Cited by 209DNA Repair MechanismsHIV Research and TreatmentVirus-based gene therapy research

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Repair of Gaps in Retroviral DNA Integration Intermediates

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Yoder, Kristine E., Bushman, Frederic D.·2000·Journal of Virology

DOI 10.1128/jvi.74.23.11191-11200.2000PMC PMC113210

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Abstract

Diverse mobile DNA elements are believed to pirate host cell enzymes to complete DNA transfer. Prominent examples are provided by retroviral cDNA integration and transposon insertion. These reactions initially involve the attachment of each element 3′ DNA end to staggered sites in the host DNA by element-encoded integrase or transposase enzymes. Unfolding of such intermediates yields DNA gaps at each junction. It has been widely assumed that host DNA repair enzymes complete attachment of the remaining DNA ends, but the enzymes involved have not been identified for any system. We have synthesized DNA substrates containing the expected gap and 5′ two-base flap structure present in retroviral integration intermediates and tested candidate enzymes for the ability to support repair in vitro. We find three required activities, two of which can be satisfied by multiple enzymes. These are a polymerase (polymerase beta, polymerase delta and its cofactor PCNA, or reverse transcriptase), a nuclease (flap endonuclease), and a ligase (ligase I, III, or IV and its cofactor XRCC4). A proposed pathway involving retroviral integrase and reverse transcriptase did not carry out repair under the conditions tested. In addition, prebinding of integrase protein to gapped DNA inhibited repair reactions, indicating that gap repair in vivo may require active disassembly of the integrase complex.

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Background

Authors: Yoder, K. E., & Bushman, F. D.
Affiliations: Salk Institute for Biological Studies (US)
ORCID: Yoder, Kristine E.
Bushman, Frederic D.
Venue: Journal of Virology
Publisher: American Society for Microbiology
Published: 2000-12
Volume: 74
Issue: 23
Pages: 11191-11200
ISSN: 0022-538X (ISSN-L)
1098-5514
DOI: 10.1128/jvi.74.23.11191-11200.2000
PMC: PMC113210
OpenAlex: W2062774485
Cited by: 209
References: 0
Citations by year: 2026: 2 · 2025: 3 · 2024: 3 · 2023: 2 · 2022: 4 · 2021: 7 · 2020: 2 · 2019: 5 · 2018: 5 · 2017: 2 · 2016: 3 · 2015: 10 · 2014: 8 · 2013: 9 · 2012: 8
FWCI: 4.22
Type: journal article
Language: en
Open access: green
europepmc.org
Licence: journals.asm.org/non-commercial-tdm-license (tdm)
Locations: Journal of Virology (publishedVersion)
Europe PMC (PubMed Central) (publishedVersion)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
Funders: Leukemia and Lymphoma Society
James B. Pendleton Charitable Trust
National Institutes of Health (5p01gm056553-05)
National Institute of General Medical Sciences (GM 56553)
National Institute of Allergy and Infectious Diseases (AI 34786, R01AI034786)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
Life Sciences › Immunology and Microbiology › Virology › HIV Research and Treatment
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Virus-based gene therapy research
Keywords: retroviral integration, integrase, reverse transcriptase, flap endonuclease, DNA ligase, DNA polymerase beta, DNA polymerase delta, PCNA, XRCC4, mobile DNA elements, transposon insertion
MeSH terms: DNA Ligase ATP, Base Sequence, DNA Repair, DNA-Binding Proteins, Molecular Sequence Data, DNA Ligases, Retroviridae, RNA-Directed DNA Polymerase, Virus Integration, Protein Serine-Threonine Kinases, Integrases, DNA-Activated Protein Kinase

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Repair of Gaps in Retroviral DNA Integration Intermediates

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