Blunt-ended DNA double-strand breaks induced by endonucleases PvuII and EcoRV are poor substrates for repair in Saccharomyces cerevisiae

DNA Repair

Volumn 9, Issue 6, 2010, Pages 617-626

  Westmoreland, James W ^b   Summers, Jennifer A ^a   Holland, Cory L ^a   Resnick, Michael A ^b   Lewis, L Kevin ^a  

^a Texas State University San Marcos   (United States)

^b NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES   (United States)

Author keywords

DNA repair; Double strand break; End joining; Endonuclease; Homologous recombination

Indexed keywords

BETA GALACTOSIDASE; DOUBLE STRANDED DNA; PROTEIN RAD9; RAD52 PROTEIN; SINGLE STRANDED DNA; TYPE II SITE SPECIFIC DEOXYRIBONUCLEASE; CAGCTG-SPECIFIC TYPE II DEOXYRIBONUCLEASES; FUNGAL DNA; GATATC-SPECIFIC TYPE II DEOXYRIBONUCLEASES;

ARTICLE; CELL CYCLE ARREST; CELL CYCLE G2 PHASE; CELL CYCLE M PHASE; CELL KILLING; CHROMOSOME 12; CHROMOSOME DELETION; CONTROLLED STUDY; DIPLOIDY; DNA REPAIR; DNA STRAND BREAKAGE; ENZYME ACTIVITY; ENZYME SUBSTRATE; GENETIC RECOMBINATION; GROWTH INHIBITION; HAPLOIDY; HOMOLOGOUS RECOMBINATION; IN VIVO STUDY; IONIZING RADIATION; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN EXPRESSION; PULSED FIELD GEL ELECTROPHORESIS; SACCHAROMYCES CEREVISIAE; SENSITIVITY ANALYSIS; WILD TYPE; YEAST CELL; CELL SURVIVAL; CYTOLOGY; DNA FRAGMENTATION; DOUBLE STRANDED DNA BREAK; ENZYME SPECIFICITY; GENE EXPRESSION; GENETICS; METABOLISM;

CELL SURVIVAL; DEOXYRIBONUCLEASES, TYPE II SITE-SPECIFIC; DIPLOIDY; DNA BREAKS, DOUBLE-STRANDED; DNA FRAGMENTATION; DNA REPAIR; DNA, FUNGAL; GENE EXPRESSION; HAPLOIDY; SACCHAROMYCES CEREVISIAE; SUBSTRATE SPECIFICITY;

SACCHAROMYCES CEREVISIAE;

EID: 77952582707     PISSN: 15687864     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.dnarep.2010.02.008     Document Type: Article

References (52)

1. Obe G., Johannes C., and Schulte-Frohlinde D. DNA double-strand breaks induced by sparsely ionizing radiation and endonucleases as critical lesions for cell death, chromosomal aberrations, mutations and oncogenic transformation. Mutagenesis 7 (1992) 3-12
2. Branzei D., and Foiani M. Interplay of replication checkpoints and repair proteins at stalled replication forks. DNA Repair (Amst.) 6 (2007) 994-1003
3. Shikazono N., Noguchi M., Fujii K., Urushibara A., and Yokoya A. The yield, processing, and biological consequences of clustered DNA damage induced by ionizing radiation. J. Radiat. Res. (Tokyo) 50 (2009) 27-36
4. Krogh B.O., and Symington L.S. Recombination proteins in yeast. Annu. Rev. Genet. 38 (2004) 233-271
5. Li X., and Heyer W.D. Homologous recombination in DNA repair and DNA damage tolerance. Cell Res. 18 (2008) 99-113
6. San Filippo J., Sung P., and Klein H. Mechanism of eukaryotic homologous recombination. Annu. Rev. Biochem. 77 (2008) 229-257
7. Shrivastav M., De Haro L.P., and Nickoloff J.A. Regulation of DNA double-strand break repair pathway choice. Cell Res. 18 (2008) 134-147
8. Zhu Z., Chung W.H., Shim E.Y., Lee S.E., and Ira G. Sgs1 helicase and two nucleases Dna2 and Exo1 resect DNA double-strand break ends. Cell 134 (2008) 981-994
9. Mimitou E.P., and Symington L.S. Sae2, Exo1 and Sgs1 collaborate in DNA double-strand break processing. Nature 455 (2008) 770-774
10. Ira G., Pellicioli A., Balijja A., Wang X., Fiorani S., Carotenuto W., Liberi G., Bressan D., Wan L., Hollingsworth N.M., Haber J.E., and Foiani M. DNA end resection, homologous recombination and DNA damage checkpoint activation require CDK1. Nature 431 (2004) 1011-1017
11. Lewis L.K., Karthikeyan G., Cassiano J., and Resnick M.A. Reduction of nucleosome assembly during new DNA synthesis impairs both major pathways of double-strand break repair. Nucleic Acids Res. 33 (2005) 4928-4939
12. Sonoda E., Hochegger H., Saberi A., Taniguchi Y., and Takeda S. Differential usage of non-homologous end-joining and homologous recombination in double strand break repair. DNA Repair (Amst.) 5 (2006) 1021-1029
13. Wyman C., and Kanaar R. DNA double-strand break repair: all's well that ends well. Annu. Rev. Genet. 40 (2006) 363-383
14. Shim E.Y., Hong S.J., Oum J.H., Yanez Y., Zhang Y., and Lee S.E. RSC mobilizes nucleosomes to improve accessibility of repair machinery to the damaged chromatin. Mol. Cell Biol. 27 (2007) 1602-1613
15. Daley J.M., Palmbos P.L., Wu D., and Wilson T.E. Nonhomologous end joining in yeast. Annu. Rev. Genet. 39 (2005) 431-451
16. Hefferin M.L., and Tomkinson A.E. Mechanism of DNA double-strand break repair by non-homologous end joining. DNA Repair 4 (2005) 639-648
17. Rogers-Bald M., Sargent R.G., and Bryant P.E. Production of chromatid breaks by a single DSB: evidence supporting the signal model. Int. J. Radiat. Biol. 76 (2000) 23-29
18. Johannes C., Horstmann M., Durante M., Chudoba I., and Obe G. Chromosome intrachanges and interchanges detected by multicolor banding in lymphocytes: searching for clastogen signatures in the human genome. Radiat. Res. 161 (2004) 540-548
19. Bryant P.E. Use of restriction endonucleases to study relationships between DNA double-strand breaks, chromosomal aberrations and other end-points in mammalian cells. Int. J. Radiat. Biol. 54 (1988) 869-890
20. Costa N.D., and Bryant P.E. Differences in accumulation of blunt- and cohesive-ended double-strand breaks generated by restriction endonucleases in electroporated CHO cells. Mutat. Res. 254 (1991) 239-246
21. Venditti S., and Camilloni G. In vivo analysis of chromatin following nystatin-mediated import of active enzymes into Saccharomyces cerevisiae. Mol. Genet. Genom. 242 (1994) 100-104
22. Lewis L.K., Westmoreland J.W., and Resnick M.A. Repair of endonuclease-induced double-strand breaks in Saccharomyces cerevisiae: essential role for genes associated with nonhomologous end-joining. Genetics 152 (1999) 1513-1529
23. Mills K.D., Sinclair D.A., and Guarente L. MEC1-dependent redistribution of the Sir3 silencing protein from telomeres to DNA double-strand breaks. Cell 97 (1999) 609-620
24. Schär P., Fäsi M., and Jessberger R. SMC1 coordinates DNA double-strand break repair pathways. Nucleic Acids Res. 32 (2004) 3921-3929
25. Yamana Y., Maeda T., Ohba H., Usui T., Ogawa H.I., and Kusano K. Regulation of homologous integration in yeast by the DNA repair proteins Ku70 and RecQ. Mol. Genet. Genom. 273 (2005) 167-176
26. Grenon M., Magill C.P., Lowndes N.F., and Jackson S.P. Double-strand breaks trigger MRX- and Mec1-dependent, but Tel1-independent, checkpoint activation. FEMS Yeast Res. 6 (2006) 836-847
27. Lewis L.K., Lobachev K., Westmoreland J.W., Karthikeyan G., Williamson K.M., Jordan J.J., and Resnick M.A. Use of a restriction endonuclease cytotoxicity assay to identify inducible GAL1 promoter variants with reduced basal activity. Gene 363 (2005) 183-192
28. Sugawara N., and Haber J.E. Repair of DNA double strand breaks: in vivo biochemistry. Methods Enzymol. 408 (2006) 416-429
29. Signon L., Malkova A., Naylor M.L., Klein H., and Haber J.E. Genetic requirements for RAD51- and RAD54-independent break-induced replication repair of a chromosomal double-strand break. Mol. Cell Biol. 21 (2001) 2048-2056
30. Hovland P., Flick J., Johnston M., and Sclafani R.A. Galactose as a gratuitous inducer of GAL gene expression in yeasts growing on glucose. Gene 83 (1989) 57-64
31. Blumenthal R.M., Gregory S.A., and Cooperider J.S. Cloning of a restriction-modification system from Proteus vulgaris and its use in analyzing a methylase-sensitive phenotype in Escherichia coli. J. Bacteriol. 164 (1985) 501-509
32. Gietz R.D., and Woods R.A. Transformation of yeast by lithium acetate/single-stranded carrier DNA/polyethylene glycol method. Methods Enzymol. 350 (2002) 87-96
33. Lewis L.K., Kirchner J.M., and Resnick M.A. Requirement for end-joining and checkpoint functions, but not RAD52-mediated recombination, after EcoRI endonuclease cleavage of Saccharomyces cerevisiae DNA. Mol. Cell Biol. 18 (1998) 1891-1902
34. Toh G.W., and Lowndes N.F. Role of the Saccharomyces cerevisiae Rad9 protein in sensing and responding to DNA damage. Biochem. Soc. Trans. 31 Pt 1 (2003) 242-246
35. Harrison J.C., and Haber J.E. Surviving the breakup: the DNA damage checkpoint. Annu. Rev. Genet. 40 (2006) 209-235
36. Kim Y.H., Ishikawa D., Ha H.P., Sugiyama M., Kaneko Y., and Harashima S. Chromosome XII context is important for rDNA function in yeast. Nucleic Acids Res. 34 (2006) 2914-2924
37. Winckler K., Bach B., and Obe G. Survival of Saccharomyces cerevisiae after treatment with the restriction endonuclease Alu I. Int. J. Radiat. Biol. 54 (1988) 563-566
38. Boulton S.J., and Jackson S.P. Saccharomyces cerevisiae Ku70 potentiates illegitimate DNA double-strand break repair and serves as a barrier to error-prone DNA repair pathways. EMBO J. 15 (1996) 5093-5103
39. Boulton S.J., and Jackson S.P. Identification of a Saccharomyces cerevisiae Ku80 homologue: roles in DNA double strand break rejoining and in telomeric maintenance. Nucleic Acids Res. 24 (1996) 4639-4648
40. Tsukamoto Y., Kato J., and Ikeda H. Silencing factors participate in DNA repair and recombination in Saccharomyces cerevisiae. Nature 388 (1997) 900-903
41. Herrmann G., Lindahl T., and Schär P. Saccharomyces cerevisiae LIF1: a function involved in DNA double-strand break repair related to mammalian XRCC4. EMBO J. 17 (1998) 4188-4198
42. Daley J.M., and Wilson T.E. Rejoining of DNA double-strand breaks as a function of overhang length. Mol. Cell Biol. 25 (2005) 896-906
43. Ganesh A., North P., and Thacker J. Repair and misrepair of site-specific DNA double-strand breaks by human cell extracts. Mutat. Res. 299 (1993) 251-259
44. de Jager M., Dronkert M.L., Modesti M., Beerens C.E., Kanaar R., and van Gent D.C. DNA-binding and strand-annealing activities of human Mre11: implications for its roles in DNA double-strand break repair pathways. Nucleic Acids Res. 29 (2001) 1317-1325
45. Fisher T.S., and Zakian V.A. Ku: a multifunctional protein involved in telomere maintenance. DNA Repair (Amst.) 4 (2005) 1215-1226
46. Boulé J.B., and Zakian V.A. Roles of Pif1-like helicases in the maintenance of genomic stability. Nucleic Acids Res. 34 (2006) 4147-4153
47. Wu Y., Siino J.S., Sugiyama T., and Kowalczykowski S.C. The DNA binding preference of RAD52 and RAD59 proteins: implications for RAD52 and RAD59 protein function in homologous recombination. J. Biol. Chem. 281 (2006) 40001-40009
48. Pingoud A., Fuxreiter M., Pingoud V., and Wende W. Type II restriction endonucleases: structure and mechanism. Cell Mol. Life Sci. 62 (2005) 685-707
49. Gros L., and Saparbaev M.K. Enzymology of the repair of free radicals-induced DNA damage. Oncogene 21 (2002) 8905-8925
50. Karumbati A.S., Deshpande R.A., Jilani A., Vance J.R., Ramotar D., and Wilson T.E. The role of yeast DNA 3′-phosphatase Tpp1 and Rad1/Rad10 endonuclease in processing spontaneous and induced base lesions. J. Biol. Chem. 278 (2003) 31434-31443
51. Argueso J.L., Westmoreland J., Mieczkowski P.A., Gawel M., Petes T.D., and Resnick M.A. Double-strand breaks associated with repetitive DNA can reshape the genome. Proc. Natl. Acad. Sci. U.S.A. 105 (2008) 11845-11850
52. Westmoreland J., Ma W., Yan Y., Van Hulle K., Malkova A., and Resnick M.A. RAD50 is required for efficient initiation of resection and recombinational repair at random, gamma-induced double-strand break ends. PLoS Genet. 5 9 (2009) e1000656