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DNA ligase III is critical for mtDNA integrity but not Xrcc1-mediated nuclear DNA repair


DNA replication and repair in mammalian cells involves three distinct DNA ligases: ligase I (Lig1), ligase III (Lig3) and ligase IV (Lig4)1. Lig3 is considered a key ligase during base excision repair because its stability depends upon its nuclear binding partner Xrcc1, a critical factor for this DNA repair pathway2,3. Lig3 is also present in the mitochondria, where its role in mitochondrial DNA (mtDNA) maintenance is independent of Xrcc1 (ref. 4). However, the biological role of Lig3 is unclear as inactivation of murine Lig3 results in early embryonic lethality5. Here we report that Lig3 is essential for mtDNA integrity but dispensable for nuclear DNA repair. Inactivation of Lig3 in the mouse nervous system resulted in mtDNA loss leading to profound mitochondrial dysfunction, disruption of cellular homeostasis and incapacitating ataxia. Similarly, inactivation of Lig3 in cardiac muscle resulted in mitochondrial dysfunction and defective heart-pump function leading to heart failure. However, Lig3 inactivation did not result in nuclear DNA repair deficiency, indicating essential DNA repair functions of Xrcc1 can occur in the absence of Lig3. Instead, we found that Lig1 was critical for DNA repair, but acted in a cooperative manner with Lig3. Additionally, Lig3 deficiency did not recapitulate the hallmark features of neural Xrcc1 inactivation such as DNA damage-induced cerebellar interneuron loss6, further underscoring functional separation of these DNA repair factors. Therefore, our data reveal that the critical biological role of Lig3 is to maintain mtDNA integrity and not Xrcc1-dependent DNA repair.

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Figure 1: Lig3 inactivation throughout the nervous system leads to a phenotype different to Xrcc1 loss.
Figure 2: Mitochondrial function is disrupted in the Lig3 Nes-cre brain.
Figure 3: Lig3 inactivation causes cardiac failure associated with defective mitochondrial function.
Figure 4: Lig3 is not essential for nuclear DNA repair.


  1. Ellenberger, T. & Tomkinson, A. E. Eukaryotic DNA ligases: structural and functional insights. Annu. Rev. Biochem. 77, 313–338 (2008)

    Article  CAS  Google Scholar 

  2. Caldecott, K. W., McKeown, C. K., Tucker, J. D., Ljungquist, S. & Thompson, L. H. An interaction between the mammalian DNA repair protein XRCC1 and DNA ligase III. Mol. Cell. Biol. 14, 68–76 (1994)

    Article  CAS  Google Scholar 

  3. Ljungquist, S., Kenne, K., Olsson, L. & Sandstrom, M. Altered DNA ligase III activity in the CHO EM9 mutant. Mutat. Res. 314, 177–186 (1994)

    Article  CAS  Google Scholar 

  4. Lakshmipathy, U. & Campbell, C. Mitochondrial DNA ligase III function is independent of Xrcc1. Nucleic Acids Res. 28, 3880–3886 (2000)

    Article  CAS  Google Scholar 

  5. Puebla-Osorio, N., Lacey, D. B., Alt, F. W. & Zhu, C. Early embryonic lethality due to targeted inactivation of DNA ligase III. Mol. Cell. Biol. 26, 3935–3941 (2006)

    Article  CAS  Google Scholar 

  6. Lee, Y. et al. The genesis of cerebellar interneurons and the prevention of neural DNA damage require XRCC1. Nature Neurosci. 12, 973–980 (2009)

    Article  CAS  Google Scholar 

  7. Almeida, K. H. & Sobol, R. W. A unified view of base excision repair: lesion-dependent protein complexes regulated by post-translational modification. DNA Repair (Amst.) 6, 695–711 (2007)

    Article  CAS  Google Scholar 

  8. Caldecott, K. W. Single-strand break repair and genetic disease. Nature Rev. Genet. 9, 619–631 (2008)

    Article  CAS  Google Scholar 

  9. Wang, H. et al. DNA ligase III as a candidate component of backup pathways of nonhomologous end joining. Cancer Res. 65, 4020–4030 (2005)

    Article  CAS  Google Scholar 

  10. Lakshmipathy, U. & Campbell, C. The human DNA ligase III gene encodes nuclear and mitochondrial proteins. Mol. Cell. Biol. 19, 3869–3876 (1999)

    Article  CAS  Google Scholar 

  11. Lakshmipathy, U. & Campbell, C. Antisense-mediated decrease in DNA ligase III expression results in reduced mitochondrial DNA integrity. Nucleic Acids Res. 29, 668–676 (2001)

    Article  CAS  Google Scholar 

  12. Pinz, K. G. & Bogenhagen, D. F. Efficient repair of abasic sites in DNA by mitochondrial enzymes. Mol. Cell. Biol. 18, 1257–1265 (1998)

    Article  CAS  Google Scholar 

  13. Krishnan, K. J. et al. What causes mitochondrial DNA deletions in human cells? Nature Genet. 40, 275–279 (2008)

    Article  CAS  Google Scholar 

  14. LeDoux, S. P. et al. Repair of mitochondrial DNA after various types of DNA damage in Chinese hamster ovary cells. Carcinogenesis 13, 1967–1973 (1992)

    Article  CAS  Google Scholar 

  15. Liu, P. et al. Removal of oxidative DNA damage via FEN1-dependent long-patch base excision repair in human cell mitochondria. Mol. Cell. Biol. 28, 4975–4987 (2008)

    Article  CAS  Google Scholar 

  16. Tomkinson, A. E., Bonk, R. T. & Linn, S. Mitochondrial endonuclease activities specific for apurinic/apyrimidinic sites in DNA from mouse cells. J. Biol. Chem. 263, 12532–12537 (1988)

    CAS  PubMed  Google Scholar 

  17. Van Houten, B., Woshner, V. & Santos, J. H. Role of mitochondrial DNA in toxic responses to oxidative stress. DNA Repair (Amst.) 5, 145–152 (2006)

    Article  CAS  Google Scholar 

  18. Tyynismaa, H. & Suomalainen, A. Mouse models of mitochondrial DNA defects and their relevance for human disease. EMBO Rep. 10, 137–143 (2009)

    Article  CAS  Google Scholar 

  19. Wallace, D. C. & Fan, W. The pathophysiology of mitochondrial disease as modeled in the mouse. Genes Dev. 23, 1714–1736 (2009)

    Article  CAS  Google Scholar 

  20. Trifunovic, A. et al. Premature ageing in mice expressing defective mitochondrial DNA polymerase. Nature 429, 417–423 (2004)

    Article  ADS  CAS  Google Scholar 

  21. Wallace, D. C., Fan, W. & Procaccio, V. Mitochondrial energetics and therapeutics. Annu. Rev. Pathol. 5, 297–348 (2010)

    Article  CAS  Google Scholar 

  22. DiMauro, S. & Schon, E. A. Mitochondrial disorders in the nervous system. Annu. Rev. Neurosci. 31, 91–123 (2008)

    Article  CAS  Google Scholar 

  23. Chan, D. C. Mitochondrial dynamics in disease. N. Engl. J. Med. 356, 1707–1709 (2007)

    Article  ADS  CAS  Google Scholar 

  24. Chan, S. S. & Copeland, W. C. DNA polymerase gamma and mitochondrial disease: understanding the consequence of POLG mutations. Biochim. Biophys. Acta 1787, 312–319 (2009)

    Article  CAS  Google Scholar 

  25. Moser, J. et al. Sealing of chromosomal DNA nicks during nucleotide excision repair requires XRCC1 and DNA ligase IIIα in a cell-cycle-specific manner. Mol. Cell 27, 311–323 (2007)

    Article  CAS  Google Scholar 

  26. Reynolds, J. J. et al. Defective DNA ligation during short-patch single-strand break repair in ataxia oculomotor apraxia 1. Mol. Cell. Biol. 29, 1354–1362 (2009)

    Article  CAS  Google Scholar 

  27. Bentley, D. J. et al. DNA ligase I null mouse cells show normal DNA repair activity but altered DNA replication and reduced genome stability. J. Cell Sci. 115, 1551–1561 (2002)

    CAS  PubMed  Google Scholar 

  28. Sleeth, K. M., Robson, R. L. & Dianov, G. L. Exchangeability of mammalian DNA ligases between base excision repair pathways. Biochemistry 43, 12924–12930 (2004)

    Article  CAS  Google Scholar 

  29. Wang, J. et al. Dilated cardiomyopathy and atrioventricular conduction blocks induced by heart-specific inactivation of mitochondrial DNA gene expression. Nature Genet. 21, 133–137 (1999)

    Article  CAS  Google Scholar 

  30. Nakai, A. et al. Developmental changes in mitochondrial activity and energy metabolism in fetal and neonatal rat brain. Brain Res. Dev. Brain Res. 121, 67–72 (2000)

    Article  CAS  Google Scholar 

  31. Simsek, D. et al. Crucial role for DNA ligase III in mitochondria but not in Xrcc1-dependent repair. Nature 10.1038/nature09794 (this issue)

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We thank the Hartwell Center for biotechnology support, the Transgenic Core Facility for blastocyst injections and the Animal Resources Center for animal husbandry. We also acknowledge the Light Microscopy Core, the Electron Microscopy Core and C. Calabrese and the Animal Imaging Core for magnetic resonance imaging and echocardiography analysis. P.J.M. is supported by the National Institutes of Health (NS-37956, CA-21765), a Cancer Center Support Grant (P30 CA21765) and the American Lebanese and Syrian Associated Charities of St Jude Children’s Research Hospital. S.K. is a Neoma Boadway AP Endowed Fellow.

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Authors and Affiliations



Y.G., S.K. and Y.L. performed all experiments characterizing the Lig3-deficient mouse and contributed to writing the manuscript. Y.G. and H.R.R. generated the targeted embryonic stem cells for blastocyst injection and were responsible for colony production and maintenance with assistance from S.K. and Y.L. S.K. and J.Z. established the functional analyses of ligases. J.E.R. provided pathology analysis. P.J.M. was project leader and produced the final version of the manuscript.

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Correspondence to Peter J. McKinnon.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Figures

The file contains Supplementary Figures 1-8 with legends. (PDF 9838 kb)

Supplementary Movie 1

This movie shows three Lig3Nes-cre mice at twelve days of age (P12) that have developed profound ataxia, compared with a wild-type littermate. (MOV 15516 kb)

Supplementary Movie 2

This movie shows loss of Lig3 affects mitochondrial function, using Mitotracker Red staining of astrocytes isolated from the Lig3Nes-cre brain by live-cell confocal imaging. While control astrocytes show a pattern of streaming mitochondria, the Lig3 mutant cells show altered mitochondrial dynamics with a static and pulsating appearance. (MOV 7322 kb)

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Gao, Y., Katyal, S., Lee, Y. et al. DNA ligase III is critical for mtDNA integrity but not Xrcc1-mediated nuclear DNA repair. Nature 471, 240–244 (2011).

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