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Bacterial Nonhomologous End Joining Ligases Preferentially Seal Breaks with a 3′-OH Monoribonucleotide*

By Hui Zhu and Stewart Shuman

Abstract

Many bacterial species have a nonhomologous end joining system of DNA repair driven by dedicated DNA ligases (LigD and LigC). LigD is a multifunctional enzyme composed of a ligase domain fused to two other catalytic modules: a polymerase that preferentially adds ribonucleotides to double-strand break ends and a phosphoesterase that trims 3′-oligoribonucleotide tracts until only a single 3′-ribonucleotide remains. LigD and LigC have a feeble capacity to seal 3′-OH/5′-PO4 DNA nicks. Here, we report that nick sealing by LigD and LigC enzymes is stimulated by the presence of a single ribonucleotide at the broken 3′-OH end. The ribonucleotide effect on LigD and LigC is specific for the 3′-terminal nucleotide and is either diminished or abolished when additional vicinal ribonucleotides are present. No such 3′-ribonucleotide effect is observed for bacterial LigA or Chlorella virus ligase. We found that in vitro repair of a double-strand break by Pseudomonas LigD requires the polymerase module and results in incorporation of an alkali-labile ribonucleotide at the repair junction. These results illuminate an underlying logic for the domain organization of LigD, whereby the polymerase and phosphoesterase domains can heal the broken 3′-end to generate the monoribonucleotide terminus favored by the nonhomologous end joining ligases

Topics: DNA: Replication, Repair, Recombination, and Chromosome Dynamics
Publisher: American Society for Biochemistry and Molecular Biology
OAI identifier: oai:pubmedcentral.nih.gov:2276377
Provided by: PubMed Central
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