Mechanism of stimulation of DNA binding of the transcription factors by human apurinic/apyrimidinic endonuclease 1, APE1

Milena Bazlekowa-Karaban, Paulina Prorok, Sonia Baconnais, Sabira Taipakova, Zhiger Akishev, Dominika Zembrzuska, Alexander V. Popov, Anton V. Endutkin, Regina Groisman, Alexander A. Ishchenko, Bakhyt Matkarimov, Amangeldy Bissenbaev, Eric Le Cam, Dmitry O. Zharkov, Barbara Tudek, Murat Saparbaev

Research output: Contribution to journalArticle

Abstract

Aerobic respiration generates reactive oxygen species (ROS), which can damage nucleic acids, proteins and lipids. A number of transcription factors (TFs) contain redox-sensitive cysteine residues at their DNA-binding sites, hence ROS-induced thiol oxidation strongly inhibits their recognition of the cognate DNA sequences. Major human apurinic/apyrimidinic (AP) endonuclease 1 (APE1/APEX1/HAP-1), referred also as a redox factor 1 (Ref-1), stimulates the DNA binding activities of the oxidized TFs such as AP-1 and NF-κB. Also, APE1 participates in the base excision repair (BER) and nucleotide incision repair (NIR) pathways to remove oxidative DNA base damage. At present, the molecular mechanism underlying the TF-stimulating/redox function of APE1 and its biological role remains disputed. Here, we provide evidence that, instead of direct cysteine reduction in TFs by APE1, APE1-catalyzed NIR and TF-stimulating activities may be based on transient cooperative binding of APE1 to DNA and induction of conformational changes in the helix. The structure of DNA duplex strongly influences NIR and TF-stimulating activities. Homologous plant AP endonucleases lacking conserved cysteine residues stimulate DNA binding of the p50 subunit of NF-κB. APE1 acts synergistically with low-molecular-weight reducing agents on TFs. Finally, APE1 stimulates DNA binding of the redox-insensitive p50-C62S mutant protein. Electron microscopy imaging of APE1 complexes with DNA revealed preferential polymerization of APE1 on the gapped and intrinsically curved DNA duplexes. Molecular modeling offers a structural explanation how full-length APE1 can oligomerize on DNA. In conclusion, we propose that DNA-directed APE1 oligomerization can be regarded as a substitute for diffusion of APE1 along the DNA contour to probe for anisotropic flexibility. APE1 oligomers exacerbate pre-existing distortions in DNA and enable both NIR activity and DNA binding by TFs regardless of their oxidation state.

Original languageEnglish
Article number102698
JournalDNA Repair
Volume82
DOIs
Publication statusPublished - Oct 1 2019

Fingerprint

DNA-(Apurinic or Apyrimidinic Site) Lyase
Endonucleases
Transcription Factors
DNA
Oxidation-Reduction
Repair
Nucleotides
Cysteine
DNA Repair
Reactive Oxygen Species
Reducing Agents
Oxidation
Oligomerization
Mutant Proteins
Molecular modeling
Sulfhydryl Compounds
DNA sequences
Polymerization
Nucleic Acids
DNA Damage

Keywords

  • AP endonuclease
  • Base excision repair
  • Nucleotide incision repair
  • Oxidative damage
  • Redox regulation
  • Transcription factors

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Cell Biology

Cite this

Bazlekowa-Karaban, M., Prorok, P., Baconnais, S., Taipakova, S., Akishev, Z., Zembrzuska, D., ... Saparbaev, M. (2019). Mechanism of stimulation of DNA binding of the transcription factors by human apurinic/apyrimidinic endonuclease 1, APE1. DNA Repair, 82, [102698]. https://doi.org/10.1016/j.dnarep.2019.102698

Mechanism of stimulation of DNA binding of the transcription factors by human apurinic/apyrimidinic endonuclease 1, APE1. / Bazlekowa-Karaban, Milena; Prorok, Paulina; Baconnais, Sonia; Taipakova, Sabira; Akishev, Zhiger; Zembrzuska, Dominika; Popov, Alexander V.; Endutkin, Anton V.; Groisman, Regina; Ishchenko, Alexander A.; Matkarimov, Bakhyt; Bissenbaev, Amangeldy; Le Cam, Eric; Zharkov, Dmitry O.; Tudek, Barbara; Saparbaev, Murat.

In: DNA Repair, Vol. 82, 102698, 01.10.2019.

Research output: Contribution to journalArticle

Bazlekowa-Karaban, M, Prorok, P, Baconnais, S, Taipakova, S, Akishev, Z, Zembrzuska, D, Popov, AV, Endutkin, AV, Groisman, R, Ishchenko, AA, Matkarimov, B, Bissenbaev, A, Le Cam, E, Zharkov, DO, Tudek, B & Saparbaev, M 2019, 'Mechanism of stimulation of DNA binding of the transcription factors by human apurinic/apyrimidinic endonuclease 1, APE1', DNA Repair, vol. 82, 102698. https://doi.org/10.1016/j.dnarep.2019.102698
Bazlekowa-Karaban, Milena ; Prorok, Paulina ; Baconnais, Sonia ; Taipakova, Sabira ; Akishev, Zhiger ; Zembrzuska, Dominika ; Popov, Alexander V. ; Endutkin, Anton V. ; Groisman, Regina ; Ishchenko, Alexander A. ; Matkarimov, Bakhyt ; Bissenbaev, Amangeldy ; Le Cam, Eric ; Zharkov, Dmitry O. ; Tudek, Barbara ; Saparbaev, Murat. / Mechanism of stimulation of DNA binding of the transcription factors by human apurinic/apyrimidinic endonuclease 1, APE1. In: DNA Repair. 2019 ; Vol. 82.
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AU - Baconnais, Sonia

AU - Taipakova, Sabira

AU - Akishev, Zhiger

AU - Zembrzuska, Dominika

AU - Popov, Alexander V.

AU - Endutkin, Anton V.

AU - Groisman, Regina

AU - Ishchenko, Alexander A.

AU - Matkarimov, Bakhyt

AU - Bissenbaev, Amangeldy

AU - Le Cam, Eric

AU - Zharkov, Dmitry O.

AU - Tudek, Barbara

AU - Saparbaev, Murat

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N2 - Aerobic respiration generates reactive oxygen species (ROS), which can damage nucleic acids, proteins and lipids. A number of transcription factors (TFs) contain redox-sensitive cysteine residues at their DNA-binding sites, hence ROS-induced thiol oxidation strongly inhibits their recognition of the cognate DNA sequences. Major human apurinic/apyrimidinic (AP) endonuclease 1 (APE1/APEX1/HAP-1), referred also as a redox factor 1 (Ref-1), stimulates the DNA binding activities of the oxidized TFs such as AP-1 and NF-κB. Also, APE1 participates in the base excision repair (BER) and nucleotide incision repair (NIR) pathways to remove oxidative DNA base damage. At present, the molecular mechanism underlying the TF-stimulating/redox function of APE1 and its biological role remains disputed. Here, we provide evidence that, instead of direct cysteine reduction in TFs by APE1, APE1-catalyzed NIR and TF-stimulating activities may be based on transient cooperative binding of APE1 to DNA and induction of conformational changes in the helix. The structure of DNA duplex strongly influences NIR and TF-stimulating activities. Homologous plant AP endonucleases lacking conserved cysteine residues stimulate DNA binding of the p50 subunit of NF-κB. APE1 acts synergistically with low-molecular-weight reducing agents on TFs. Finally, APE1 stimulates DNA binding of the redox-insensitive p50-C62S mutant protein. Electron microscopy imaging of APE1 complexes with DNA revealed preferential polymerization of APE1 on the gapped and intrinsically curved DNA duplexes. Molecular modeling offers a structural explanation how full-length APE1 can oligomerize on DNA. In conclusion, we propose that DNA-directed APE1 oligomerization can be regarded as a substitute for diffusion of APE1 along the DNA contour to probe for anisotropic flexibility. APE1 oligomers exacerbate pre-existing distortions in DNA and enable both NIR activity and DNA binding by TFs regardless of their oxidation state.

AB - Aerobic respiration generates reactive oxygen species (ROS), which can damage nucleic acids, proteins and lipids. A number of transcription factors (TFs) contain redox-sensitive cysteine residues at their DNA-binding sites, hence ROS-induced thiol oxidation strongly inhibits their recognition of the cognate DNA sequences. Major human apurinic/apyrimidinic (AP) endonuclease 1 (APE1/APEX1/HAP-1), referred also as a redox factor 1 (Ref-1), stimulates the DNA binding activities of the oxidized TFs such as AP-1 and NF-κB. Also, APE1 participates in the base excision repair (BER) and nucleotide incision repair (NIR) pathways to remove oxidative DNA base damage. At present, the molecular mechanism underlying the TF-stimulating/redox function of APE1 and its biological role remains disputed. Here, we provide evidence that, instead of direct cysteine reduction in TFs by APE1, APE1-catalyzed NIR and TF-stimulating activities may be based on transient cooperative binding of APE1 to DNA and induction of conformational changes in the helix. The structure of DNA duplex strongly influences NIR and TF-stimulating activities. Homologous plant AP endonucleases lacking conserved cysteine residues stimulate DNA binding of the p50 subunit of NF-κB. APE1 acts synergistically with low-molecular-weight reducing agents on TFs. Finally, APE1 stimulates DNA binding of the redox-insensitive p50-C62S mutant protein. Electron microscopy imaging of APE1 complexes with DNA revealed preferential polymerization of APE1 on the gapped and intrinsically curved DNA duplexes. Molecular modeling offers a structural explanation how full-length APE1 can oligomerize on DNA. In conclusion, we propose that DNA-directed APE1 oligomerization can be regarded as a substitute for diffusion of APE1 along the DNA contour to probe for anisotropic flexibility. APE1 oligomers exacerbate pre-existing distortions in DNA and enable both NIR activity and DNA binding by TFs regardless of their oxidation state.

KW - AP endonuclease

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KW - Nucleotide incision repair

KW - Oxidative damage

KW - Redox regulation

KW - Transcription factors

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