DNA Ligase IV Supports Imprecise End Joining Independently of Its Catalytic Activity

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DNA ligase IV (Dnl4 in budding yeast) is a specialized ligase used in non-homologous end joining (NHEJ) of DNA double-strand breaks (DSBs). Although point and truncation mutations arise in the human ligase IV syndrome, the roles of Dnl4 in DSB repair have mainly been examined using gene deletions. Here, Dnl4 catalytic point mutants were generated that were severely defective in auto-adenylation in vitro and NHEJ activity in vivo, despite being hyper-recruited to DSBs and supporting wild-type levels of Lif1 interaction and assembly of a Ku- and Lif1-containing complex at DSBs. Interestingly, residual levels of especially imprecise NHEJ were markedly higher in a deletion-based assay with Dnl4 catalytic mutants than with a gene deletion strain, suggesting a role of DSB-bound Dnl4 in supporting a mode of NHEJ catalyzed by a different ligase. Similarly, next generation sequencing of repair joints in a distinct single-DSB assay showed that dnl4-K466A mutation conferred a significantly different imprecise joining profile than wild-type Dnl4 and that such repair was rarely observed in the absence of Dnl4. Enrichment of DNA ligase I (Cdc9 in yeast) at DSBs was observed in wild-type as well as dnl4 point mutant strains, with both Dnl4 and Cdc9 disappearing from DSBs upon 5′ resection that was unimpeded by the presence of catalytically inactive Dnl4. These findings indicate that Dnl4 can promote mutagenic end joining independently of its catalytic activity, likely by a mechanism that involves Cdc9.

Vyšlo v časopise: DNA Ligase IV Supports Imprecise End Joining Independently of Its Catalytic Activity. PLoS Genet 9(6): e32767. doi:10.1371/journal.pgen.1003599
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1003599

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Zdroje

1. LieberMR (2010) The mechanism of double-strand DNA break repair by the nonhomologous DNA end-joining pathway. Annu Rev Biochem 79: 181–211.

2. ChiruvellaKK, LiangZ, WilsonTE (2013) Repair of double strand breaks by end-joining. Cold Spring Harb Perspect Biol 5(5): a012757.

3. DaleyJM, PalmbosPL, WuD, WilsonTE (2005) Nonhomologous end joining in yeast. Annu Rev Genet 39: 431–451.

4. EllenbergerT, TomkinsonAE (2008) Eukaryotic DNA ligases: structural and functional insights. Annu Rev Biochem 77: 313–338.

5. PascalJM, O'BrienPJ, TomkinsonAE, EllenbergerT (2004) Human DNA ligase I completely encircles and partially unwinds nicked DNA. Nature 432: 473–478.

6. PascalJM, TsodikovOV, HuraGL, SongW, CotnerEA, et al. (2006) A flexible interface between DNA ligase and PCNA supports conformational switching and efficient ligation of DNA. Mol Cell 24: 279–291.

7. MaY, LuH, TippinB, GoodmanMF, ShimazakiN, et al. (2004) A biochemically defined system for mammalian nonhomologous DNA end joining. Mol Cell 16: 701–713.

8. RiballoE, WoodbineL, StiffT, WalkerSA, GoodarziAA, et al. (2009) XLF-Cernunnos promotes DNA ligase IV-XRCC4 re-adenylation following ligation. Nucleic Acids Res 37: 482–492.

9. IraG, PellicioliA, BalijjaA, WangX, FioraniS, et al. (2004) DNA end resection, homologous recombination and DNA damage checkpoint activation require CDK1. Nature 431: 1011–1017.

10. SymingtonLS, GautierJ (2011) Double-strand break end resection and repair pathway choice. Annu Rev Genet 45: 247–71.

11. ZhangY, HefferinML, ChenL, ShimEY, TsengHM, et al. (2007) Role of Dnl4-Lif1 in nonhomologous end-joining repair complex assembly and suppression of homologous recombination. Nat Struct Mol Biol 14: 639–646.

12. ClericiM, MantieroD, GueriniI, LucchiniG, LongheseMP (2008) The Yku70-Yku80 complex contributes to regulate double-strand break processing and checkpoint activation during the cell cycle. EMBO Rep 9: 810–818.

13. MladenovE, IliakisG (2011) Induction and repair of DNA double strand breaks: the increasing spectrum of non-homologous end joining pathways. Mutat Res 711: 61–72.

14. SimsekD, BrunetE, WongSY, KatyalS, GaoY, et al. (2011) DNA ligase III promotes alternative nonhomologous end-joining during chromosomal translocation formation. PLoS Genet 7: e1002080.

15. Della-MariaJ, ZhouY, TsaiMS, KuhnleinJ, CarneyJ, et al. (2011) hMre11/hRad50/Nbs1 and DNA ligase IIIα/XRCC1 act together in an alternative non-homologous end joining pathway. J Biol Chem 286: 33845–33853.

16. BoboilaC, OksenychV, GostissaM, WangJH, ZhaS, et al. (2012) Robust chromosomal DNA repair via alternative end-joining in the absence of X-ray repair cross-complementing protein 1 (XRCC1). Proc Natl Acad Sci USA 109: 2473–2478.

17. O'DriscollM, CerosalettiKM, GirardPM, DaiY, StummM, et al. (2001) DNA ligase IV mutations identified in patients exhibiting developmental delay and immunodeficiency. Mol Cell 8: 1175–1185.

18. ChistiakovDA (2010) Ligase IV syndrome. Adv Exp Med Biol 685: 175–185.

19. RucciF, NotarangeloLD, FazeliA, PatriziL, HickernellT, et al. (2010) Homozygous DNA ligase IV R278H mutation in mice leads to leaky SCID and represents a model for human LIG4 syndrome. Proc Natl Acad Sci USA 107: 3024–3029.

20. SriskandaV, ShumanS (1998) Mutational analysis of Chlorella virus DNA ligase: catalytic roles of domain I and motif VI. Nucleic Acids Res 26: 4618–4625.

21. SriskandaV, ShumanS (2002) Role of nucleotidyltransferase motifs I, III and IV in the catalysis of phosphodiester bond formation by Chlorella virus DNA ligase. Nucleic Acids Res 30: 903–911.

22. NairPA, NandakumarJ, SmithP, OdellM, LimaCD, et al. (2007) Structural basis for nick recognition by a minimal pluripotent DNA ligase. Nat Struct Mol Biol 14: 770–778.

23. DoreAS, FurnhamN, DaviesOR, SibandaBL, ChirgadzeDY, et al. (2006) Structure of an Xrcc4-DNA ligase IV yeast ortholog complex reveals a novel BRCT interaction mode. DNA Repair (Amst) 5: 362–368.

24. DaleyJM, LaanRL, SureshA, WilsonTE (2005) DNA joint dependence of pol X family polymerase action in nonhomologous end joining. J Biol Chem 280: 29030–29037.

25. WilsonTE, GrawunderU, LieberMR (1997) Yeast DNA ligase IV mediates non-homologous DNA end joining. Nature 388: 495–498.

26. KarathanasisE, WilsonTE (2002) Enhancement of Saccharomyces cerevisiae end-joining efficiency by cell growth stage but not by impairment of recombination. Genetics 161: 1015–1027.

27. WuD, TopperLM, WilsonTE (2008) Recruitment and dissociation of nonhomologous end joining proteins at a DNA double-strand break in Saccharomyces cerevisiae. Genetics 178: 1237–1249.

28. PalmbosPL, WuD, DaleyJM, WilsonTE (2008) Recruitment of Saccharomyces cerevisiae Dnl4-Lif1 complex to a double-strand break requires interactions with Yku80 and the Xrs2 FHA domain. Genetics 180: 1809–1819.

29. PalmbosPL, DaleyJM, WilsonTE (2005) Mutations of the Yku80 C terminus and Xrs2 FHA domain specifically block yeast nonhomologous end joining. Mol Cell Biol 25: 10782–10790.

30. WilsonTE (2002) A genomics-based screen for yeast mutants with an altered recombination/end-joining repair ratio. Genetics 162: 677–688.

31. AndersS, HuberW (2010) Differential expression analysis for sequence count data. Genome Biol 11: R106.

32. ShimEY, HongSJ, OumJH, YanezY, ZhangY, et al. (2007) RSC mobilizes nucleosomes to improve accessibility of repair machinery to the damaged chromatin. Mol and Cell Biol 27: 1602–1613.

33. MaJL, KimEM, HaberJE, LeeSE (2003) Yeast Mre11 and Rad1 proteins define a Ku-independent mechanism to repair double-strand breaks lacking overlapping end sequences. Mol Cell Biol 23: 8820–8828.

34. ChiruvellaKK, SebastianR, SharmaS, KarandeAA, ChoudharyB, et al. (2012) Time-dependent predominance of nonhomologous DNA end-joining pathways during embryonic development in mice. J Mol Biol 417: 197–211.

35. RiballoE, DohertyAJ, DaiY, StiffT, OettingerMA, et al. (2001) Cellular and biochemical impact of a mutation in DNA ligase IV conferring clinical radiosensitivity. J Biol Chem 276: 31124–31132.

36. GirardPM, KyselaB, HarerCJ, DohertyAJ, JeggoPA (2004) Analysis of DNA ligase IV mutations found in LIG4 syndrome patients: the impact of two linked polymorphisms. Hum Mol Genet 13: 2369–2376.

37. DaleyJM, WilsonTE (2005) Rejoining of DNA double-strand breaks as a function of overhang length. Mol Cell Biol 25: 896–906.

38. GrobP, ZhangTT, HannahR, YangH, HefferinML, et al. (2012) Electron microscopy visualization of DNA-protein complexes formed by Ku and DNA ligase IV. DNA repair 11: 74–81.

39. CottarelJ, FritP, BombardeO, SallesB, NegrelA, et al. (2013) A noncatalytic function of the ligation complex during nonhomologous end joining. J Cell Biol 200: 173–186.

40. MahaneyBL, HammelM, MeekK, TainerJA, Lees-MillerSP (2013) XRCC4 and XLF form long helical protein filaments suitable for DNA end protection and alignment to facilitate DNA double strand break repair. Biochem Cell Biol 91: 31–41.

41. HammelM, YuY, FangS, Lees-MillerSP, TainerJA (2010) XLF regulates filament architecture of the XRCC4.ligase IV complex. Structure 18: 1431–1442.

42. ShibataA, ConradS, BirrauxJ, GeutingV, BartonO, et al. (2011) Factors determining DNA double-strand break repair pathway choice in G2 phase. EMBO J 30: 1079–1092.

43. OermannEK, WuJ, GuanKL, XiongY (2012) Alterations of metabolic genes and metabolites in cancer. Sem Cell Dev Biol 23: 370–380.

44. BindraRS, GogliaAG, JasinM, PowellSN (2013) Development of an assay to measure mutagenic non-homologous end-joining repair activity in mammalian cells. Nucl Acids Res doi:10.1093. Epub ahead of print

45. SrivastavaM, NambiarM, SharmaS, KarkiSS, GoldsmithG, et al. (2012) An inhibitor of nonhomologous end-joining abrogates double-strand break repair and impedes cancer progression. Cell 151: 1474–1487.

46. BrachmannCB, DaviesA, CostGJ, CaputoE, LiJ, et al. (1998) Designer deletion strains derived from Saccharomyces cerevisiae S288C: a useful set of strains and plasmids for PCR-mediated gene disruption and other applications. Yeast 14: 115–132.

47. UetzP, GiotL, CagneyG, MansfieldTA, JudsonRS, et al. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403: 623–627.

48. LangmeadB, TrapnellC, PopM, SalzbergSL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25.

49. YatesJR, EngJK, McCormackAL, SchieltzD (1995) Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database. Anal Chem 67: 1426–1436.

50. MooreJK, HaberJE (1996) Cell cycle and genetic requirements of two pathways of nonhomologous end-joining repair of double-strand breaks in Saccharomyces cerevisiae. Mol Cell Biol 16: 2164–2173.