TDP1 promotes assembly of non-homologous end joining protein complexes on DNA

Branzei, 2005, The DNA damage response during DNA replication, Curr. Opin. Cell Biol., 17, 568, 10.1016/j.ceb.2005.09.003 Lieber, 2010, The mechanism of double-strand DNA break repair by the nonhomologous DNA end-joining pathway, Annu. Rev. Biochem., 79, 181, 10.1146/annurev.biochem.052308.093131 Chiruvella, 2013, Repair of double-strand breaks by end joining, Cold Spring Harb. Perspect. Biol., 5, 10.1101/cshperspect.a012757 Mari, 2006, Dynamic assembly of end-joining complexes requires interaction between Ku70/80 and XRCC4, Proc. Natl. Acad. Sci. U. S. A., 103, 18597, 10.1073/pnas.0609061103 Yano, 2008, Ku recruits XLF to DNA double-strand breaks, EMBO Rep., 9, 91, 10.1038/sj.embor.7401137 Yano, 2008, Live cell imaging of XLF and XRCC4 reveals a novel view of protein assembly in the non-homologous end-joining pathway, Cell Cycle, 7, 1321, 10.4161/cc.7.10.5898 Yano, 2011, Functional significance of the interaction with Ku in DNA double-strand break recognition of XLF, FEBS Lett., 585, 841, 10.1016/j.febslet.2011.02.020 Costantini, 2007, Interaction of the Ku heterodimer with the DNA ligase IV/Xrcc4 complex and its regulation by DNA-PK, DNA Repair (Amst.), 6, 712, 10.1016/j.dnarep.2006.12.007 Leber, 1998, The XRCC4 gene product is a target for and interacts with the DNA-dependent protein kinase, J. Biol. Chem., 273, 1794, 10.1074/jbc.273.3.1794 Hsu, 2002, Defining interactions between DNA-PK and ligase IV/XRCC4, DNA Repair (Amst.), 1, 225, 10.1016/S1568-7864(01)00018-0 Pouliot, 1999, Yeast gene for a Tyr-DNA phosphodiesterase that repairs topoisomerase I complexes, Science, 286, 552, 10.1126/science.286.5439.552 Pommier, 2014, Tyrosyl-DNA-phosphodiesterases (TDP1 and TDP2), DNA Repair (Amst.), 19, 114, 10.1016/j.dnarep.2014.03.020 Interthal, 2001, The tyrosyl-DNA phosphodiesterase Tdp1 is a member of the phospholipase D superfamily, Proc. Natl. Acad. Sci. U. S. A., 98, 12009, 10.1073/pnas.211429198 Nitiss, 2006, Tyrosyl-DNA phosphodiesterase (Tdp1) participates in the repair of Top2-mediated DNA damage, Proc. Natl. Acad. Sci. U. S. A., 103, 8953, 10.1073/pnas.0603455103 Alagoz, 2014, TDP1 deficiency sensitizes human cells to base damage via distinct topoisomerase I and PARP mechanisms with potential applications for cancer therapy, Nucleic Acids Res., 42, 3089, 10.1093/nar/gkt1260 Murai, 2012, Tyrosyl-DNA phosphodiesterase 1 (TDP1) repairs DNA damage induced by topoisomerases I and II and base alkylation in vertebrate cells, J. Biol. Chem., 287, 12848, 10.1074/jbc.M111.333963 Inamdar, 2002, Conversion of phosphoglycolate to phosphate termini on 3′ overhangs of DNA double strand breaks by the human tyrosyl-DNA phosphodiesterase hTdp1, J. Biol. Chem., 277, 27162, 10.1074/jbc.M204688200 Zhou, 2009, Tyrosyl-DNA phosphodiesterase and the repair of 3′-phosphoglycolate-terminated DNA double-strand breaks, DNA Repair (Amst.), 8, 901, 10.1016/j.dnarep.2009.05.003 Interthal, 2005, Human Tdp1 cleaves a broad spectrum of substrates, including phosphoamide linkages, J. Biol. Chem., 280, 36518, 10.1074/jbc.M508898200 Huang, 2013, TDP1 repairs nuclear and mitochondrial DNA damage induced by chain-terminating anticancer and antiviral nucleoside analogs, Nucleic Acids Res., 41, 7793, 10.1093/nar/gkt483 Takashima, 2002, Mutation of TDP1, encoding a topoisomerase I-dependent DNA damage repair enzyme, in spinocerebellar ataxia with axonal neuropathy, Nat. Genet., 32, 267, 10.1038/ng987 Das, 2010, Role of tyrosyl-DNA phosphodiesterase (TDP1) in mitochondria, Proc. Natl. Acad. Sci. U. S. A., 107, 19790, 10.1073/pnas.1009814107 Dexheimer, 2010, The DNA binding and 3′-end preferential activity of human tyrosyl-DNA phosphodiesterase, Nucleic Acids Res., 38, 2444, 10.1093/nar/gkp1206 Interthal, 2005, SCAN1 mutant Tdp1 accumulates the enzyme – DNA intermediate and causes camptothecin hypersensitivity, EMBO J., 24, 2224, 10.1038/sj.emboj.7600694 Barthelmes, 2004, TDP1 overexpression in human cells counteracts DNA damage mediated by topoisomerases I and II, J. Biol. Chem., 279, 55618, 10.1074/jbc.M405042200 Zhou, 2005, Deficiency in 3′-phosphoglycolate processing in human cells with a hereditary mutation in tyrosyl-DNA phosphodiesterase (TDP1), Nucleic Acids Res., 33, 289, 10.1093/nar/gki170 Povirk, 2012, Processing of damaged DNA ends for double-strand break repair in mammalian cells, ISRN Mol. Biol., 2012, 1, 10.5402/2012/345805 Das, 2009, Optimal function of the DNA repair enzyme TDP1 requires its phosphorylation by ATM and/or DNA-PK, EMBO J., 28, 3667, 10.1038/emboj.2009.302 Bahmed, 2010, Yeast Tdp1 regulates the fidelity of nonhomologous end joining, Proc. Natl. Acad. Sci. U. S. A., 107, 4057, 10.1073/pnas.0909917107 Hanakahi, 2011, Effect of the inositol polyphosphate InsP(6) on DNA-PK-dependent phosphorylation, Mol. Cancer Res., 9, 1366, 10.1158/1541-7786.MCR-11-0230 Jayaram, 2008, E1B 55k-independent dissociation of the DNA ligase IV/XRCC4 complex by E4 34k during adenovirus infection, Virology, 382, 163, 10.1016/j.virol.2008.08.045 Evan, 1985, Isolation of monoclonal antibodies specific for human c-myc proto-oncogene product, Mol. Cell. Biol., 5, 3610, 10.1128/MCB.5.12.3610 Plo, 2003, Association of XRCC1 and tyrosyl DNA phosphodiesterase (Tdp1) for the repair of topoisomerase I-mediated DNA lesions, DNA Repair (Amst.), 2, 1087, 10.1016/S1568-7864(03)00116-2 Antony, 2007, Novel high-throughput electrochemiluminescent assay for identification of human tyrosyl-DNA phosphodiesterase (Tdp1) inhibitors and characterization of furamidine (NSC 305831) as an inhibitor of Tdp1, Nucleic Acids Res., 35, 4474, 10.1093/nar/gkm463 Akopiants, 2009, Requirement for XLF/Cernunnos in alignment-based gap filling by DNA polymerases lambda and mu for nonhomologous end joining in human whole-cell extracts, Nucleic Acids Res., 37, 4055, 10.1093/nar/gkp283 Lai, 1992, Ethidium bromide provides a simple tool for identifying genuine DNA-independent protein associations, Proc. Natl. Acad. Sci. U. S. A., 89, 6958, 10.1073/pnas.89.15.6958 Lechner, 1994, Inhibition of p53 DNA binding by human papillomavirus E6 proteins, J. Virol., 68, 4262, 10.1128/JVI.68.7.4262-4273.1994 Nguyen, 2006, Protein-protein interaction assays: eliminating false positive interactions, Nat. Methods, 3, 135, 10.1038/nmeth0206-135 Interthal, 2011, Effects of DNA and protein size on substrate cleavage by human tyrosyl-DNA phosphodiesterase 1, Biochem. J., 436, 559, 10.1042/BJ20101841 Debethune, 2002, Processing of nucleopeptides mimicking the topoisomerase I-DNA covalent complex by tyrosyl-DNA phosphodiesterase, Nucleic Acids Res., 30, 1198, 10.1093/nar/30.5.1198 Lu, 2007, Length-dependent binding of human XLF to DNA and stimulation of XRCC4.DNA ligase IV activity, J. Biol. Chem., 282, 11155, 10.1074/jbc.M609904200 Malivert, 2010, Delineation of the Xrcc4-interacting region in the globular head domain of cernunnos/XLF, J. Biol. Chem., 285, 26475, 10.1074/jbc.M110.138156 Andres, 2012, A human XRCC4-XLF complex bridges DNA, Nucleic Acids Res., 40, 1868, 10.1093/nar/gks022 Roy, 2012, XRCC4's interaction with XLF is required for coding (but not signal) end joining, Nucleic Acids Res., 40, 1684, 10.1093/nar/gkr1315 Hammel, 2011, XRCC4 protein interactions with XRCC4-like factor (XLF) create an extended grooved scaffold for DNA ligation and double strand break repair, J. Biol. Chem., 286, 32638, 10.1074/jbc.M111.272641 Li, 2008, Crystal structure of human XLF/Cernunnos reveals unexpected differences from XRCC4 with implications for NHEJ, EMBO J., 27, 290, 10.1038/sj.emboj.7601942 Davies, 2002, The crystal structure of human tyrosyl-DNA phosphodiesterase, Tdp1, Structure, 10, 237, 10.1016/S0969-2126(02)00707-4 Hudson, 2012, SUMO modification of the neuroprotective protein TDP1 facilitates chromosomal single-strand break repair, Nat. Commun., 3, 733, 10.1038/ncomms1739 Chiang, 2010, TDP1 serine 81 promotes interaction with DNA ligase IIIalpha and facilitates cell survival following DNA damage, Cell Cycle, 9, 588, 10.4161/cc.9.3.10598 Das, 2014, PARP1-TDP1 coupling for the repair of topoisomerase I-induced DNA damage, Nucleic Acids Res., 42, 4435, 10.1093/nar/gku088 Cui, 2005, Autophosphorylation of DNA-dependent protein kinase regulates DNA end processing and may also alter double-strand break repair pathway choice, Mol. Cell. Biol., 25, 10842, 10.1128/MCB.25.24.10842-10852.2005 Convery, 2005, Inhibition of homologous recombination by variants of the catalytic subunit of the DNA-dependent protein kinase (DNA-PKcs), Proc. Natl. Acad. Sci. U. S. A., 102, 1345, 10.1073/pnas.0406466102 Chan, 1996, The DNA-dependent protein kinase is inactivated by autophosphorylation of the catalytic subunit, J. Biol. Chem., 271, 8936, 10.1074/jbc.271.15.8936 Hammel, 2010, Ku and DNA-dependent protein kinase dynamic conformations and assembly regulate DNA binding and the initial non-homologous end joining complex, J. Biol. Chem., 285, 1414, 10.1074/jbc.M109.065615 Merkle, 2002, The DNA-dependent protein kinase interacts with DNA to form a protein-DNA complex that is disrupted by phosphorylation, Biochemistry, 41, 12706, 10.1021/bi0263558 Dobbs, 2010, A structural model for regulation of NHEJ by DNA-PKcs autophosphorylation, DNA Repair (Amst.), 9, 1307, 10.1016/j.dnarep.2010.09.019 Morris, 2011, Evidence for a remodelling of DNA-PK upon autophosphorylation from electron microscopy studies, Nucleic Acids Res., 39, 5757, 10.1093/nar/gkr146 Daley, 2005, Nonhomologous end joining in yeast, Annu. Rev. Genet., 39, 431, 10.1146/annurev.genet.39.073003.113340 Waters, 2014, Nonhomologous end joining: a good solution for bad ends, DNA Repair (Amst.), 17, 39, 10.1016/j.dnarep.2014.02.008 Betermier, 2014, Is non-homologous end-joining really an inherently error-prone process?, PLoS Genet., 10, e1004086, 10.1371/journal.pgen.1004086 Raymond, 2005, Substrate specificity of tyrosyl-DNA phosphodiesterase I (Tdp1), J. Biol. Chem., 280, 22029, 10.1074/jbc.M502148200 Pouliot, 2001, Pathways for repair of topoisomerase I covalent complexes in Saccharomyces cerevisiae, Genes Cells, 6, 677, 10.1046/j.1365-2443.2001.00452.x Li, 2008, Lymphocyte-specific compensation for XLF/cernunnos end-joining functions in V(D)J recombination, Mol. Cell, 31, 631, 10.1016/j.molcel.2008.07.017 Zha, 2011, ATM damage response and XLF repair factor are functionally redundant in joining DNA breaks, Nature, 469, 250, 10.1038/nature09604 Gapud, 2011, Ataxia telangiectasia mutated (Atm) and DNA-PKcs kinases have overlapping activities during chromosomal signal joint formation, Proc. Natl. Acad. Sci. U. S. A., 108, 2022, 10.1073/pnas.1013295108 Gapud, 2011, Unique and redundant functions of ATM and DNA-PKcs during V(D)J recombination, Cell Cycle, 10, 1928, 10.4161/cc.10.12.16011 Zha, 2011, Ataxia telangiectasia-mutated protein and DNA-dependent protein kinase have complementary V(D)J recombination functions, Proc. Natl. Acad. Sci. U. S. A., 108, 2028, 10.1073/pnas.1019293108 Hawkins, 2009, In vitro complementation of Tdp1 deficiency indicates a stabilized enzyme-DNA adduct from tyrosyl but not glycolate lesions as a consequence of the SCAN1 mutation, DNA Repair, 8, 654, 10.1016/j.dnarep.2008.12.012 Katyal, 2007, TDP1 facilitates chromosomal single-strand break repair in neurons and is neuroprotective in vivo, EMBO J., 26, 4720, 10.1038/sj.emboj.7601869 Ruscetti, 1998, Stimulation of the DNA-dependent protein kinase by poly(ADP-ribose) polymerase, J. Biol. Chem., 273, 14461, 10.1074/jbc.273.23.14461 Spagnolo, 2012, Visualization of a DNA-PK/PARP1 complex, Nucleic Acids Res., 40, 4168, 10.1093/nar/gkr1231 Beck, 2014, Poly(ADP-ribose) polymerases in double-strand break repair: focus on PARP1, PARP2 and PARP3, Exp. Cell Res., 329, 18, 10.1016/j.yexcr.2014.07.003 Schneider, 2012, Terminally differentiated astrocytes lack DNA damage response signaling and are radioresistant but retain DNA repair proficiency, Cell Death Differ., 19, 582, 10.1038/cdd.2011.129 Daley, 2014, 53BP1, BRCA1 and the choice between recombination and end joining at DNA double-strand breaks, Mol. Cell. Biol., 34, 10.1128/MCB.01639-13 Koch, 2004, Xrcc4 physically links DNA end processing by polynucleotide kinase to DNA ligation by DNA ligase IV, EMBO J., 23, 3874, 10.1038/sj.emboj.7600375 Weinfeld, 2011, Tidying up loose ends: the role of polynucleotide kinase/phosphatase in DNA strand break repair, Trends Biochem. Sci., 36, 262, 10.1016/j.tibs.2011.01.006 Mani, 2010, Dual modes of interaction between XRCC4 and polynucleotide kinase/phosphatase: implications for nonhomologous end joining, J. Biol. Chem., 285, 37619, 10.1074/jbc.M109.058719 Pawelczak, 2011, Coordination of DNA-PK activation and nuclease processing of DNA termini in NHEJ, Antioxid. Redox Signal., 14, 2531, 10.1089/ars.2010.3368 Li, 2011, Polynucleotide kinase and aprataxin-like forkhead-associated protein (PALF) acts as both a single-stranded DNA endonuclease and a single-stranded DNA 3′ exonuclease and can participate in DNA end joining in a biochemical system, J. Biol. Chem., 286, 36368, 10.1074/jbc.M111.287797 Mohapatra, 2013, Trimming of damaged 3′ overhangs of DNA double-strand breaks by the Metnase and Artemis endonucleases, DNA Repair (Amst.), 12, 422, 10.1016/j.dnarep.2013.03.005 Roberts, 2010, Ku is a 5′-dRP/AP lyase that excises nucleotide damage near broken ends, Nature, 464, 1214, 10.1038/nature08926