The lyase activity of bifunctional DNA glycosylases and the 3′-diesterase activity of APE1 contribute to the repair of oxidized bases in nucleosomes

Abstract The vast majority of oxidized bases that form in DNA are subject to base excision repair (BER). The DNA intermediates generated during successive steps in BER may prove mutagenic or lethal, making it critical that they be ‘handed’ from one BER enzyme to the next in a coordinated fashion. He...

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Published in	Nucleic acids research Vol. 47; no. 6; pp. 2922 - 2931
Main Authors	Maher, Robyn L, Wallace, Susan S, Pederson, David S
Format	Journal Article
Language	English
Published	England Oxford University Press 08.04.2019
Subjects	Chromatin - enzymology Chromatin - genetics Deoxyribonuclease (Pyrimidine Dimer) - chemistry Deoxyribonuclease (Pyrimidine Dimer) - genetics DNA - chemistry DNA - genetics DNA Damage - genetics DNA Glycosylases - chemistry DNA Glycosylases - genetics DNA Repair DNA-(Apurinic or Apyrimidinic Site) Lyase - chemistry DNA-(Apurinic or Apyrimidinic Site) Lyase - genetics Esterases - genetics Genome Integrity, Repair and Humans Lyases - chemistry Lyases - genetics Nucleosomes - enzymology Nucleosomes - genetics Oxidation-Reduction
Online Access	Get full text
ISSN	0305-1048 1362-4962 1362-4962
DOI	10.1093/nar/gky1315

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Abstract	Abstract The vast majority of oxidized bases that form in DNA are subject to base excision repair (BER). The DNA intermediates generated during successive steps in BER may prove mutagenic or lethal, making it critical that they be ‘handed’ from one BER enzyme to the next in a coordinated fashion. Here, we report that the handoff of BER intermediates that occurs during the repair of naked DNA substrates differs significantly from that in nucleosomes. During BER of oxidized bases in naked DNA, products generated by the DNA glycosylase NTHL1 were efficiently processed by the downstream enzyme, AP-endonuclease (APE1). In nucleosomes, however, NTHL1-generated products accumulated to significant levels and persisted for some time. During BER of naked DNA substrates, APE1 completely bypasses the inefficient lyase activity of NTHL1. In nucleosomes, the NTHL1-associated lyase contributes to BER, even in the presence of APE1. Moreover, in nucleosomes but not in naked DNA, APE1 was able to process NTHL1 lyase-generated substrates just as efficiently as it processed abasic sites. Thus, the lyase activity of hNTHL1, and the 3′ diesterase activity of APE1, which had been seen as relatively dispensable, may have been preserved during evolution to enhance BER in chromatin.
AbstractList	The vast majority of oxidized bases that form in DNA are subject to base excision repair (BER). The DNA intermediates generated during successive steps in BER may prove mutagenic or lethal, making it critical that they be 'handed' from one BER enzyme to the next in a coordinated fashion. Here, we report that the handoff of BER intermediates that occurs during the repair of naked DNA substrates differs significantly from that in nucleosomes. During BER of oxidized bases in naked DNA, products generated by the DNA glycosylase NTHL1 were efficiently processed by the downstream enzyme, AP-endonuclease (APE1). In nucleosomes, however, NTHL1-generated products accumulated to significant levels and persisted for some time. During BER of naked DNA substrates, APE1 completely bypasses the inefficient lyase activity of NTHL1. In nucleosomes, the NTHL1-associated lyase contributes to BER, even in the presence of APE1. Moreover, in nucleosomes but not in naked DNA, APE1 was able to process NTHL1 lyase-generated substrates just as efficiently as it processed abasic sites. Thus, the lyase activity of hNTHL1, and the 3' diesterase activity of APE1, which had been seen as relatively dispensable, may have been preserved during evolution to enhance BER in chromatin. The vast majority of oxidized bases that form in DNA are subject to base excision repair (BER). The DNA intermediates generated during successive steps in BER may prove mutagenic or lethal, making it critical that they be 'handed' from one BER enzyme to the next in a coordinated fashion. Here, we report that the handoff of BER intermediates that occurs during the repair of naked DNA substrates differs significantly from that in nucleosomes. During BER of oxidized bases in naked DNA, products generated by the DNA glycosylase NTHL1 were efficiently processed by the downstream enzyme, AP-endonuclease (APE1). In nucleosomes, however, NTHL1-generated products accumulated to significant levels and persisted for some time. During BER of naked DNA substrates, APE1 completely bypasses the inefficient lyase activity of NTHL1. In nucleosomes, the NTHL1-associated lyase contributes to BER, even in the presence of APE1. Moreover, in nucleosomes but not in naked DNA, APE1 was able to process NTHL1 lyase-generated substrates just as efficiently as it processed abasic sites. Thus, the lyase activity of hNTHL1, and the 3' diesterase activity of APE1, which had been seen as relatively dispensable, may have been preserved during evolution to enhance BER in chromatin.The vast majority of oxidized bases that form in DNA are subject to base excision repair (BER). The DNA intermediates generated during successive steps in BER may prove mutagenic or lethal, making it critical that they be 'handed' from one BER enzyme to the next in a coordinated fashion. Here, we report that the handoff of BER intermediates that occurs during the repair of naked DNA substrates differs significantly from that in nucleosomes. During BER of oxidized bases in naked DNA, products generated by the DNA glycosylase NTHL1 were efficiently processed by the downstream enzyme, AP-endonuclease (APE1). In nucleosomes, however, NTHL1-generated products accumulated to significant levels and persisted for some time. During BER of naked DNA substrates, APE1 completely bypasses the inefficient lyase activity of NTHL1. In nucleosomes, the NTHL1-associated lyase contributes to BER, even in the presence of APE1. Moreover, in nucleosomes but not in naked DNA, APE1 was able to process NTHL1 lyase-generated substrates just as efficiently as it processed abasic sites. Thus, the lyase activity of hNTHL1, and the 3' diesterase activity of APE1, which had been seen as relatively dispensable, may have been preserved during evolution to enhance BER in chromatin. Abstract The vast majority of oxidized bases that form in DNA are subject to base excision repair (BER). The DNA intermediates generated during successive steps in BER may prove mutagenic or lethal, making it critical that they be ‘handed’ from one BER enzyme to the next in a coordinated fashion. Here, we report that the handoff of BER intermediates that occurs during the repair of naked DNA substrates differs significantly from that in nucleosomes. During BER of oxidized bases in naked DNA, products generated by the DNA glycosylase NTHL1 were efficiently processed by the downstream enzyme, AP-endonuclease (APE1). In nucleosomes, however, NTHL1-generated products accumulated to significant levels and persisted for some time. During BER of naked DNA substrates, APE1 completely bypasses the inefficient lyase activity of NTHL1. In nucleosomes, the NTHL1-associated lyase contributes to BER, even in the presence of APE1. Moreover, in nucleosomes but not in naked DNA, APE1 was able to process NTHL1 lyase-generated substrates just as efficiently as it processed abasic sites. Thus, the lyase activity of hNTHL1, and the 3′ diesterase activity of APE1, which had been seen as relatively dispensable, may have been preserved during evolution to enhance BER in chromatin.
Author	Pederson, David S Maher, Robyn L Wallace, Susan S
AuthorAffiliation	Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405-0068, USA
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Author_xml	– sequence: 1 givenname: Robyn L surname: Maher fullname: Maher, Robyn L organization: Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405-0068, USA – sequence: 2 givenname: Susan S surname: Wallace fullname: Wallace, Susan S organization: Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405-0068, USA – sequence: 3 givenname: David S surname: Pederson fullname: Pederson, David S email: david.pederson@uvm.edu organization: Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405-0068, USA
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/30649547$$D View this record in MEDLINE/PubMed
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Snippet	Abstract The vast majority of oxidized bases that form in DNA are subject to base excision repair (BER). The DNA intermediates generated during successive... The vast majority of oxidized bases that form in DNA are subject to base excision repair (BER). The DNA intermediates generated during successive steps in BER...
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SubjectTerms	Chromatin - enzymology Chromatin - genetics Deoxyribonuclease (Pyrimidine Dimer) - chemistry Deoxyribonuclease (Pyrimidine Dimer) - genetics DNA - chemistry DNA - genetics DNA Damage - genetics DNA Glycosylases - chemistry DNA Glycosylases - genetics DNA Repair DNA-(Apurinic or Apyrimidinic Site) Lyase - chemistry DNA-(Apurinic or Apyrimidinic Site) Lyase - genetics Esterases - genetics Genome Integrity, Repair and Humans Lyases - chemistry Lyases - genetics Nucleosomes - enzymology Nucleosomes - genetics Oxidation-Reduction
Title	The lyase activity of bifunctional DNA glycosylases and the 3′-diesterase activity of APE1 contribute to the repair of oxidized bases in nucleosomes
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