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Bypass of Abasic Site–Peptide Cross-Links by Human Repair and Translesion DNA Polymerases

DNA–protein cross-links remain the least-studied type of DNA damage. Recently, their repair was shown to involve proteolysis; however, the fate of the peptide remnant attached to DNA is unclear. Particularly, peptide cross-links could interfere with DNA polymerases. Apurinuic/apyrimidinic (AP) sites...

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Autores principales: Yudkina, Anna V., Barmatov, Alexander E., Bulgakov, Nikita A., Boldinova, Elizaveta O., Shilkin, Evgeniy S., Makarova, Alena V., Zharkov, Dmitry O.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10341727/
https://www.ncbi.nlm.nih.gov/pubmed/37446048
http://dx.doi.org/10.3390/ijms241310877
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author Yudkina, Anna V.
Barmatov, Alexander E.
Bulgakov, Nikita A.
Boldinova, Elizaveta O.
Shilkin, Evgeniy S.
Makarova, Alena V.
Zharkov, Dmitry O.
author_facet Yudkina, Anna V.
Barmatov, Alexander E.
Bulgakov, Nikita A.
Boldinova, Elizaveta O.
Shilkin, Evgeniy S.
Makarova, Alena V.
Zharkov, Dmitry O.
author_sort Yudkina, Anna V.
collection PubMed
description DNA–protein cross-links remain the least-studied type of DNA damage. Recently, their repair was shown to involve proteolysis; however, the fate of the peptide remnant attached to DNA is unclear. Particularly, peptide cross-links could interfere with DNA polymerases. Apurinuic/apyrimidinic (AP) sites, abundant and spontaneously arising DNA lesions, readily form cross-links with proteins. Their degradation products (AP site–peptide cross-links, APPXLs) are non-instructive and should be even more problematic for polymerases. Here, we address the ability of human DNA polymerases involved in DNA repair and translesion synthesis (POLβ, POLλ, POLη, POLκ and PrimPOL) to carry out synthesis on templates containing AP sites cross-linked to the N-terminus of a 10-mer peptide (APPXL-I) or to an internal lysine of a 23-mer peptide (APPXL-Y). Generally, APPXLs strongly blocked processive DNA synthesis. The blocking properties of APPXL-I were comparable with those of an AP site, while APPXL-Y constituted a much stronger obstruction. POLη and POLκ demonstrated the highest bypass ability. DNA polymerases mostly used dNTP-stabilized template misalignment to incorporate nucleotides when encountering an APPXL. We conclude that APPXLs are likely highly cytotoxic and mutagenic intermediates of AP site–protein cross-link repair and must be quickly eliminated before replication.
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spelling pubmed-103417272023-07-14 Bypass of Abasic Site–Peptide Cross-Links by Human Repair and Translesion DNA Polymerases Yudkina, Anna V. Barmatov, Alexander E. Bulgakov, Nikita A. Boldinova, Elizaveta O. Shilkin, Evgeniy S. Makarova, Alena V. Zharkov, Dmitry O. Int J Mol Sci Article DNA–protein cross-links remain the least-studied type of DNA damage. Recently, their repair was shown to involve proteolysis; however, the fate of the peptide remnant attached to DNA is unclear. Particularly, peptide cross-links could interfere with DNA polymerases. Apurinuic/apyrimidinic (AP) sites, abundant and spontaneously arising DNA lesions, readily form cross-links with proteins. Their degradation products (AP site–peptide cross-links, APPXLs) are non-instructive and should be even more problematic for polymerases. Here, we address the ability of human DNA polymerases involved in DNA repair and translesion synthesis (POLβ, POLλ, POLη, POLκ and PrimPOL) to carry out synthesis on templates containing AP sites cross-linked to the N-terminus of a 10-mer peptide (APPXL-I) or to an internal lysine of a 23-mer peptide (APPXL-Y). Generally, APPXLs strongly blocked processive DNA synthesis. The blocking properties of APPXL-I were comparable with those of an AP site, while APPXL-Y constituted a much stronger obstruction. POLη and POLκ demonstrated the highest bypass ability. DNA polymerases mostly used dNTP-stabilized template misalignment to incorporate nucleotides when encountering an APPXL. We conclude that APPXLs are likely highly cytotoxic and mutagenic intermediates of AP site–protein cross-link repair and must be quickly eliminated before replication. MDPI 2023-06-29 /pmc/articles/PMC10341727/ /pubmed/37446048 http://dx.doi.org/10.3390/ijms241310877 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Yudkina, Anna V.
Barmatov, Alexander E.
Bulgakov, Nikita A.
Boldinova, Elizaveta O.
Shilkin, Evgeniy S.
Makarova, Alena V.
Zharkov, Dmitry O.
Bypass of Abasic Site–Peptide Cross-Links by Human Repair and Translesion DNA Polymerases
title Bypass of Abasic Site–Peptide Cross-Links by Human Repair and Translesion DNA Polymerases
title_full Bypass of Abasic Site–Peptide Cross-Links by Human Repair and Translesion DNA Polymerases
title_fullStr Bypass of Abasic Site–Peptide Cross-Links by Human Repair and Translesion DNA Polymerases
title_full_unstemmed Bypass of Abasic Site–Peptide Cross-Links by Human Repair and Translesion DNA Polymerases
title_short Bypass of Abasic Site–Peptide Cross-Links by Human Repair and Translesion DNA Polymerases
title_sort bypass of abasic site–peptide cross-links by human repair and translesion dna polymerases
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10341727/
https://www.ncbi.nlm.nih.gov/pubmed/37446048
http://dx.doi.org/10.3390/ijms241310877
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