The role of the N-terminal domain of human apurinic/apyrimidinic endonuclease 1, APE1, in DNA glycosylase stimulation

• Published in: DNA repair 2018-04, Vol.64, p.10-25
• Main Authors: Kladova, Olga A., Bazlekowa-Karaban, Milena, Baconnais, Sonia, Piétrement, Olivier, Ishchenko, Alexander A., Matkarimov, Bakhyt T., Iakovlev, Danila A., Vasenko, Andrey, Fedorova, Olga S., Le Cam, Eric, Tudek, Barbara, Kuznetsov, Nikita A., Saparbaev, Murat
• Format: Article
• Language: English
• Subjects: AP endonuclease; AP lyase; Apurinic/apyrimidinic site; Base excision repair; Biochemistry, Molecular Biology; DNA glycosylase; Life Sciences; Molecular biology; Oxidative DNA damage; Redox function
• ISSN: 1568-7864; 1568-7856
• DOI: 10.1016/j.dnarep.2018.02.001

[Display omitted] •The redox domain of APE1 is required for DNA glycosylase activity stimulation.•APE1 stabilizes enzyme–substrate and stimulates disruption of enzyme–product complexes.•APE1 forms multiprotein oligomers along an undamaged DNA duplex.•APE1 shows DNA length dependence with preferential cleavage of short DNA duplexes.•APE1 stimulates DNA glycosylases via a conformational selection mechanism. The base excision repair (BER) pathway consists of sequential action of DNA glycosylase and apurinic/apyrimidinic (AP) endonuclease necessary to remove a damaged base and generate a single-strand break in duplex DNA. Human multifunctional AP endonuclease 1 (APE1, a.k.a. APEX1, HAP-1, or Ref-1) plays essential roles in BER by acting downstream of DNA glycosylases to incise a DNA duplex at AP sites and remove 3′-blocking sugar moieties at DNA strand breaks. Human 8-oxoguanine-DNA glycosylase (OGG1), methyl-CpG-binding domain 4 (MBD4, a.k.a. MED1), and alkyl-N-purine-DNA glycosylase (ANPG, a.k.a. Aag or MPG) excise a variety of damaged bases from DNA. Here we demonstrated that the redox-deficient truncated APE1 protein lacking the first N-terminal 61 amino acid residues (APE1-NΔ61) cannot stimulate DNA glycosylase activities of OGG1, MBD4, and ANPG on duplex DNA substrates. Electron microscopy imaging of APE1–DNA complexes revealed oligomerization of APE1 along the DNA duplex and APE1-mediated DNA bridging followed by DNA aggregation. APE1 polymerizes on both undamaged and damaged DNA in cooperative mode. Association of APE1 with undamaged DNA may enable scanning for damage; however, this event reduces effective concentration of the enzyme and subsequently decreases APE1-catalyzed cleavage rates on long DNA substrates. We propose that APE1 oligomers on DNA induce helix distortions thereby enhancing molecular recognition of DNA lesions by DNA glycosylases via a conformational proofreading/selection mechanism. Thus, APE1-mediated structural deformations of the DNA helix stabilize the enzyme–substrate complex and promote dissociation of human DNA glycosylases from the AP site with a subsequent increase in their turnover rate. The major human apurinic/apyrimidinic (AP) endonuclease, APE1, stimulates DNA glycosylases by increasing their turnover rate on duplex DNA substrates. At present, the mechanism of the stimulation remains unclear. We report that the redox domain of APE1 is necessary for the active mode of stimulation of DNA glycosylases. Electron microscopy