Replication restart: A pathway for (CTG)·(CAG) repeat deletion in Escherichia coli

Mutation Research - Fundamental and Molecular Mechanisms of Mutagenesis

Volumn 595, Issue 1-2, 2006, Pages 5-22

  Kim, Seung Hwan ^a   Pytlos, Małgorzata J ^a   Sinden, Richard R ^a  

^a TEXAS A AND M HEALTH SCIENCE CENTER   (United States)

Author keywords

DNA secondary structure; Genome instability; Repeat deletion; Repeat instability; Replication restart; Triplet repeats

Indexed keywords

BACTERIAL PROTEIN; PROTEIN PRIA; PROTEIN RECG; PROTEIN RECO; PROTEIN RUVAB; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL STRAIN; CONTROLLED STUDY; DNA REPLICATION; DNA REPLICATION ORIGIN; DNA STRAND; DNA STRUCTURE; DNA TEMPLATE; ESCHERICHIA COLI; GENE DELETION; GENE EXPRESSION; MUTATION; NONHUMAN; PRIORITY JOURNAL; WILD TYPE;

ADENOSINE TRIPHOSPHATASES; BASE SEQUENCE; DNA HELICASES; DNA REPLICATION; DNA, BACTERIAL; DNA-BINDING PROTEINS; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; MUTATION; NUCLEIC ACID CONFORMATION; PROTEIN BINDING; SEQUENCE DELETION; SUBSTRATE SPECIFICITY; TRINUCLEOTIDE REPEAT EXPANSION;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 33244486739     PISSN: 00275107     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mrfmmm.2005.07.010     Document Type: Article

References (73)

1. J.D. Cleary, and C.E. Pearson The contribution of CIS-elements to disease-associated repeat instability: clinical and experimental evidence Cytogenet. Genome Res. 100 2003 25 55
2. H.Y. Zoghbi, and H.T. Orr Polyglutamine diseases: protein cleavage and aggregation Curr. Opin. Neurobiol. 9 1999 566 570
3. S. Kang, A. Jaworski, K. Ohshima, and R.D. Wells Expansion and deletion of CTG triplet repeats from human disease genes are determined by the direction of replication in E. coli Nat. Genet. 10 1995 213 218
4. J.D. Cleary, K. Nichol, Y.H. Wang, and C.E. Pearson Evidence of cis-acting factors in replication-mediated trinucleotide repeat instability in primate cells Nat. Genet. 31 2002 37 46
5. I.V. Kovtun, and C.T. McMurray Trinucleotide expansion in haploid germ cells by gap repair Nat. Genet. 27 2001 407 411
6. C.H. Freudenreich, J.B. Stavenhagen, and V.A. Zakian Stability of a CTG/CAG trinucleotide repeat in yeast is dependent on its orientation in the genome Mol. Cell Biol. 17 1997 2090 2098
7. C.H. Freudenreich, S.M. Kantrow, and V.A. Zakian Expansion and length-dependent fragility of CTG repeats in yeast Science 279 1998 853 856
8. R.R. Sinden Biological implications of the DNA structures associated with disease-causing triplet repeats Am. J. Hum. Genet. 64 1999 346 353
9. R.R. Sinden, V.N. Potaman, E.A. Oussatcheva, C.E. Pearson, Y.L. Lyubchenko, and L.S. Shlyakhtenko Triplet repeat DNA structures and human genetic disease: dynamic mutations from dynamic DNA J. Biosci. 27 2002 53 65
10. J.P. Jakupciak, and R.D. Wells Genetic instabilities in (CTG)·(CAG) repeats occur by recombination J. Biol. Chem. 274 1999 23468 23479
11. V.I. Hashem, M.J. Pytlos, E.A. Klysik, K. Tsuji, M. Khajavi, T. Ashizawa, and R.R. Sinden Chemotherapeutic deletion of CTG repeats in lymphoblast cells from DM1 patients Nucl. Acids Res. 32 2004 6334 6346
12. V.I. Hashem, and R.R. Sinden Chemotherapeutically induced deletion of expanded triplet repeats Mutat. Res. 508 2002 107 119
13. E. Pineiro, L. Fernandez-Lopez, J. Gamez, R. Marcos, J. Surralles, and A. Velazquez Mutagenic stress modulates the dynamics of CTG repeat instability associated with myotonic dystrophy type 1 Nucl. Acids Res. 31 2003 6733 6740
14. V. Gorbunova, A. Seluanov, V. Dion, Z. Sandor, J.L. Meservy, and J.H. Wilson Selectable system for monitoring the instability of CTG/CAG triplet repeats in mammalian cells Mol. Cell Biol. 23 2003 4485 4493
15. Z. Yang, R. Lau, J.L. Marcadier, D. Chitayat, and C.E. Pearson Replication inhibitors modulate instability of an expanded trinucleotide repeat at the myotonic dystrophy type 1 disease locus in human cells Am. J. Hum. Genet. 73 2003 1092 1105
16. M. Gomes-Pereira, and D.G. Monckton Chemically induced increases and decreases in the rate of expansion of a CAG*CTG triplet repeat Nucl. Acids Res. 32 2004 2865 2872
17. V.I. Hashem, W.A. Rosche, and R.R. Sinden Genetic assays for measuring rates of (CAG)·(CTG) repeat instability in Escherichia coli Mutat. Res. 502 2002 25 37
18. M.J. Ireland, S.S. Reinke, and D.M. Livingston The impact of lagging strand replication mutations on the stability of CAG repeat tracts in yeast Genetics 155 2000 1657 1665
19. J.J. Miret, L. Pessoa-Brandao, and R.S. Lahue Orientation-dependent and sequence-specific expansions of CTG/CAG trinucleotide repeats in Saccharomyces cerevisiae Proc. Natl. Acad. Sci. U.S.A. 95 1998 12438 12443
20. S. Bhattacharyya, and R.S. Lahue Saccharomyces cerevisiae Srs2 DNA helicase selectively blocks expansions of trinucleotide repeats Mol. Cell Biol. 24 2004 7324 7330
21. M.L. Rolfsmeier, M.J. Dixon, L. Pessoa-Brandao, R. Pelletier, J.J. Miret, and R.S. Lahue Cis-elements governing trinucleotide repeat instability in Saccharomyces cerevisiae Genetics 157 2001 1569 1579
22. Y. Liu, H. Zhang, J. Veeraraghavan, R.A. Bambara, and C.H. Freudenreich Saccharomyces cerevisiae flap endonuclease 1 uses flap equilibration to maintain triplet repeat stability Mol. Cell Biol. 24 2004 4049 4064
23. J.K. Schweitzer, and D.M. Livingston Expansions of CAG repeat tracts are frequent in a yeast mutant defective in Okazaki fragment maturation Hum. Mol. Genet. 7 1998 69 74
24. J.K. Schweitzer, and D.M. Livingston The effect of DNA replication mutations on CAG tract stability in yeast Genetics 152 1999 953 963
25. S. Lee, and M.S. Park Human FEN-1 can process the 5′-flap DNA of CTG/CAG triplet repeat derived from human genetic diseases by length and sequence dependent manner Exp. Mol. Med. 34 2002 313 317
26. G.B. Panigrahi, J.D. Cleary, and C.E. Pearson In vitro (CTG)·(CAG) expansions and deletions by human cell extracts J. Biol. Chem. 277 2002 13926 13934
27. J.L. Marcadier, and C.E. Pearson Fidelity of primate cell repair of a double-strand break within a (CTG)·(CAG) tract. Effect of slipped DNA structures J. Biol. Chem. 278 2003 33848 33856
28. T.Q. Trinh, and R.R. Sinden Preferential DNA secondary structure mutagenesis in the lagging strand of replication in E. coli Nature 352 1991 544 547
29. R.R. Sinden, G. Zheng, R.G. Brankamp, and K.N. Allen On the deletion of inverted repeated DNA in Escherichia coli: effects of length, thermal stability, and cruciform formation in vivo Genetics 129 1991 991 1005
30. n repeats in E. coli Mutat. Res. 554 2004 95 109
31. R. Pelletier, M.M. Krasilnikova, G.M. Samadashwily, R. Lahue, and S.M. Mirkin Replication and expansion of trinucleotide repeats in yeast Mol. Cell Biol. 23 2003 1349 1357
32. G.M. Samadashwily, G. Raca, and S.M. Mirkin Trinucleotide repeats affect DNA replication in vivo Nat. Genet. 17 1997 298 304
33. n repeats in vivo Mol. Cell Biol. 24 2004 2286 2295
34. S. Kang, K. Ohshima, M. Shimizu, S. Amirhaeri, and R.D. Wells Pausing of DNA synthesis in vitro at specific loci in CTG and CGG triplet repeats from human hereditary disease genes J. Biol. Chem. 270 1995 27014 27021
35. K. Usdin, and K.J. Woodford CGG repeats associated with DNA instability and chromosome fragility form structures that block DNA synthesis in vitro Nucl. Acids Res. 23 1995 4202 4209
36. M.J. Hartenstine, M.F. Goodman, and J. Petruska Base stacking and even/odd behavior of hairpin loops in DNA triplet repeat slippage and expansion with DNA polymerase J. Biol. Chem. 275 2000 18382 18390
37. B.L. Heidenfelder, A.M. Makhov, and M.D. Topal Hairpin formation in Friedreich's ataxia triplet repeat expansion J. Biol. Chem. 278 2003 2425 2431
38. n repeats at neutral pH Nucl. Acids Res. 32 2004 1224 1231
39. E. Grabczyk, and K. Usdin The GAA·TTC triplet repeat expanded in Friedreich's ataxia impedes transcription elongation by T7 RNA polymerase in a length and supercoil dependent manner Nucl. Acids Res. 28 2000 2815 2822
40. M.M. Cox, M.F. Goodman, K.N. Kreuzer, D.J. Sherratt, S.J. Sandler, and K.J. Marians The importance of repairing stalled replication forks Nature 404 2000 37 41
41. P. McGlynn, and R.G. Lloyd Recombinational repair and restart of damaged replication forks Nat. Rev. Mol. Cell Biol. 3 2002 859 870
42. M.M. Cox Recombinational DNA repair of damaged replication forks in Escherichia coli: questions Annu. Rev. Genet. 35 2001 53 82
43. K.J. Marians PriA-directed replication fork restart in Escherichia coli Trends Biochem. Sci. 25 2000 185 189
44. M. Seigneur, V. Bidnenko, S.D. Ehrlich, and B. Michel RuvAB acts at arrested replication forks Cell 95 1998 419 430
45. M.J. Flores, H. Bierne, S.D. Ehrlich, and B. Michel Impairment of lagging strand synthesis triggers the formation of a RuvABC substrate at replication forks EMBO J. 20 2001 619 629
46. P. McGlynn, R.G. Lloyd, and K.J. Marians Formation of Holliday junctions by regression of nascent DNA in intermediates containing stalled replication forks: RecG stimulates regression even when the DNA is negatively supercoiled Proc. Natl. Acad. Sci. U.S.A. 98 2001 8235 8240
47. R.J. Bennett, H.J. Dunderale, and S.C. West Resolution of Holliday junctions by RuvC resolvase: cleavage specificity and DNA distortion Cell 74 1993 1021 1031
48. H. Iwasaki, M. Takahagi, T. Shiba, A. Nakata, and H. Shinagawa Escherichia coli RuvC protein is an endonuclease that resolves the Holliday structure EMBO J. 10 1991 4381 4389
49. J. Courcelle, J.R. Donaldson, K.H. Chow, and C.T. Courcelle DNA damage-induced replication fork regression and processing in Escherichia coli Science 299 2003 1064 1067
50. J. Courcelle, and P.C. Hanawalt RecA-dependent recovery of arrested DNA replication forks Annu. Rev. Genet. 37 2003 611 646
51. J. Courcelle, and P.C. Hanawalt RecQ and RecJ process blocked replication forks prior to the resumption of replication in UV-irradiated Escherichia coli Mol. Gen. Genet. 262 1999 543 551
52. K. Umezu, and R.D. Kolodner Protein interactions in genetic recombination in Escherichia coli. Interactions involving RecO and RecR overcome the inhibition of RecA by single-stranded DNA-binding protein J. Biol. Chem. 269 1994 30005 30013
53. J.M. Bork, M.M. Cox, and R.B. Inman The RecOR proteins modulate RecA protein function at 5′ ends of single-stranded DNA EMBO J. 20 2001 7313 7322
54. B.L. Webb, M.M. Cox, and R.B. Inman Recombinational DNA repair: the RecF and RecR proteins limit the extension of RecA filaments beyond single-strand DNA gaps Cell 91 1997 347 356
55. N. Kantake, M.V. Madiraju, T. Sugiyama, and S.C. Kowalczykowski Escherichia coli RecO protein anneals ssDNA complexed with its cognate ssDNA-binding protein: a common step in genetic recombination Proc. Natl. Acad. Sci. U.S.A. 99 2002 15327 15332
56. K.H. Chow, and J. Courcelle RecO acts with RecF and RecR to protect and maintain replication forks blocked by UV-induced DNA damage in Escherichia coli J. Biol. Chem. 279 2004 3492 3496
57. J.W. Drake A constant rate of spontaneous mutation in DNA-based microbes Proc. Natl. Acad. Sci. U.S.A. 88 1991 7160 7164
58. J.H. Zar Biostatistical Analysis 1999 Prentice-Hall
59. A.V. Gregg, P. McGlynn, R.P. Jaktaji, and R.G. Lloyd Direct rescue of stalled DNA replication forks via the combined action of PriA and RecG helicase activities Mol. Cell 9 2002 241 251
60. M. Mitas Trinucleotide repeats associated with human disease Nucl. Acids Res. 25 1997 2245 2253
61. E.A. Oussatcheva, L.S. Shlyakhtenko, R. Glass, R.R. Sinden, Y.L. Lyubchenko, and V.N. Potaman Structure of branched DNA molecules: gel retardation and atomic force microscopy studies J. Mol. Biol. 292 1999 75 86
62. D.M.J. Lilley, and R.M. Clegg The structure of branched DNA species Quart. Rev. Biophys. 26 1993 131 175
63. R.P. Jaktaji, and R.G. Lloyd PriA supports two distinct pathways for replication restart in UV-irradiated Escherichia coli cells Mol. Microbiol. 47 2003 1091 1100
64. P. McGlynn, A.A. Al-Deib, J. Liu, K.J. Marians, and R.G. Lloyd The DNA replication protein PriA and the recombination protein RecG bind D-loops J. Mol. Biol. 270 1997 212 221
65. E.A. Oussatcheva, V.I. Hashem, Y. Zou, R.R. Sinden, and V.N. Potaman Involvement of the nucleotide excision repair protein UvrA in instability of (CAG)·(CTG) repeat sequences in E. coli J. Biol. Chem. 276 2001 30878 30884
66. C.E. Pearson, and R.R. Sinden Trinucleotide repeat DNA structures: dynamic mutations from dynamic DNA Curr. Opin. Struct. Biol. 8 1998 321 330
67. J.M. Darlow, and D.R.F. Leach Secondary structures in d(CGG) and d(CCG) repeat tracts J. Mol. Biol. 275 1998 3 16
68. C.E. Pearson, and R.R. Sinden Alternative structures in duplex DNA formed within the trinucleotide repeats of the myotonic dystrophy and fragile X loci Biochemistry 35 1996 5041 5053
69. K. Morimatsu, and S.C. Kowalczykowski RecFOR proteins load RecA protein onto gapped DNA to accelerate DNA strand exchange: a universal step of recombinational repair Mol. Cell 11 2003 1337 1347
70. P. McGlynn, and R.G. Lloyd Genome stability and the processing of damaged replication forks by RecG Trends Genet. 18 2002 413 419
71. C.E. Pearson, A. Ewel, S. Acharya, R.A. Fishel, and R.R. Sinden Human MSH2 binds to trinucleotide repeat DNA structures associated with neurodegenerative diseases Hum. Mol. Genet. 6 1997 1117 1123
72. M. Tam, M.S. Erin, M. Kekis, S.B. David, G.B. Price, and C.E. Pearson Slipped (CTG)·(CAG) repeats of the myotonic dystrophy locus: surface probing with anti-DNA antibodies J. Mol. Biol. 332 2003 585 600
73. J.D. McCool, and S.J. Sandler Effects of mutations involving cell division, recombination, and chromosome dimer resolution on a priA2::kan mutant Proc. Natl. Acad. Sci. U.S.A. 98 2001 8203 8210