title: Repair of gaps in retroviral DNA integration intermediates.
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.
authors.affiliation: Infectious Disease Laboratory, The Salk Institute, La Jolla, California 92037, USA.
authors.forename: K E
authors.initials: KE
authors.lastname: Yoder
authors.forename: F D
authors.initials: FD
authors.lastname: Bushman
mesh_terms: D001483:Base Sequence; D000072481:DNA Ligase ATP; D011088:DNA Ligases / Q000494:pharmacology; D004260:DNA Repair; D051747:DNA-Activated Protein Kinase; D004268:DNA-Binding Proteins; D019426:Integrases / Q000494:pharmacology; D008969:Molecular Sequence Data; D017346:Protein Serine-Threonine Kinases / Q000502:physiology; D012194:RNA-Directed DNA Polymerase / Q000494:pharmacology; D012190:Retroviridae / Q000235:genetics*; D016662:Virus Integration
chemical_list: D004268:DNA-Binding Proteins; D051747:DNA-Activated Protein Kinase; D017346:Protein Serine-Threonine Kinases; D019426:Integrases; D012194:RNA-Directed DNA Polymerase; D011088:DNA Ligases; D000072481:DNA Ligase ATP