Mechanisms of tandem repeat instability in bacteria

Mutation Research - Fundamental and Molecular Mechanisms of Mutagenesis

Volumn 598, Issue 1-2, 2006, Pages 144-163

  Bichara, M ^b   Wagner, J ^b   Lambert, I B ^a  

^a CARLETON UNIVERSITY   (Canada)

^b UNIVERSITÉ DE STRASBOURG   (France)

Author keywords

Bacterial fitness; Deletion; DNA instability; DNA repair; Expansion; Microsatellite; Mutation; Phase variation; Recombination; Replication; Review; Tandem repeat; TLS polymerases; Triplet repeat

Indexed keywords

DNA DIRECTED DNA POLYMERASE ALPHA; DNA POLYMERASE; DNA POLYMERASE IV; DNA POLYMERASE V; NUCLEOTIDE; SINGLE STRANDED DNA; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; BACTERIAL GENOME; CHROMOSOME ANALYSIS; COMPARATIVE GENE MAPPING; DISEASE ASSOCIATION; DNA DAMAGE; DNA REPAIR; DNA REPLICATION; DNA SEQUENCE; DNA STRAND; DNA STRUCTURE; ESCHERICHIA COLI; EXCISION REPAIR; EXPERIMENT; GENE MUTATION; GENE REPLICATION; GENETIC MODEL; GENETIC RECOMBINATION; GENETIC TRANSCRIPTION; HAEMOPHILUS INFLUENZAE; HUMAN; HUMAN GENOME; MAMMALIAN GENETICS; MICROSATELLITE INSTABILITY; MISMATCH REPAIR; MOLECULAR BIOLOGY; NEISSERIA MENINGITIDIS; NONHUMAN; PLASMID; PRIORITY JOURNAL; PROKARYOTE; PROTEIN SECONDARY STRUCTURE; REVIEW; SIMPLE SEQUENCE REPEAT; STATISTICAL SIGNIFICANCE; TANDEM REPEAT; TRANSCRIPTION REGULATION;

BASE SEQUENCE; DNA REPEAT EXPANSION; GENES, BACTERIAL; GENETIC DISEASES, INBORN; GENOMIC INSTABILITY; HUMANS; MODELS, MOLECULAR; PLASMIDS; SEQUENCE DELETION; TANDEM REPEAT SEQUENCES; TRINUCLEOTIDE REPEATS;

ESCHERICHIA COLI; EUKARYOTA; PROKARYOTA;

EID: 33744939499     PISSN: 00275107     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mrfmmm.2006.01.020     Document Type: Review

References (148)

1. Debrauwere H., Gendrel C.G., Lechat S., and Dutreix M. Differences and similarities between various tandem repeat sequences: minisatellites and microsatellites. Biochimie 79 (1997) 577-586
2. Li Y.C., Korol A.B., Fahima T., Beiles A., and Nevo E. Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review. Mol. Ecol. 11 (2002) 2453-2465
3. Li Y.C., Korol A.B., Fahima T., and Nevo E. Microsatellites within genes: structure, function, and evolution. Mol. Biol. Evol. 21 (2004) 991-1007
4. Sia E.A., Jinks-Robertson S., and Petes T.D. Genetic control of microsatellite stability. Mutat. Res. 383 (1997) 61-70
5. Strauss B.S. Frameshift mutation, microsatellites and mismatch repair. Mutat. Res. 437 (1999) 195-203
6. Cummings C.J., and Zoghbi H.Y. Trinucleotide repeats: mechanisms and pathophysiology. Annu. Rev. Genomics Hum. Genet. 1 (2000) 281-328
7. Cummings C.J., and Zoghbi H.Y. Fourteen and counting: unraveling trinucleotide repeat diseases. Hum. Mol. Genet. 9 (2000) 909-916
8. Wells R.D., Dere R., Hebert M.L., Napierala M., and Son L.S. Advances in mechanisms of genetic instability related to hereditary neurological diseases. Nucl. Acids Res. 33 (2005) 3785-3798
9. Umar A., Risinger J.I., Hawk E.T., and Barrett J.C. Testing guidelines for hereditary non-polyposis colorectal cancer. Nat. Rev. Cancer 4 (2004) 153-158
10. Bennett P. Demystified. microsatellites. Mol. Pathol. 53 (2000) 177-183
11. Butler J.M., Buel E., Crivellente F., and McCord B.R. Forensic DNA typing by capillary electrophoresis using the ABI Prism 310 and 3100 genetic analyzers for STR analysis. Electrophoresis 25 (2004) 1397-1412
12. Wickenheiser R.A. Trace DNA: a review, discussion of theory, and application of the transfer of trace quantities of DNA through skin contact. J. Forensic Sci. 47 (2002) 442-450
13. van Belkum A., Scherer S., van Alphen L., and Verbrugh H. Short-sequence DNA repeats in prokaryotic genomes. Microbiol. Mol. Biol. Rev. 62 (1998) 275-293
14. Fouet A., Smith K.L., Keys C., Vaissaire J., Le Doujet C., Levy M., Mock M., and Keim P. Diversity among French Bacillus anthracis isolates. J. Clin. Microbiol. 40 (2002) 4732-4734
15. Frothingham R., and Meeker-O'Connell W.A. Genetic diversity in the Mycobacterium tuberculosis complex based on variable numbers of tandem DNA repeats. Microbiology 144 (1998) 1189-1196
16. Lindstedt B.A. Multiple-locus variable number tandem repeats analysis for genetic fingerprinting of pathogenic bacteria. Electrophoresis 26 (2005) 2567-2582
17. van Belkum A., Scherer S., van Leeuwen W., Willemse D., van Alphen L., and Verbrugh H. Variable number of tandem repeats in clinical strains of Haemophilus influenzae. Infect. Immun. 65 (1997) 5017-5027
18. Renders N., Licciardello L., IJsseldijk C., Sijmons M., van Alphen L., Verbrugh H., and van Belkum A. Variable numbers of tandem repeat loci in genetically homogeneous Haemophilus influenzae strains alter during persistent colonisation of cystic fibrosis patients. FEMS Microbiol. Lett. 173 (1999) 95-102
19. Bayliss C.D., Field D., and Moxon E.R. The simple sequence contingency loci of Haemophilus influenzae and Neisseria meningitidis. J. Clin. Invest 107 (2001) 657-662
20. Bayliss C.D., Dixon K.M., and Moxon E.R. Simple sequence repeats (microsatellites): mutational mechanisms and contributions to bacterial pathogenesis. A meeting review. FEMS Immunol. Med. Microbiol. 40 (2004) 11-19
21. van der Woude M.W., and Baumler A.J. Phase and antigenic variation in bacteria. Clin. Microbiol. Rev. 17 (2004) 581-611
22. Martin P., Makepeace K., Hill S.A., Hood D.W., and Moxon E.R. Microsatellite instability regulates transcription factor binding and gene expression. Proc. Natl. Acad. Sci. U.S.A 102 (2005) 3800-3804
23. Weiser J.N., Love J.M., and Moxon E.R. The molecular mechanism of phase variation of H. influenzae lipopolysaccharide. Cell 59 (1989) 657-665
24. Weiser J.N., and Pan N. Adaptation of Haemophilus influenzae to acquired and innate humoral immunity based on phase variation of lipopolysaccharide. Mol. Microbiol. 30 (1998) 767-775
25. Gatchel J.R., and Zoghbi H.Y. Diseases of unstable repeat expansion: mechanisms and common principles. Nat. Rev. Genet. 6 (2005) 743-755
26. Freund A.M., Bichara M., and Fuchs R.P. Z-DNA-forming sequences are spontaneous deletion hot spots. Proc. Natl. Acad. Sci. U.S.A. 86 (1989) 7465-7469
27. Jackson A.L., Chen R., and Loeb L.A. Induction of microsatellite instability by oxidative DNA damage. Proc. Natl. Acad. Sci. U.S.A. 95 (1998) 12468-12473
28. Hashem V.I., Rosche W.A., and Sinden R.R. Genetic assays for measuring rates of (CAG). (CTG) repeat instability in Escherichia coli. Mutat. Res. 502 (2002) 25-37
29. Sinden R.R., Potaman V.N., Oussatcheva E.A., Pearson C.E., Lyubchenko Y.L., and Shlyakhtenko L.S. Triplet repeat DNA structures and human genetic disease: dynamic mutations from dynamic DNA. J. Biosci. 27 (2002) 53-65
30. Schumacher S., Pinet I., and Bichara M. Modulation of transcription reveals a new mechanism of triplet repeat instability in Escherichia coli. J. Mol. Biol. 307 (2001) 39-49
31. Hashem V.I., Klysik E.A., Rosche W.A., and Sinden R.R. Instability of repeated DNAs during transformation in Escherichia coli. Mutat. Res. 502 (2002) 39-46
32. Jakupciak J.P., and Wells R.D. Genetic instabilities in (CTG.CAG) repeats occur by recombination. J. Biol. Chem. 274 (1999) 23468-23479
33. Jakupciak J.P., and Wells R.D. Gene conversion (recombination) mediates expansions of CTG.CAG repeats. J. Biol. Chem. 275 (2000) 40003-40013
34. Napierala M., Parniewski P., Pluciennik A., and Wells R.D. Long CTG.CAG repeat sequences markedly stimulate intramolecular recombination. J. Biol. Chem. 277 (2002) 34087-34100
35. Pluciennik A., Iyer R.R., Napierala M., Larson J.E., Filutowicz M., and Wells R.D. Long CTG.CAG repeats from myotonic dystrophy are preferred sites for intermolecular recombination. J. Biol. Chem. 277 (2002) 34074-34086
36. Morel P., Reverdy C., Michel B., Ehrlich S.D., and Cassuto E. The role of SOS and flap processing in microsatellite instability in Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 95 (1998) 10003-10008
37. Bayliss C.D., van de V., and Moxon E.R. Mutations in polI but not mutSLH destabilize Haemophilus influenzae tetranucleotide repeats. EMBO J. 21 (2002) 1465-1476
38. Bayliss C.D., Sweetman W.A., and Moxon E.R. Destabilization of tetranucleotide repeats in Haemophilus influenzae mutants lacking RnaseHI or the Klenow domain of PolI. Nucl. Acids Res. 33 (2005) 400-408
39. De Bolle X., Bayliss C.D., Field D., van de V., Saunders N.J., Hood D.W., and Moxon E.R. The length of a tetranucleotide repeat tract in Haemophilus influenzae determines the phase variation rate of a gene with homology to type III DNA methyltransferases. Mol. Microbiol. 35 (2000) 211-222
40. Bayliss C.D., Sweetman W.A., and Moxon E.R. Mutations in Haemophilus influenzae mismatch repair genes increase mutation rates of dinucleotide repeat tracts but not dinucleotide repeat-driven pilin phase variation rates. J. Bacteriol. 186 (2004) 2928-2935
41. Wells R.D. Molecular basis of genetic instability of triplet repeats. J. Biol. Chem. 271 (1996) 2875-2878
42. Wells R.D., Parniewski P., Pluciennik A., Bacolla A., Gellibolian R., and Jaworski A. Small slipped register genetic instabilities in Escherichia coli in triplet repeat sequences associated with hereditary neurological diseases. J. Biol. Chem. 273 (1998) 19532-19541
43. Streisinger G., Okada Y., Emrich J., Newton J., Tsugita A., Terzaghi E., and Inouye M. Frameshift mutations and the genetic code. Cold Spring Harb. Symp. Quant. Biol. 31 (1966) 77-84
44. Bebenek K., and Kunkel T.A. Streisinger revisited: DNA synthesis errors mediated by substrate misalignments. Cold Spring Harb. Symp. Quant. Biol. 65 (2000) 81-91
45. Lahue R.S., and Slater D.L. DNA repair and trinucleotide repeat instability. Front Biosci. 8 (2003) s653-s665
46. Kang S., Jaworski A., Ohshima K., and Wells R.D. Expansion and deletion of CTG repeats from human disease genes are determined by the direction of replication in E. coli. Nat. Genet. 10 (1995) 213-218
47. Ohshima K., Montermini L., Wells R.D., and Pandolfo M. Inhibitory effects of expanded GAA.TTC triplet repeats from intron I of the Friedreich ataxia gene on transcription and replication in vivo. J. Biol. Chem. 273 (1998) 14588-14595
48. Rosche W.A., Trinh T.Q., and Sinden R.R. Differential DNA secondary structure-mediated deletion mutation in the leading and lagging strands. J. Bacteriol. 177 (1995) 4385-4391
49. Schumacher S., Fuchs R.P., and Bichara M. Two distinct models account for short and long deletions within sequence repeats in Escherichia coli. J. Bacteriol. 179 (1997) 6512-6517
50. Shimizu M., Gellibolian R., Oostra B.A., and Wells R.D. Cloning, characterization and properties of plasmids containing CGG triplet repeats from the FMR-1 gene. J. Mol. Biol. 258 (1996) 614-626
51. Bowater R.P., Rosche W.A., Jaworski A., Sinden R.R., and Wells R.D. Relationship between Escherichia coli growth and deletions of CTG.CAG triplet repeats in plasmids. J. Mol. Biol. 264 (1996) 82-96
52. Bichara M., Pinet I., Schumacher S., and Fuchs R.P. Mechanisms of dinucleotide repeat instability in Escherichia coli. Genetics 154 (2000) 533-542
53. Schumacher S., Fuchs R.P., and Bichara M. Expansion of CTG repeats from human disease genes is dependent upon replication mechanisms in Escherichia coli: the effect of long patch mismatch repair revisited. J. Mol. Biol. 279 (1998) 1101-1110
54. Levinson G., and Gutman G.A. High frequencies of short frameshifts in poly-CA/TG tandem repeats borne by bacteriophage M13 in Escherichia coli K-12. Nucl. Acids Res. 15 (1987) 5323-5338
55. Parniewski P., Jaworski A., Wells R.D., and Bowater R.P. Length of CTG.CAG repeats determines the influence of mismatch repair on genetic instability. J. Mol. Biol. 299 (2000) 865-874
56. Schmidt K.H., Abbott C.M., and Leach D.R. Two opposing effects of mismatch repair on CTG repeat instability in Escherichia coli. Mol. Microbiol. 35 (2000) 463-471
57. Samadashwily G.M., Raca G., and Mirkin S.M. Trinucleotide repeats affect DNA replication in vivo. Nat. Genet. 17 (1997) 298-304
58. da Silva E.F., and Reha-Krantz L.J. Dinucleotide repeat expansion catalyzed by bacteriophage T4 DNA polymerase in vitro. J. Biol. Chem. 275 (2000) 31528-31535
59. Iyer R.R., and Wells R.D. Expansion and deletion of triplet repeat sequences in Escherichia coli occur on the leading strand of DNA replication. J. Biol. Chem. 274 (1999) 3865-3877
60. Ji J., Clegg N.J., Peterson K.R., Jackson A.L., Laird C.D., and Loeb L.A. In vitro expansion of GGC.GCC repeats: identification of the preferred strand of expansion. Nucl. Acids Res. 24 (1996) 2835-2840
61. Kang S., Ohshima K., Shimizu M., Amirhaeri S., and Wells R.D. 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
62. Ohshima K., and Wells R.D. Hairpin formation during DNA synthesis primer realignment in vitro in triplet repeat sequences from human hereditary disease genes. J. Biol. Chem. 272 (1997) 16798-16806
63. Petruska J., Hartenstine M.J., and Goodman M.F. Analysis of strand slippage in DNA polymerase expansions of CAG/CTG triplet repeats associated with neurodegenerative disease. J. Biol. Chem. 273 (1998) 5204-5210
64. Usdin K., and Woodford K.J. CGG repeats associated with DNA instability and chromosome fragility form structures that block DNA synthesis in vitro. Nucl. Acids Res. 23 (1995) 4202-4209
65. Bierne H., Vilette D., Ehrlich S.D., and Michel B. Isolation of a dnaE mutation which enhances RecA-independent homologous recombination in the Escherichia coli chromosome. Mol. Microbiol. 24 (1997) 1225-1234
66. Iyer R.R., Pluciennik A., Rosche W.A., Sinden R.R., and Wells R.D. DNA polymerase III proofreading mutants enhance the expansion and deletion of triplet repeat sequences in Escherichia coli. J. Biol. Chem. 275 (2000) 2174-2184
67. Morag A.S., Saveson C.J., and Lovett S.T. Expansion of DNA repeats in Escherichia coli: effects of recombination and replication functions. J. Mol. Biol. 289 (1999) 21-27
68. Saveson C.J., and Lovett S.T. Enhanced deletion formation by aberrant DNA replication in Escherichia coli. Genetics 146 (1997) 457-470
69. Strauss B.S., Sagher D., and Acharya S. Role of proofreading and mismatch repair in maintaining the stability of nucleotide repeats in DNA. Nucl. Acids Res. 25 (1997) 806-813
70. Rosche W.A., Jaworski A., Kang S., Kramer S.F., Larson J.E., Geidroc D.P., Wells R.D., and Sinden R.R. Single-stranded DNA-binding protein enhances the stability of CTG triplet repeats in Escherichia coli. J. Bacteriol. 178 (1996) 5042-5044
71. Petruska J., Arnheim N., and Goodman M.F. Stability of intrastrand hairpin structures formed by the CAG/CTG class of DNA triplet repeats associated with neurological diseases. Nucl. Acids Res. 24 (1996) 1992-1998
72. Smith G.K., Jie J., Fox G.E., and Gao X. DNA CTG triplet repeats involved in dynamic mutations of neurologically related gene sequences form stable duplexes. Nucl. Acids Res. 23 21 (1995) 4303-4311
73. 15 adopts a hairpin conformation. Nucl. Acids Res. 23 (1995) 2706-2714
74. Trinh T.Q., and Sinden R.R. Preferential DNA secondary structure mutagenesis in the lagging strand of replication in E. coli. Nature 352 (1991) 544-547
75. Kornberg A., and Baker T.A. Plasmids and organelles DNA Replication (1992), W.H. Freeman and Company, New York pp. 637-647
76. Viguera E., Canceill D., and Ehrlich S.D. Replication slippage involves DNA polymerase pausing and dissociation. EMBO J. 20 (2001) 2587-2595
77. Pages V., and Fuchs R.P. How DNA lesions are turned into mutations within cells?. Oncogene 21 (2002) 8957-8966
78. Napolitano R., Janel-Bintz R., Wagner J., and Fuchs R.P. All three SOS-inducible DNA polymerases (Pol II, Pol IV and Pol V) are involved in induced mutagenesis. EMBO J. 19 (2000) 6259-6265
79. Wagner J., Etienne H., Janel-Bintz R., and Fuchs R.P. Genetics of mutagenesis in E. coli: various combinations of translesion polymerases (Pol II, IV and V) deal with lesion/sequence context diversity. DNA Rep. (Amsterdam) 1 (2002) 159-167
80. Kim S.R., Matsui K., Yamada M., Gruz P., and Nohmi T. Roles of chromosomal and episomal dinB genes encoding DNA PolIV in targeted and untargeted mutagenesis in Escherichia coli. Mol. Genet. Genom. 266 (2001) 207-215
81. Kim S.R., Maenhaut-Michel G., Yamada M., Yamamoto Y., Matsui K., Sofuni T., Nohmi T., and Ohmori H. Multiple pathways for SOS-induced mutagenesis in Escherichia coli: an overexpression of dinB/dinP results in strongly enhancing mutagenesis in the absence of any exogenous treatment to damage DNA. Proc. Natl. Acad. Sci. U.S.A. 94 (1997) 13792-13797
82. Wagner J., and Nohmi T. Escherichia coli DNA polymerase IV mutator activity: genetic requirements and mutational specificity. J. Bacteriol. 182 (2000) 4587-4595
83. Fuchs R.P., Fujii S., and Wagner J. Properties and functions of Escherichia coli: Pol IV and Pol V. Adv. Protein Chem. 69 (2004) 229-264
84. Dixon M.J., and Lahue R.S. Examining the potential role of DNA polymerases eta and zeta in triplet repeat instability in yeast. DNA Rep. (Amsterdam) 1 (2002) 763-770
85. Sweetman W.A., Moxon E.R., and Bayliss C.D. Induction of the SOS regulon of Haemophilus influenzae does not affect phase variation rates at tetranucleotide or dinucleotide repeats. Microbiology 151 (2005) 2751-2763
86. Martin P., Sun L., Hood D.W., and Moxon E.R. Involvement of genes of genome maintenance in the regulation of phase variation frequencies in Neisseria meningitidis. Microbiology 150 (2004) 3001-3012
87. Cox M.M. Recombinational DNA repair of damaged replication forks in Escherichia coli: questions. Annu. Rev. Genet. 35 (2001) 53-82
88. Cox M.M. The nonmutagenic repair of broken replication forks via recombination. Mutat. Res. 510 (2002) 107-120
89. Kowalczykowski S.C., Dixon D.A., Eggleston A.K., Lauder S.D., and Rehrauer W.M. Biochemistry of homologous recombination in Escherichia coli. Microbiol. Rev. 58 (1994) 401-465
90. Kuzminov A. Recombinational repair of DNA damage in Escherichia coli and bacteriophage lambda. Microbiol. Mol. Biol. Rev. 63 (1999) 751-813
91. McGlynn P., and Lloyd R.G. Recombinational repair and restart of damaged replication forks. Nat. Rev. Mol. Cell Biol. 3 (2002) 859-870
92. Pages V., and Fuchs R.P. Uncoupling of leading- and lagging-strand DNA replication during lesion bypass in vivo. Science 300 (2003) 1300-1303
93. Bierne H., Ehrlich S.D., and Michel B. Competition between parental and recombinant plasmids affects the measure of recombination frequencies. Plasmid 33 (1995) 101-112
94. Jakupciak J.P., and Wells R.D. Genetic instabilities of triplet repeat sequences by recombination. IUBMB. Life 50 (2000) 355-359
95. Sopher B.L., Myrick S.B., Hong J.Y., Smith A.C., and La Spada A.R. In vivo expansion of trinucleotide repeats yields plasmid and YAC constructs for targeting and transgenesis. Gene 261 (2000) 383-390
96. Hebert M.L., Spitz L.A., and Wells R.D. DNA double-strand breaks induce deletion of CTG.CAG repeats in an orientation-dependent manner in Escherichia coli. J. Mol. Biol. 336 3 (2004) 655-672
97. n repeats in E. coli. Mutat. Res. 554 (2004) 95-109
98. Pearson C.E., Tam M., Wang Y.H., Montgomery S.E., Dar A.C., Cleary J.D., and Nichol K. Slipped-strand DNAs formed by long (CAG)*(CTG) repeats: slipped-out repeats and slip-out junctions. Nucl. Acids Res. 30 (2002) 4534-4547
99. Dere R., Napierala M., Ranum L.P., and Wells R.D. Hairpin structure-forming propensity of the (CCTG.CAGG) tetranucleotide repeats contributes to the genetic instability associated with myotonic dystrophy type 2. J. Biol. Chem. 279 (2004) 41715-41726
100. Cleary J.D., and Pearson C.E. Replication fork dynamics and dynamic mutations: the fork-shift model of repeat instability. Trends Genet. 21 (2005) 272-280
101. Schofield M.J., and Hsieh P. DNA mismatch repair: molecular mechanisms and biological function. Annu. Rev. Microbiol. 57 (2003) 579-608
102. Eisen J.A., and Hanawalt P.C. A phylogenomic study of DNA repair genes, proteins, and processes. Mutat. Res. 435 (1999) 171-213
103. Richardson A.R., and Stojiljkovic I. Mismatch repair and the regulation of phase variation in Neisseria meningitidis. Mol. Microbiol. 40 (2001) 645-655
104. Richardson A.R., Yu Z., Popovic T., and Stojiljkovic I. Mutator clones of Neisseria meningitidis in epidemic serogroup A disease. Proc. Natl. Acad. Sci. U.S.A. 99 (2002) 6103-6107
105. Eckert K.A., and Yan G. Mutational analyses of dinucleotide and tetranucleotide microsatellites in Escherichia coli: influence of sequence on expansion mutagenesis. Nucl. Acids Res. 28 (2000) 2831-2838
106. n triplet repeats from human hereditary diseases. Proc. Natl. Acad. Sci. U.S.A. 92 (1995) 11019-11023
107. Kline K.A., Sechman E.V., Skaar E.P., and Seifert H.S. Recombination, repair and replication in the pathogenic Neisseriae: the 3 R's of molecular genetics of two human-specific bacterial pathogens. Mol. Microbiol. 50 (2003) 3-13
108. Mizrahi V., and Andersen S.J. DNA repair in Mycobacterium tuberculosis. What have we learnt from the genome sequence?. Mol. Microbiol. 29 (1998) 1331-1339
109. Oussatcheva E.A., Hashem V.I., Zou Y., Sinden R.R., and Potaman V.N. Involvement of the nucleotide excision repair protein UvrA in instability of CAG*CTG repeat sequences in Escherichia coli. J. Biol. Chem. 276 (2001) 30878-30884
110. Parniewski P., Bacolla A., Jaworski A., and Wells R.D. Nucleotide excision repair affects the stability of long transcribed (CTG*CAG) tracts in an orientation-dependent manner in Escherichia coli. Nucl. Acids Res. 27 (1999) 616-623
111. Leach D.R. Long DNA palindromes, cruciform structures, genetic instability and secondary structure repair. Bioessays 16 (1994) 893-900
112. Sarkar P.S., Chang H.C., Boudi F.B., and Reddy S. CTG repeats show bimodal amplification in E. coli. Cell 95 (1998) 531-540
113. Pan X., and Leach D.R. The roles of mutS, sbcCD and recA in the propagation of TGG repeats in Escherichia coli. Nucl. Acids Res. 28 (2000) 3178-3184
114. Chastain P.D., Eichler E.E., Kang S., Nelson D.L., Levene S.D., and Sinden R.R. Anomalous rapid electrophoretic mobility of DNA containing triplet repeats associated with human disease genes. Biochemistry 34 (1995) 16125-16131
115. Pearson C.E., and Sinden R.R. Alternative structures in duplex DNA formed within the trinucleotide repeats of the myotonic dystrophy and fragile X loci. Biochemistry 35 (1996) 5041-5053
116. Pearson C.E., Eichler E.E., Lorenzetti D., Kramer S.F., Zoghbi H.Y., Nelson D.L., and Sinden R.R. Interruptions in the triplet repeats of SCA1 and FRAXA reduce the propensity and complexity of slipped strand DNA (S-DNA) formation. Biochemistry 37 (1998) 2701-2708
117. n repeats from the myotonic dystrophy locus. Nucl. Acids Res. 26 (1998) 816-823
118. Bowater R.P., Jaworski A., Larson J.E., Parniewski P., and Wells R.D. Transcription increases the deletion frequency of long CTG.CAG triplet repeats from plasmids in Escherichia coli. Nucl. Acids Res. 25 (1997) 2861-2868
119. Mochmann L.H., and Wells R.D. Transcription influences the types of deletion and expansion products in an orientation-dependent manner from GAC*GTC repeats. Nucl. Acids Res. 32 (2004) 4469-4479
120. Sakamoto N., Larson J.E., Iyer R.R., Montermini L., Pandolfo M., and Wells R.D. GGA*TCC-interrupted triplets in long GAA*TTC repeats inhibit the formation of triplex and sticky DNA structures, alleviate transcription inhibition, and reduce genetic instabilities. J. Biol. Chem. 276 (2001) 27178-27187
121. Sakamoto N., Ohshima K., Montermini L., Pandolfo M., and Wells R.D. Sticky DNA, a self-associated complex formed at long GAA*TTC repeats in intron 1 of the frataxin gene, inhibits transcription. J. Biol. Chem. 276 (2001) 27171-27177
122. Choong C.S., Kemppainen J.A., Zhou Z.X., and Wilson E.M. Reduced androgen receptor gene expression with first exon CAG repeat expansion. Mol. Endocrinol. 10 (1996) 1527-1535
123. Klesert T.R., Otten A.D., Bird T.D., and Tapscott S.J. Trinucleotide repeat expansion at the myotonic dystrophy locus reduces expression of DMAHP. Nat. Genet. 16 (1997) 402-406
124. Maron D.M., and Ames B.N. Revised methods for the Salmonella mutagenicity test. Mutat. Res. 113 (1983) 173-215
125. Cupples C.G., and Miller J.H. A set of lacZ mutations in Escherichia coli that allow rapid detection of each of the six base substitutions. Proc. Natl. Acad. Sci. U.S.A. 86 (1989) 5345-5349
126. Cupples C.G., Cabrera M., Cruz C., and Miller J.H. A set of lacZ mutations in Escherichia coli that allow rapid detection of specific frameshift mutations. Genetics 125 (1990) 275-280
127. Jackson A.L., and Loeb L.A. Microsatellite instability induced by hydrogen peroxide in Escherichia coli. Mutat. Res. 447 (2000) 187-198
128. Hashem V.I., and Sinden R.R. Chemotherapeutically induced deletion of expanded triplet repeats. Mutat. Res. 508 (2002) 107-119
129. Pearson C.E., Edamura K.N., and Cleary J.D. Repeat instability: mechanisms of dynamic mutations. Nat. Rev. Genet. 6 (2005) 729-742
130. Wagner J., Gruz P., Kim S.R., Yamada M., Matsui K., Fuchs R.P., and Nohmi T. The dinB gene encodes a novel E. coli DNA polymerase, DNA PolIV, involved in mutagenesis. Mol. Cell 4 (1999) 281-286
131. Reuven N.B., Arad G., Maor-Shoshani A., and Livneh Z. The mutagenesis protein UmuC is a DNA polymerase activated by UmuD', RecA, and SSB and is specialized for translesion replication. J. Biol. Chem. 274 (1999) 31763-31766
132. 2)C is an error-prone DNA polymerase, Escherichia coli pol V. Proc. Natl. Acad. Sci. U.S.A. 96 (1999) 8919-8924
133. Cordonnier A.M., and Fuchs R.P. Replication of damaged DNA: molecular defect in xeroderma pigmentosum variant cells. Mutat. Res. 435 (1999) 111-119
134. Becherel O.J., Fuchs R.P., and Wagner J. Pivotal role of the beta-clamp in translesion DNA synthesis and mutagenesis in E. coli cells. DNA Rep. (Amsterdam) 1 (2002) 703-708
135. Lenne-Samuel N., Wagner J., Etienne H., and Fuchs R.P. The processivity factor beta controls DNA polymerase IV traffic during spontaneous mutagenesis and translesion synthesis in vivo. EMBO Rep. 3 (2002) 45-49
136. Michel B., Grompone G., Flores M.J., and Bidnenko V. Multiple pathways process stalled replication forks. Proc. Natl. Acad. Sci. U.S.A. 101 (2004) 12783-12788
137. van Ham S.M., van Alphen L., Mooi F.R., and van Putten J.P. Phase variation of H. influenzae fimbriae: transcriptional control of two divergent genes through a variable combined promoter region. Cell 73 (1993) 1187-1196
138. Maskell D.J., Szabo M.J., Butler P.D., Williams A.E., and Moxon E.R. Phase variation of lipopolysaccharide in Haemophilus influenzae. Res. Microbiol. 142 (1991) 719-724
139. Hood D.W., Deadman M.E., Jennings M.P., Bisercic M., Fleischmann R.D., Venter J.C., and Moxon E.R. DNA repeats identify novel virulence genes in Haemophilus influenzae. Proc. Natl. Acad. Sci. U.S.A. 93 (1996) 11121-11125
140. Banerjee A., Wang R., Uljon S.N., Rice P.A., Gotschlich E.C., and Stein D.C. Identification of the gene (lgtG) encoding the lipooligosaccharide beta chain synthesizing glucosyl transferase from Neisseria gonorrhoeae. Proc. Natl. Acad. Sci. U.S.A. 95 (1998) 10872-10877
141. Meyer T.F., and van Putten J.P. Genetic mechanisms and biological implications of phase variation in pathogenic Neisseriae. Clin. Microbiol. Rev. 2 Suppl (1989) S139-S145
142. Heidenfelder B.L., Makhov A.M., and Topal M.D. Hairpin formation in Friedreich's ataxia triplet repeat expansion. J. Biol. Chem. 278 (2003) 2425-2431
143. Kim S.H., Cai L., Pytlos M.J., Edwards S.F., and Sinden R.R. Generation of long tracts of disease-associated DNA repeats. Biotechniques 38 (2005) 247-253
144. Machuca-Tzili L., Brook D., and Hilton-Jones D. Clinical and molecular aspects of the myotonic dystrophies: a review. Muscle Nerve 32 (2005) 1-18
145. Potaman V.N., Lushnikov A.Y., Sinden R.R., and Lyubchenko Y.L. Site-specific labeling of supercoiled DNA at the A + T rich sequences. Biochemistry 41 (2002) 13198-13206
146. Escarceller M., Hicks J., Gudmundsson G., Trump G., Touati D., Lovett S., Foster P.L., McEntee K., and Goodman M.F. Involvement of Escherichia coli DNA polymerase II in response to oxidative damage and adaptive mutation. J. Bacteriol. 176 (1994) 6221-6228
147. Woodgate R. Construction of a umuDC operon substitution mutation in Escherichia coli. Mutat. Res. 281 (1992) 221-225
148. Mount D.W. A mutant of Escherichia coli showing constitutive expression of the lysogenic induction and error-prone DNA repair pathways. Proc. Natl. Acad. Sci. U.S.A. 74 (1977) 300-304