TY - JOUR

T1 - Comparative Analysis of Exo-and Endonuclease Activities of APE1-like Enzymes

AU - Davletgildeeva, Anastasiia T.

AU - Kuznetsova, Alexandra A.

AU - Novopashina, Darya S.

AU - Ishchenko, Alexander A.

AU - Saparbaev, Murat

AU - Fedorova, Olga S.

AU - Kuznetsov, Nikita A.

N1 - Funding Information: Funding: This work was supported partially by a Russian-Government-funded project (no. 121031300041-4), by Electricité de France (RB 2020-02 and RB 2021-05, to M.S.), by the French National Research Agency (ANR-18-CE44-0008), and Fondation ARC (PJA-2021060003796) to A.A.I. The part of the work involving the analysis of 3′-5′ exonuclease and endoribonuclease activities was specifically funded by the Russian Science Foundation, grant no. 21-64-00017. A.T.D. was supported by Ph.D. grant no. 20-34-90008 from the Russian Foundation for Basic Research. Publisher Copyright: © 2022 by the authors. Licensee MDPI, Basel, Switzerland.

PY - 2022/3/1

Y1 - 2022/3/1

N2 - Apurinic/apyrimidinic (AP)-endonucleases are multifunctional enzymes that are required for cell viability. AP-endonucleases incise DNA 5′ to an AP-site; can recognize and process some damaged nucleosides; and possess 3′-phosphodiesterase, 3′-phosphatase, and endoribonu-clease activities. To elucidate the mechanism of substrate cleavage in detail, we analyzed the effect of mono-and divalent metal ions on the exo-and endonuclease activities of four homologous APE1-like endonucleases (from an insect (Rrp1), amphibian (xAPE1), fish (zAPE1), and from hu-mans (hAPE1)). It was found that the enzymes had similar patterns of dependence on metal ions’ concentrations in terms of AP-endonuclease activity, suggesting that the main biological function (AP-site cleavage) was highly conserved among evolutionarily distant species. The efficiency of the 3′-5′ exonuclease activity was the highest in hAPE1 among these enzymes. In contrast, the en-doribonuclease activity of the enzymes could be ranked as hAPE1 ≈ zAPE1 ≤ xAPE1 ≤ Rrp1. Taken together, the results revealed that the tested enzymes differed significantly in their capacity for substrate cleavage, even though the most important catalytic and substrate-binding amino acid residues were conserved. It can be concluded that substrate specificity and cleavage efficiency were controlled by factors external to the catalytic site, e.g., the N-terminal domain of these enzymes.

AB - Apurinic/apyrimidinic (AP)-endonucleases are multifunctional enzymes that are required for cell viability. AP-endonucleases incise DNA 5′ to an AP-site; can recognize and process some damaged nucleosides; and possess 3′-phosphodiesterase, 3′-phosphatase, and endoribonu-clease activities. To elucidate the mechanism of substrate cleavage in detail, we analyzed the effect of mono-and divalent metal ions on the exo-and endonuclease activities of four homologous APE1-like endonucleases (from an insect (Rrp1), amphibian (xAPE1), fish (zAPE1), and from hu-mans (hAPE1)). It was found that the enzymes had similar patterns of dependence on metal ions’ concentrations in terms of AP-endonuclease activity, suggesting that the main biological function (AP-site cleavage) was highly conserved among evolutionarily distant species. The efficiency of the 3′-5′ exonuclease activity was the highest in hAPE1 among these enzymes. In contrast, the en-doribonuclease activity of the enzymes could be ranked as hAPE1 ≈ zAPE1 ≤ xAPE1 ≤ Rrp1. Taken together, the results revealed that the tested enzymes differed significantly in their capacity for substrate cleavage, even though the most important catalytic and substrate-binding amino acid residues were conserved. It can be concluded that substrate specificity and cleavage efficiency were controlled by factors external to the catalytic site, e.g., the N-terminal domain of these enzymes.

KW - 3′-5′ exonuclease activity

KW - Abasic site

KW - Apurinic/apyrimidinic endonuclease

KW - Damaged nucleotide

KW - DNA repair

KW - Endonuclease activity

UR - http://www.scopus.com/inward/record.url?scp=85125576961&partnerID=8YFLogxK

U2 - 10.3390/ijms23052869

DO - 10.3390/ijms23052869

M3 - Article

C2 - 35270011

AN - SCOPUS:85125576961

VL - 23

JO - International Journal of Molecular Sciences

JF - International Journal of Molecular Sciences

SN - 1661-6596

IS - 5

M1 - 2869

ER -