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A human 5′-tyrosyl DNA phosphodiesterase that repairs topoisomerase-mediated DNA damage


Topoisomerases regulate DNA topology and are fundamental to many aspects of chromosome metabolism1,2. Their activity involves the transient cleavage of DNA, which, if it occurs near sites of endogenous DNA damage or in the presence of topoisomerase poisons, can result in abortive topoisomerase-induced DNA strand breaks3,4,5. These breaks feature covalent linkage of the enzyme to the DNA termini by a 3′- or 5′-phosphotyrosyl bond and are implicated in hereditary human disease6,7,8, chromosomal instability and cancer4,9, and underlie the clinical efficacy of an important class of anti-tumour poisons3,9,10. The importance of liberating DNA termini from trapped topoisomerase is illustrated by the progressive neurodegenerative disease observed in individuals containing a mutation in tyrosyl-DNA phosphodiesterase 1 (TDP1), an enzyme that cleaves 3′-phosphotyrosyl bonds6,7,8. However, a complementary human enzyme that cleaves 5′-phosphotyrosyl bonds has not been reported, despite the effect of DNA double-strand breaks containing such termini on chromosome instability and cancer6,7,8. Here we identify such an enzyme in human cells and show that this activity efficiently restores 5′-phosphate termini at DNA double-strand breaks in preparation for DNA ligation. This enzyme, TTRAP, is a member of the Mg2+/Mn2+-dependent family of phosphodiesterases. Cellular depletion of TTRAP results in increased susceptibility and sensitivity to topoisomerase-II-induced DNA double-strand breaks. TTRAP is, to our knowledge, the first human 5′-tyrosyl DNA phosphodiesterase to be identified, and we suggest that this enzyme is denoted tyrosyl DNA phosphodiesterase-2 (TDP2).

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Figure 1: Human TTRAP suppresses the sensitivity of yeast to Top1-induced DNA damage.
Figure 2: TTRAP possesses 3′- and 5′-tyrosyl DNA phosphodiesterase (TDP) activity.
Figure 3: Reduced 5′-TDP activity in TTRAP-deficient human cell extracts.
Figure 4: TTRAP affects etoposide sensitivity and DNA damage accumulation.


  1. Champoux, J. J. DNA topoisomerases: structure, function, and mechanism. Annu. Rev. Biochem. 70, 369–413 (2001)

    Article  CAS  Google Scholar 

  2. Wang, J. C. Cellular roles of DNA topoisomerases: a molecular perspective. Nature Rev. Mol. Cell Biol. 3, 430–440 (2002)

    Article  CAS  Google Scholar 

  3. Li, T. K. & Liu, L. F. Tumor cell death induced by topoisomerase-targeting drugs. Annu. Rev. Pharmacol. Toxicol. 41, 53–77 (2001)

    Article  Google Scholar 

  4. Deweese, J. E. & Osheroff, N. The DNA cleavage reaction of topoisomerase II: wolf in sheep’s clothing. Nucleic Acids Res. 37, 738–748 (2009)

    Article  CAS  Google Scholar 

  5. Pourquier, P. & Pommier, Y. Topoisomerase I-mediated DNA damage. Adv. Cancer Res. 80, 189–216 (2001)

    Article  CAS  Google Scholar 

  6. El-Khamisy, S. F. et al. Defective DNA single-strand break repair in spinocerebellar ataxia with axonal neuropathy-1. Nature 434, 108–113 (2005)

    Article  ADS  CAS  Google Scholar 

  7. Takashima, H. et al. Mutation of TDP1, encoding a topoisomerase I-dependent DNA damage repair enzyme, in spinocerebellar ataxia with axonal neuropathy. Nature Genet. 32, 267–272 (2002)

    Article  CAS  Google Scholar 

  8. Yang, S. W. et al. A eukaryotic enzyme that can disjoin dead-end covalent complexes between DNA and type I topoisomerases. Proc. Natl Acad. Sci. USA 93, 11534–11539 (1996)

    Article  ADS  CAS  Google Scholar 

  9. Nitiss, J. L. Targeting DNA topoisomerase II in cancer chemotherapy. Nature Rev. Cancer 9, 338–350 (2009)

    Article  CAS  Google Scholar 

  10. Pommier, Y. Topoisomerase I inhibitors: camptothecins and beyond. Nature Rev. Cancer 6, 789–802 (2006)

    Article  CAS  Google Scholar 

  11. Vance, J. R. & Wilson, T. E. Yeast Tdp1 and Rad1-Rad10 function as redundant pathways for repairing Top1 replicative damage. Proc. Natl Acad. Sci. USA 99, 13669–13674 (2002)

    Article  ADS  CAS  Google Scholar 

  12. Liu, C., Pouliot, J. J. & Nash, H. A. Repair of topoisomerase I covalent complexes in the absence of the tyrosyl-DNA phosphodiesterase Tdp1. Proc. Natl Acad. Sci. USA 99, 14970–14975 (2002)

    Article  ADS  CAS  Google Scholar 

  13. Pype, S. et al. TTRAP, a novel protein that associates with CD40, tumor necrosis factor (TNF) receptor-75 and TNF receptor-associated factors (TRAFs), and that inhibits nuclear factor-κB activation. J. Biol. Chem. 275, 18586–18593 (2000)

    Article  CAS  Google Scholar 

  14. Rodrigues-Lima, F., Josephs, M., Katan, M. & Cassinat, B. Sequence analysis identifies TTRAP, a protein that associates with CD40 and TNF receptor-associated factors, as a member of a superfamily of divalent cation-dependent phosphodiesterases. Biochem. Biophys. Res. Commun. 285, 1274–1279 (2001)

    Article  CAS  Google Scholar 

  15. Nitiss, J. L. et al. Amsacrine and etoposide hypersensitivity of yeast cells overexpressing DNA topoisomerase II. Cancer Res. 52, 4467–4472 (1992)

    CAS  PubMed  Google Scholar 

  16. Xu, G. L. et al. TTRAP is a novel PML nuclear bodies-associated protein. Biochem. Biophys. Res. Commun. 375, 395–398 (2008)

    Article  CAS  Google Scholar 

  17. Mielke, C., Christensen, M. O., Barthelmes, H. U. & Boege, F. Enhanced processing of UVA-irradiated DNA by human topoisomerase II in living cells. J. Biol. Chem. 279, 20559–20562 (2004)

    Article  CAS  Google Scholar 

  18. Mielke, C., Kalfalah, F. M., Christensen, M. O. & Boege, F. Rapid and prolonged stalling of human DNA topoisomerase I in UVA-irradiated genomic areas. DNA Repair (Amst.) 6, 1757–1763 (2007)

    Article  CAS  Google Scholar 

  19. Kingma, P. S. & Osheroff, N. The response of eukaryotic topoisomerases to DNA damage. Biochim. Biophys. Acta 1400, 223–232 (1998)

    Article  CAS  Google Scholar 

  20. Connelly, J. C. & Leach, D. R. Repair of DNA covalently linked to protein. Mol. Cell 13, 307–316 (2004)

    Article  CAS  Google Scholar 

  21. Hartsuiker, E., Neale, M. J. & Carr, A. M. Distinct requirements for the Rad32(Mre11) nuclease and Ctp1(CtIP) in the removal of covalently bound topoisomerase I and II from DNA. Mol. Cell 33, 117–123 (2009)

    Article  CAS  Google Scholar 

  22. Pei, H. et al. EAPII interacts with ETS1 and modulates its transcriptional function. Oncogene 22, 2699–2709 (2003)

    Article  CAS  Google Scholar 

  23. Esguerra, C. V. et al. Ttrap is an essential modulator of Smad3-dependent Nodal signaling during zebrafish gastrulation and left-right axis determination. Development 134, 4381–4393 (2007)

    Article  CAS  Google Scholar 

  24. Zucchelli, S. et al. Aggresome-forming TTRAP mediates pro-apoptotic properties of Parkinson’s disease-associated DJ-1 missense mutations. Cell Death Differ. 16, 428–438 (2009)

    Article  CAS  Google Scholar 

  25. Vance, J. R. & Wilson, T. E. Repair of DNA strand breaks by the overlapping functions of lesion-specific and non-lesion-specific DNA 3′ phosphatases. Mol. Cell. Biol. 21, 7191–7198 (2001)

    Article  CAS  Google Scholar 

  26. Nitiss, K. C., Malik, M., He, X., White, S. W. & Nitiss, J. L. Tyrosyl-DNA phosphodiesterase (Tdp1) participates in the repair of Top2-mediated DNA damage. Proc. Natl Acad. Sci. USA 103, 8953–8958 (2006)

    Article  ADS  CAS  Google Scholar 

  27. Whitehouse, C. J. et al. XRCC1 stimulates human polynucleotide kinase activity at damaged DNA termini and accelerates DNA single-strand break repair. Cell 104, 107–117 (2001)

    Article  CAS  Google Scholar 

  28. Parsons, J. L., Dianova, I. I. & Dianov, G. L. APE1 is the major 3′-phosphoglycolate activity in human cell extracts. Nucleic Acids Res. 32, 3531–3536 (2004)

    Article  CAS  Google Scholar 

  29. 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 (2008)

    Article  Google Scholar 

  30. Katyal, S. et al. TDP1 facilitates chromosomal single-strand break repair in neurons and is neuroprotective in vivo . EMBO J. 26, 4720–4731 (2007)

    Article  CAS  Google Scholar 

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This work was funded by the MRC (G0600776), the BBSRC (BB/C516595/1), and CR-UK (C6563/A10192). S.F.E.K. and F.C.L. were also funded by Fellowships from the Wellcome Trust (S.F.E.K.; 085284), Marie Curie (FCL; 2007-2-1-IEF-221222) and EMBO (FCL; ALTF 956-2006). We thank T. Wilson, H. Nash, M. Neale, J. Nitiss and E. Hoffmann for materials.

Author Contributions F.C.L. developed the genetic screen and conducted the mammalian cell experiments. M.C.Z. and F.C.L. conducted the yeast experiments. K.O. and S.F.E.K. prepared the recombinant proteins, and S.F.E.K. conducted the biochemical experiments. K.W.C., F.C.L. and S.F.E.K. designed and interpreted the experiments. K.W.C. coordinated the project and wrote the manuscript.

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Correspondence to Felipe Cortes Ledesma or Keith W. Caldecott.

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Ledesma, F., El Khamisy, S., Zuma, M. et al. A human 5′-tyrosyl DNA phosphodiesterase that repairs topoisomerase-mediated DNA damage. Nature 461, 674–678 (2009).

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