TY - JOUR

T1 - An Insight into the Mechanism of DNA Cleavage by DNA Endonuclease from the Hyperthermophilic Archaeon Pyrococcus furiosus

AU - Davletgildeeva, Anastasiia T.

AU - Kuznetsova, Aleksandra A.

AU - Ishchenko, Alexander A.

AU - Saparbaev, Murat

AU - Kuznetsov, Nikita A.

N1 - The work was supported by the Ministry of Science and Higher Education of the Russian Federation, agreement No. 075-15-2021-1085.

PY - 2024/8

Y1 - 2024/8

N2 - Hyperthermophilic archaea such as Pyrococcus furiosus survive under very aggressive environmental conditions by occupying niches inaccessible to representatives of other domains of life. The ability to survive such severe living conditions must be ensured by extraordinarily efficient mechanisms of DNA processing, including repair. Therefore, in this study, we compared kinetics of conformational changes of DNA Endonuclease Q from P. furiosus during its interaction with various DNA substrates containing an analog of an apurinic/apyrimidinic site (F-site), hypoxanthine, uracil, 5,6-dihydrouracil, the α-anomer of adenosine, or 1,N6-ethenoadenosine. Our examination of DNA cleavage activity and fluorescence time courses characterizing conformational changes of the dye-labeled DNA substrates during the interaction with EndoQ revealed that the enzyme induces multiple conformational changes of DNA in the course of binding. Moreover, the obtained data suggested that the formation of the enzyme–substrate complex can proceed through dissimilar kinetic pathways, resulting in different types of DNA conformational changes, which probably allow the enzyme to perform its biological function at an extreme temperature.

AB - Hyperthermophilic archaea such as Pyrococcus furiosus survive under very aggressive environmental conditions by occupying niches inaccessible to representatives of other domains of life. The ability to survive such severe living conditions must be ensured by extraordinarily efficient mechanisms of DNA processing, including repair. Therefore, in this study, we compared kinetics of conformational changes of DNA Endonuclease Q from P. furiosus during its interaction with various DNA substrates containing an analog of an apurinic/apyrimidinic site (F-site), hypoxanthine, uracil, 5,6-dihydrouracil, the α-anomer of adenosine, or 1,N6-ethenoadenosine. Our examination of DNA cleavage activity and fluorescence time courses characterizing conformational changes of the dye-labeled DNA substrates during the interaction with EndoQ revealed that the enzyme induces multiple conformational changes of DNA in the course of binding. Moreover, the obtained data suggested that the formation of the enzyme–substrate complex can proceed through dissimilar kinetic pathways, resulting in different types of DNA conformational changes, which probably allow the enzyme to perform its biological function at an extreme temperature.

KW - DNA repair

KW - abasic site

KW - apurinic/apyrimidinic endonuclease

KW - damaged nucleotide

KW - endonuclease activity

KW - exonuclease activity

KW - pre-steady-state enzyme kinetics

KW - Pyrococcus furiosus/enzymology

KW - DNA Cleavage

KW - Kinetics

KW - Archaeal Proteins/metabolism

KW - Substrate Specificity

KW - Nucleic Acid Conformation

KW - DNA/metabolism

UR - https://www.scopus.com/record/display.uri?eid=2-s2.0-85202612602&origin=inward&txGid=88cff6a30ae72d62c9278d4cbd33e3b4

UR - https://www.mendeley.com/catalogue/f6672892-0652-3459-bfd8-41818a9ae2c3/

U2 - 10.3390/ijms25168897

DO - 10.3390/ijms25168897

M3 - Article

C2 - 39201583

VL - 25

JO - International Journal of Molecular Sciences

JF - International Journal of Molecular Sciences

SN - 1661-6596

IS - 16

M1 - 8897

ER -