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

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

  • DNA Repair (Amst). 2018 Apr;64:10-25. doi: 10.1016/j.dnarep.2018.02.001.
Olga A Kladova 1,  Milena Bazlekowa-Karaban 2,  Sonia Baconnais 3,  Olivier Piétrement 3,  Alexander A Ishchenko 4,  Bakhyt T Matkarimov 5,  Danila A Iakovlev 1,  Andrey Vasenko 6,  Olga S Fedorova 1,  Eric Le Cam 3,  Barbara Tudek 7,  Nikita A Kuznetsov 8,  Murat Saparbaev 9
Affiliations

Affiliations

  • 1 SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia.
  • 2 Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland; Groupe «Réparation de l'ADN», Equipe Labellisée par la Ligue Nationale contre le Cancer, CNRS UMR8200, Université Paris-Sud, Gustave Roussy Cancer Campus, F-94805 Villejuif Cedex, France; Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland.
  • 3 CNRS UMR8126, Université Paris-Sud, Université Paris-Saclay, Gustave Roussy, F-94805 Villejuif Cedex, France.
  • 4 Groupe «Réparation de l'ADN», Equipe Labellisée par la Ligue Nationale contre le Cancer, CNRS UMR8200, Université Paris-Sud, Gustave Roussy Cancer Campus, F-94805 Villejuif Cedex, France.
  • 5 National laboratory Astana, Nazarbayev University, Astana 010000, Kazakhstan.
  • 6 National Research University Higher School of Economics, 101000 Moscow, Russia.
  • 7 Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland; Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland.
  • 8 SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia. Electronic address: [email protected].
  • 9 Groupe «Réparation de l'ADN», Equipe Labellisée par la Ligue Nationale contre le Cancer, CNRS UMR8200, Université Paris-Sud, Gustave Roussy Cancer Campus, F-94805 Villejuif Cedex, France. Electronic address: [email protected].
PMID: 29475157 DOI: 10.1016/j.dnarep.2018.02.001
Abstract

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.

Significance statement: 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 revealed that full-length APE1 oligomerizes on DNA possibly via cooperative binding to DNA. Consequently, APE1 shows DNA length dependence with preferential repair of short DNA duplexes. We propose that APE1-catalyzed oligomerization along DNA induces helix distortions, which in turn enable conformational selection and stimulation of DNA glycosylases. This new biochemical property of APE1 sheds LIGHT on the mechanism of redox function and its role in DNA repair.

Keywords

AP endonuclease; AP lyase; Apurinic/apyrimidinic site; Base excision repair; DNA glycosylase; Oxidative DNA damage; Redox function.

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