Variable Termination Sites of DNA Polymerases Encountering a DNA–Protein Cross-Link | Sciact - CRIS-system of Boreskov Institute of Catalysis

Variable Termination Sites of DNA Polymerases Encountering a DNA–Protein Cross-Link Full article

Journal

PLoS One
ISSN: 1932-6203

Output data

Year: 2018, Volume: 13, Number: 6, Article number : e0198480, Pages count : 17 DOI: 10.1371/journal.pone.0198480

Tags

BASE EXCISION-REPAIR; STRAND-DISPLACEMENT; GENOMIC INSTABILITY; REPLICATION BYPASS; ESCHERICHIA-COLILESION-BYPASS; MAJOR GROOVE; MECHANISM; BETA; PEPTIDE

Authors

Yudkina Anna V. ^1,2 , Dvornikova Antonina P. ¹ , Zharkov Dmitry O. ^1,2

Affiliations

1	Laboratory of Genome and Protein Engineering, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
2	Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia

DNA-protein cross-links (DPCs) are important DNA lesions induced by endogenous crosslinking agents such as formaldehyde or acetaldehyde, as well as ionizing radiation, cancer chemotherapeutic drugs, and abortive action of some enzymes. Due to their very bulky nature, they are expected to interfere with DNA and RNA synthesis and DNA repair. DPCs are highly genotoxic and the ability of cells to deal with them is relevant for many chemotherapeutic interventions. However, interactions of DNA polymerases with DPCs have been poorly studied due to the lack of a convenient experimental model. We have used NaBH4-induced trapping of E. coli formamidopyrimidine-DNA glycosylase with DNA to construct model DNA polymerase substrates containing a DPC in single-stranded template, or in the template strand of double-stranded DNA, or in the non-template (displaced) strand of double-stranded DNA. Nine DNA polymerases belonging to families A, B, X, and Y were studied with respect to their behavior upon encountering a DPC: Klenow fragment of E. coli DNA polymerase I, Thermus aquaticus DNA polymerase I, Pyrococcus furiosus DNA polymerase, Sulfolobus solfataricus DNA polymerase IV, human DNA polymerases β, κ and λ, and DNA polymerases from bacteriophages T4 and RB69. Although none were able to fully bypass DPCs in any context, Family B DNA polymerases (T4, RB69) and Family Y DNA polymerase IV were able to elongate the primer up to the site of the cross-link if a DPC was located in single-stranded template or in the displaced strand. In other cases, DNA synthesis stopped 4–5 nucleotides before the site of the cross-link in single-stranded template or in double-stranded DNA if the polymerases could displace the downstream strand. We suggest that termination of DNA polymerases on a DPC is mostly due to the unrelieved conformational strain experienced by the enzyme when pressing against the cross-linked protein molecule

Yudkina A.V. , Dvornikova A.P. , Zharkov D.O.
Variable Termination Sites of DNA Polymerases Encountering a DNA–Protein Cross-Link
PLoS One. 2018. V.13. N6. e0198480 :1-17. DOI: 10.1371/journal.pone.0198480 WOS Scopus OpenAlex

Submitted:	Mar 9, 2018
Accepted:	May 18, 2018
Published print:	Jun 1, 2018
Published online:	Jun 1, 2018

Web of science:	WOS:000433900800128
Scopus:	2-s2.0-85048039410
OpenAlex:	W2805829106

DB	Citing
Web of science	19
OpenAlex	19
Scopus	20