TY - JOUR

T1 - Distinct Mechanisms of Target Search by Endonuclease VIII-like DNA Glycosylases

AU - Diatlova, Evgeniia A.

AU - Mechetin, Grigory V.

AU - Zharkov, Dmitry O.

N1 - Funding Information: This research was funded by the Russian Foundation for Basic Research (grant number 20-04-00554-a). Partial salary support from the Russian Ministry of Science and Higher Education (State funded budget project 121031300056-8 to D.O.Z.) is acknowledged. Publisher Copyright: © 2022 by the authors.

PY - 2022/10

Y1 - 2022/10

N2 - Proteins that recognize specific DNA sequences or structural elements often find their cognate DNA lesions in a processive mode, in which an enzyme binds DNA non-specifically and then slides along the DNA contour by one-dimensional diffusion. Opposite to the processive mechanism is distributive search, when an enzyme binds, samples and releases DNA without significant lateral movement. Many DNA glycosylases, the repair enzymes that excise damaged bases from DNA, use processive search to find their cognate lesions. Here, using a method based on correlated cleavage of multiply damaged oligonucleotide substrates we investigate the mechanism of lesion search by three structurally related DNA glycosylases—bacterial endonuclease VIII (Nei) and its mammalian homologs NEIL1 and NEIL2. Similarly to another homologous enzyme, bacterial formamidopyrimidine–DNA glycosylase, NEIL1 seems to use a processive mode to locate its targets. However, the processivity of Nei was notably lower, and NEIL2 exhibited almost fully distributive action on all types of substrates. Although one-dimensional diffusion is often regarded as a universal search mechanism, our results indicate that even proteins sharing a common fold may be quite different in the ways they locate their targets in DNA.

AB - Proteins that recognize specific DNA sequences or structural elements often find their cognate DNA lesions in a processive mode, in which an enzyme binds DNA non-specifically and then slides along the DNA contour by one-dimensional diffusion. Opposite to the processive mechanism is distributive search, when an enzyme binds, samples and releases DNA without significant lateral movement. Many DNA glycosylases, the repair enzymes that excise damaged bases from DNA, use processive search to find their cognate lesions. Here, using a method based on correlated cleavage of multiply damaged oligonucleotide substrates we investigate the mechanism of lesion search by three structurally related DNA glycosylases—bacterial endonuclease VIII (Nei) and its mammalian homologs NEIL1 and NEIL2. Similarly to another homologous enzyme, bacterial formamidopyrimidine–DNA glycosylase, NEIL1 seems to use a processive mode to locate its targets. However, the processivity of Nei was notably lower, and NEIL2 exhibited almost fully distributive action on all types of substrates. Although one-dimensional diffusion is often regarded as a universal search mechanism, our results indicate that even proteins sharing a common fold may be quite different in the ways they locate their targets in DNA.

KW - DNA glycosylases

KW - DNA repair

KW - endonuclease VIII

KW - facilitated diffusion

KW - NEIL1

KW - NEIL2

KW - target search

KW - DNA-Formamidopyrimidine Glycosylase/genetics

KW - DNA Glycosylases/genetics

KW - DNA/metabolism

KW - Oligonucleotides

KW - Deoxyribonuclease (Pyrimidine Dimer)/genetics

KW - Animals

KW - DNA Repair

KW - Mammals/metabolism

UR - http://www.scopus.com/inward/record.url?scp=85140577469&partnerID=8YFLogxK

UR - https://www.mendeley.com/catalogue/8e26bbeb-0183-35db-a5c5-4a19af19776a/

U2 - 10.3390/cells11203192

DO - 10.3390/cells11203192

M3 - Article

C2 - 36291061

AN - SCOPUS:85140577469

VL - 11

JO - Cells

JF - Cells

SN - 2073-4409

IS - 20

M1 - 3192

ER -