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

Abstract

HIGHLIGHTS-APE1 forms a stable complex with ssDNA longer than 15 mer; -APE1-catalyzed repair and TF-stimulating activities depend on the structure of DNA duplex; -APE1 acts synergistically with reducing agents to stimulate DNA binding of AP-1 and p50; -APE1 stimulates DNA binding of p50-C62S redox-insensitive mutant; -APE1 forms stable multiprotein oligomers on intrinsically curved DNA regions. ABBREVIATIONSROS, reactive oxygen species; AP, apurinic/apyrimidinic site; THF, 3-hydroxy-2hydroxymethyltetrahydrofuran or tetrahydrofuran; αdA, α-anomeric 2′-deoxyadenosine; Z, 3nitropyrrole; BER, base excision repair; NIR, nucleotide incision repair; APE1 (a.k.a. APEX1, HAP-1, or Ref-1), human major AP endonuclease 1; Nfo, Escherichia coli endonuclease IV; ARP, Arabidopsis thaliana major AP endonuclease; wARP, wheat Triticum aestivum AP endonuclease. Milena BAZLEKOWA-KARABAN et al., Mechanism of stimulation of DNA binding of the transcription factors by human apurinic/apyrimidinic endonuclease 1, APE1.

The Enigma of Substrate Recognition and Catalytic Efficiency of APE1-Like Enzymes

“…By contrast, this domain affects both the rate of formation and the stability of the initial complex in the cases of NIR and 3 →5 exonuclease activities (Gros et al, 2004;Daviet et al, 2007;Timofeyeva et al, 2009). Multiple studies also underscore that the N-terminal domain may functionally interact with different proteins involved in DNA repair (Kladova et al, 2018a;Moor et al, 2020;Popov et al, 2020), transcription (Georgiadis et al, 2008;Kelley et al, 2011;Bazlekowa-Karaban et al, 2019), and RNA metabolism (Vascotto et al, 2009;Tell et al, 2010;Poletto et al, 2013). Summarizing the literature data, we can conclude that the N-terminal domain may be required for the preliminary low-affinity binding process in search of the proper lesion in DNA or a cleavage site in RNA and proteinprotein interactions.…”

APE1 distinguishes DNA substrates in exonucleolytic cleavage by induced space-filling

“…Although earlier studies showed that in the middle-binding mode, APE1 can excise the mismatched 3′-end of a dsDNA substrate 20,24,25,37,38 , whether the physiologically more relevant matched dsDNA substrates are also vulnerable to the exonuclease activity of APE1 has not been established. Our results show that the matched dsDNA substrates can indeed be digested by mAPE1, albeit they have higher recalcitrance than the mismatched counterpart (Fig.…”

“…On the gel, the band of protein-DNA complex similar to that in the aforementioned substrates is also observed. This band is rather smeared, though, reflecting the likelihood of more than one APE1 attaching to a dsDNA substrate in the case of terminal binding 37 . For the binding of mAPE1 with AP site-containing dsDNA and gapped dsDNA, on the other hand, an additional band for a lower molecular weight protein-DNA complex is observed at the lower protein concentration of 0.5 μM (Fig.…”

Reading Targeted DNA Damage in the Active Demethylation Pathway: Role of Accessory Domains of Eukaryotic AP Endonucleases and Thymine-DNA Glycosylases

“…Recent observations brought forward a somewhat unexpected hypothesis that unifies all these functions under a model of APE1 multimerization on DNA. Transmission electron microscopy and atomic force microscopy revealed that the full-length APE1 can form filaments on both undamaged and damaged DNA fragments and introduce bends and kinks that can be used to detect an AP site [149,189]. Several APE1 molecules was observed to bind both undamaged and damaged oligonucleotides in an apparently cooperative mode, with single-stranded DNA or nicks acting as preferential binding sites [189].…”