Key Points
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DNA double-strand breaks (DSBs) pose an acute threat to the survival of all cells. There are two major pathways of DSB repair — homologous recombination (HR) and non-homologous end joining (NHEJ).
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In HR, one or both of the DNA ends are resected by an exonuclease to generate a 3′ single-strand extension that invades the intact sister chromatid. The invading strand serves as a primer for DNA synthesis. HR is generally error-free, which allows the rescue of collapsed DNA-replication forks and provides a defence against exogenous DNA-damaging agents. In NHEJ, there is no requirement for a homologous DNA template. Instead, DSBs are approximated by the DNA-end-binding protein Ku and then at least one of the broken ends is sealed by a specialized DNA ligase. NHEJ can be faithful or mutagenic, depending on whether the ends are sealed directly or remodelled by nucleases or polymerases before sealing. The central role of a dedicated DNA ligase is a distinctive feature of NHEJ.
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For many years it was thought that bacteria contained only a single DNA ligase and relied solely on HR for DSB repair. However, over the past five years this has been overturned by evidence that many bacterial genera, including Mycobacterium, Pseudomonas, Bacillus and Agrobacterium, contain an NHEJ system that depends on Ku and the dedicated DNA ligase LigD. Biochemical, structural and genetic studies of the bacterial ligases and Ku proteins are beginning to define an NHEJ pathway that has distinctive features and enzymatic components.
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LigD is a large, multifunctional enzyme that differs from all other DNA ligases in that it has multiple catalytic activities in a single polypeptide. LigD consists of an ATP-dependent ligase domain, a polymerase (POL) domain and a phosphoesterase domain. The minimal LigC ligases have been characterized only in mycobacteria and Agrobacterium tumefaciens, and comprise only nucleotidyltransferase (NTase) and oligonucleotide-binding (OB) domains. The complexity of the bacterial NHEJ apparatus ranges from the simple state found in Pseudomonas aeruginosa (which has one Ku, one LigD and no LigC), to progressively more complex forms, such as that found in Mycobacterium tuberculosis (which has one Ku, one LigD and one LigC), Mycobacterium smegmatis (which has one Ku, one LigD and two LigCs) and A. tumefaciens (which has three Ku paralogues, two LigDs and three LigCs).
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Bacterial NHEJ has been studied in most detail in mycobacteria, in which the fate of DSBs that have been repaired by mycobacterial NHEJ has illuminated the broad outlines and distinctive features of the bacterial NHEJ pathway.
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The crystal structures of the POL domains of P. aeruginosa LigD bound to ATP and M. tuberculosis LigD bound to GTP have been solved.
Abstract
The capacity to rectify DNA double-strand breaks (DSBs) is crucial for the survival of all species. DSBs can be repaired either by homologous recombination (HR) or non-homologous end joining (NHEJ). The long-standing notion that bacteria rely solely on HR for DSB repair has been overturned by evidence that mycobacteria and other genera have an NHEJ system that depends on a dedicated DNA ligase, LigD, and the DNA-end-binding protein Ku. Recent studies have illuminated the role of NHEJ in protecting the bacterial chromosome against DSBs and other clastogenic stresses. There is also emerging evidence of functional crosstalk between bacterial NHEJ proteins and components of other DNA-repair pathways. Although still a young field, bacterial NHEJ promises to teach us a great deal about the nexus of DNA repair and bacterial pathogenesis.
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Acknowledgements
NHEJ research in the laboratories of S.S. and M.S.G. is suported by National Institutes of Health grants A1064693 and GM63611.
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DATABASES
Entrez Genome Project
Protein Data Bank
Mycobacterium tuberculosis LigD LIG
Mycobacterium tuberculosis LigD POL
FURTHER INFORMATION
Glossary
- Abasic site
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A common form of DNA damage in which a base is removed from a strand of DNA by the action of DNA-repair enzymes, such as uracil glycosylase, leaving the phosphodiester bond intact.
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Shuman, S., Glickman, M. Bacterial DNA repair by non-homologous end joining. Nat Rev Microbiol 5, 852–861 (2007). https://doi.org/10.1038/nrmicro1768
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DOI: https://doi.org/10.1038/nrmicro1768
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