TY - JOUR

T1 - Displacement of Slow-Turnover DNA Glycosylases by Molecular Traffic on DNA

AU - Yudkina, Anna V.

AU - Endutkin, Anton V.

AU - Diatlova, Eugenia A.

AU - Moor, Nina A.

AU - Vokhtantsev, Ivan P.

AU - Grin, Inga R.

AU - Zharkov, Dmitry O.

N1 - Publisher Copyright: © 2020 by the authors. Licensee MDPI, Basel, Switzerland. Copyright: Copyright 2020 Elsevier B.V., All rights reserved.

PY - 2020/8

Y1 - 2020/8

N2 - In the base excision repair pathway, the initiating enzymes, DNA glycosylases, remove damaged bases and form long-living complexes with the abasic DNA product, but can be displaced by AP endonucleases. However, many nuclear proteins can move along DNA, either actively (such as DNA or RNA polymerases) or by passive one-dimensional diffusion. In most cases, it is not clear whether this movement is disturbed by other bound proteins or how collisions with moving proteins affect the bound proteins, including DNA glycosylases. We have used a two-substrate system to study the displacement of human OGG1 and NEIL1 DNA glycosylases by DNA polymerases in both elongation and diffusion mode and by D4, a passively diffusing subunit of a viral DNA polymerase. The OGG1-DNA product complex was disrupted by DNA polymerase β (POLβ) in both elongation and diffusion mode, Klenow fragment (KF) in the elongation mode and by D4. NEIL1, which has a shorter half-life on DNA, was displaced more efficiently. Hence, both possibly specific interactions with POLβ and nonspecific collisions (KF, D4) can displace DNA glycosylases from DNA. The protein movement along DNA was blocked by very tightly bound Cas9 RNA-targeted nuclease, providing an upper limit on the efficiency of obstacle clearance.

AB - In the base excision repair pathway, the initiating enzymes, DNA glycosylases, remove damaged bases and form long-living complexes with the abasic DNA product, but can be displaced by AP endonucleases. However, many nuclear proteins can move along DNA, either actively (such as DNA or RNA polymerases) or by passive one-dimensional diffusion. In most cases, it is not clear whether this movement is disturbed by other bound proteins or how collisions with moving proteins affect the bound proteins, including DNA glycosylases. We have used a two-substrate system to study the displacement of human OGG1 and NEIL1 DNA glycosylases by DNA polymerases in both elongation and diffusion mode and by D4, a passively diffusing subunit of a viral DNA polymerase. The OGG1-DNA product complex was disrupted by DNA polymerase β (POLβ) in both elongation and diffusion mode, Klenow fragment (KF) in the elongation mode and by D4. NEIL1, which has a shorter half-life on DNA, was displaced more efficiently. Hence, both possibly specific interactions with POLβ and nonspecific collisions (KF, D4) can displace DNA glycosylases from DNA. The protein movement along DNA was blocked by very tightly bound Cas9 RNA-targeted nuclease, providing an upper limit on the efficiency of obstacle clearance.

KW - DNA damage

KW - DNA polymerases

KW - DNA repair

KW - facilitated diffusion

KW - molecular traffic

KW - tight protein–DNA complexes

KW - PROTEIN

KW - ENDONUCLEASE-III

KW - XRCC1

KW - tight protein-DNA complexes

KW - POLYMERASE-BETA

KW - AP LYASE ACTIVITY

KW - HUMAN 8-OXOGUANINE-DNA GLYCOSYLASE

KW - SUBSTRATE-SPECIFICITY

KW - REPLICATION

KW - BASE EXCISION-REPAIR

KW - BINDING

UR - http://www.scopus.com/inward/record.url?scp=85089131803&partnerID=8YFLogxK

U2 - 10.3390/genes11080866

DO - 10.3390/genes11080866

M3 - Article

C2 - 32751599

AN - SCOPUS:85089131803

VL - 11

SP - 1

EP - 21

JO - Genes

JF - Genes

SN - 2073-4425

IS - 8

M1 - 866

ER -