Mechanism of nonhomologous end-joining in mycobacteria: a low-fidelity repair system driven by Ku, ligase D and ligase C

Nat Struct Mol Biol. 2005 Apr;12(4):304-12. doi: 10.1038/nsmb915. Epub 2005 Mar 20.


DNA double-strand breaks (DSBs) can be repaired either via homologous recombination (HR) or nonhomologous end-joining (NHEJ). Both pathways are operative in eukaryotes, but bacteria had been thought to rely on HR alone. Here we provide direct evidence that mycobacteria have a robust NHEJ pathway that requires Ku and a specialized polyfunctional ATP-dependent DNA ligase (LigD). NHEJ of blunt-end and complementary 5'-overhang DSBs is highly mutagenic ( approximately 50% error rate). Analysis of the recombination junctions ensuing from individual NHEJ events highlighted the participation of several DNA end-remodeling activities, including template-dependent fill-in of 5' overhangs, nontemplated addition of single nucleotides at blunt ends, and nucleolytic resection. LigD itself has the template-dependent and template-independent polymerase functions in vitro that compose the molecular signatures of NHEJ in vivo. Another ATP-dependent DNA ligase (LigC) provides a backup mechanism for LigD-independent error-prone repair of blunt-end DSBs. We speculate that NHEJ allows mycobacteria to evade genotoxic host defense.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Antigens, Nuclear / metabolism*
  • Bacterial Proteins / metabolism*
  • Base Sequence
  • DNA / chemistry
  • DNA / genetics
  • DNA / metabolism
  • DNA Damage
  • DNA Ligase ATP
  • DNA Ligases / genetics
  • DNA Ligases / metabolism*
  • DNA Repair / genetics*
  • DNA-Binding Proteins / metabolism*
  • Ku Autoantigen
  • Mutation / genetics
  • Mycobacterium smegmatis / genetics
  • Mycobacterium smegmatis / metabolism*
  • Protein Binding
  • Recombination, Genetic / genetics*
  • Templates, Genetic


  • Antigens, Nuclear
  • Bacterial Proteins
  • DNA-Binding Proteins
  • DNA
  • Ku Autoantigen
  • DNA Ligases
  • DNA Ligase ATP