDNA for ATR-Chk1 DDR pathway activation and subsequent SSB repair. (C) DSB generation and DSB repair including HR and NHEJ sub-pathways. APE2 may promotes DSB generation when the two AP sites are close to each other. APE2 may also promote Rad51 recruitment to ssDNA for strand invasion for HR.