Immigration control of DNA in bacteria: self versus non-self

References

1. Abadjieva, A., Patel, J., Webb, M., Zinkevich, V. & Firman, K. ( 1993; ). A deletion mutant of the type IC restriction endonuclease EcoR1241 expressing a novel DNA specificity. Nucleic Acids Res 21, 4435-4443.[CrossRef]
   [Google Scholar]
2. Atanasiu, C., Byron, O., McMiken, H., Sturrock, S. S. & Dryden, D. T. F. ( 2001; ). Characterisation of the structure of ocr, the gene 0.3 protein of bacteriophage T7. Nucleic Acids Res 29, 3059-3068.[CrossRef]
   [Google Scholar]
3. Arber, W. ( 2000; ). Genetic variation: molecular mechanisms and impact on microbial evolution. FEMS Microbiol Rev 24, 1-7.[CrossRef]
   [Google Scholar]
4. Arber, W. & Dussoix, D. ( 1962; ). Host specificity of DNA produced by Escherichia coli. I. Host controlled modification of bacteriophage lambda. J Mol Biol 5, 18-36.[CrossRef]
   [Google Scholar]
5. Arber, W. & Morse, M. L. ( 1965; ). Host specificity of DNA produced by Escherichia coli. VI. Effects on bacterial conjugation. Genetics 51, 137-148.
   [Google Scholar]
6. Bandyopadhyay, P. K., Studier, F. W., Hamilton, D. L. & Yuan, R. ( 1985; ). Inhibition of the type I restriction-modification enzymes EcoB and EcoK by the gene 0.3 protein of bacteriophage T7. J Mol Biol 182, 567-578.[CrossRef]
   [Google Scholar]
7. Barcus, V. A. & Murray, N. E. ( 1995; ). Barriers to recombination: restriction. In Population Genetics of Bacteria (Society for General Microbiology symposium no. 52) , pp. 31-58. Edited by S. Baumberg, J. P. W. Young, E. M. H. Wellington & J. R. Saunders. Cambridge:Cambridge University Press.
8. Barcus, V. A., Titheradge, A. J. & Murray, N. E. ( 1995; ). The diversity of alleles at the hsd locus in natural populations of Escherichia coli. Genetics 140, 1187-1197.
   [Google Scholar]
9. Bates, S., Roscoe, R. A., Althorpe, N. J., Brammar, W. J. & Wilkins, B. M. ( 1999; ). Expression of leading region genes on IncI1 plasmid ColIb-P9: genetic evidence for single-stranded DNA transcription. Microbiology 145, 2655-2662.
   [Google Scholar]
10. Belogurov, A. A. & Delver, E. P. ( 1995; ). A motif conserved among the type I restriction-modification enzymes and antirestriction proteins: a possible basis for mechanism of action of plasmid-encoded antirestriction functions. Nucleic Acids Res 23, 785-787.[CrossRef]
    [Google Scholar]
11. Bertani, G. & Weigle, J. J. ( 1953; ). Host controlled variation in bacterial viruses. J Bacteriol 65, 113-121.
    [Google Scholar]
12. Biaudet, V., El Karoui, M. & Gruss, A. ( 1998; ). Codon usage can explain GT-rich islands surrounding Chi sites on the Escherichia coli genome. Mol Microbiol 29, 666-669.[CrossRef]
    [Google Scholar]
13. Bickle, T. A. (1987). Restriction and modification systems. In Escherichia coli and Salmonella, 1st edn, pp. 692–696. Edited by F. C. Neidhardt and others. Washington, DC: American Society for Microbiology.
14. Bickle, T. A. & Krüger, D. H. ( 1993; ). Biology of DNA restriction. Microbiol Rev 57, 434-450.
    [Google Scholar]
15. Blattner, F. R., Plunkett, G., III, Bloch, C. A & 14 other authors ( 1997; ). The complete genome sequence of Escherichia coli K-12. Science 277, 1453–1474.[CrossRef]
    [Google Scholar]
16. Boyer, H. ( 1964; ). Genetic control of restriction and modification in Escherichia coli. J Bacteriol 88, 1652-1660.
    [Google Scholar]
17. Boyer, H. W. & Roulland-Dussoix, D. ( 1969; ). A complementation analysis of the restriction and modification of DNA in Escherichia coli. J Mol Biol 41, 459-472.[CrossRef]
    [Google Scholar]
18. Brammar, W. J., Murray, N. E. & Winton, S. ( 1974; ). Restriction of λtrp bacteriophages by Escherichia coli K. J Mol Biol 90, 633-647.[CrossRef]
    [Google Scholar]
19. Bullas, L. R., Colson, C. & Van Pel, A. ( 1976; ). DNA restriction and modification systems in Salmonella: SQ, a new system derived by recombination between the SB system of Salmonella typhimurium and the SP system of Salmonella potsdam. J Gen Microbiol 95, 166-172.[CrossRef]
    [Google Scholar]
20. Bullas, L. R., Colson, C. & Neufeld, B. ( 1980; ). Deoxyribonucleic acid restriction and modification systems in Salmonella: chromosomally located systems of different serotypes. J Bacteriol 141, 275-292.
    [Google Scholar]
21. Burland, V., Plunkett, G.III, Daniels, D. L. & Blattner, F. R. ( 1993; ). DNA sequence and analysis of 136 kilobases of the Escherichia coli genome: organizational symmetry around the origin of replication. Genomics 16, 551-561.[CrossRef]
    [Google Scholar]
22. Chang, A. C. Y. & Cohen, S. N. ( 1977; ). In vivo site-specific genetic recombination promoted by the EcoRI restriction endonuclease. Proc Natl Acad Sci USA 74, 4811-4815.[CrossRef]
    [Google Scholar]
23. Chedin, F., Ehrlich, S. D. & Kowalczykowski, S. C. ( 2000; ). The Bacillus subtilis AddAB helicase/nuclease is regulated by its cognate Chi sequence in vitro. J Mol Biol 298, 7-20.[CrossRef]
    [Google Scholar]
24. Colbert, T., Taylor, A. F. & Smith, G. R. ( 1998; ). Genomics, Chi sites and codons: islands of preferred DNA pairing are oceans of ORFs. Trends Genet 14, 485-488.[CrossRef]
    [Google Scholar]
25. Cowan, G. M., Gann, A. A. & Murray, N. E. ( 1989; ). Conservation of complex DNA recognition domains between families of restriction enzymes. Cell 56, 103-109.[CrossRef]
    [Google Scholar]
26. Cromie, G. A. & Leach, D. R. ( 2001; ). Recombination repair of chromosomal DNA double-strand breaks generated by a restriction endonuclease. Mol Microbiol 41, 873-884.
    [Google Scholar]
27. Dabert, P., Ehrlich, S. D. & Gruss, A. ( 1992; ). χ sequence protects against RecBCD degradation of DNA in vivo. Proc Natl Acad Sci USA 89, 12073-12077.[CrossRef]
    [Google Scholar]
28. Davies, G. P., Powell, L. M., Webb, J. L., Cooper, L. P. & Murray, N. E. ( 1998; ). EcoKI with an amino acid substitution in any one of seven DEAD-box motifs has impaired ATPase and endonuclease activities. Nucleic Acids Res 26, 4828-4836.[CrossRef]
    [Google Scholar]
29. Davies, G. P., Kemp, P., Molineux, I. J. & Murray, N. E. ( 1999a; ). The DNA translocation and ATPase activities of restriction-deficient mutants of EcoKI. J Mol Biol 292, 787-796.[CrossRef]
    [Google Scholar]
30. Davies, G. P., Martin, L., Sturrock, S. S., Cronshaw, A., Murray, N. E. & Dryden, D. T. ( 1999b; ). On the structure and operation of type I DNA restriction enzymes. J Mol Biol 290, 565-579.[CrossRef]
    [Google Scholar]
31. Davison, J. & Brunel, F. ( 1979; ). Restriction insensitivity in bacteriophage T5. I. Genetic characterization of mutants sensitive to EcoRI restriction. J Virol 29, 11-16.
    [Google Scholar]
32. Dixon, D. A. & Kowalczykowski, S. C. ( 1993; ). The recombination hotspot χ is a regulatory sequence that acts by attenuating the nuclease activity of the E. coli RecBCD enzyme. Cell 73, 87-96.[CrossRef]
    [Google Scholar]
33. Dorner, L. F., Bitinaite, J., Whitaker, R. D. & Schildkraut, I. ( 1999; ). Genetic analysis of the base-specific contacts of BamHI restriction endonuclease. J Mol Biol 285, 1515-1523.[CrossRef]
    [Google Scholar]
34. Doronina, V. A. & Murray, N. E. ( 2001; ). The proteolytic control of restriction activity in Escherichia coli K-12. Mol Microbiol 39, 416-428.[CrossRef]
    [Google Scholar]
35. Dreier, J., MacWilliams, M. P. & Bickle, T. A. ( 1996; ). DNA cleavage by the type IC restriction-modification enzyme EcoR124II. J Mol Biol 264, 722-733.[CrossRef]
    [Google Scholar]
36. Dryden, D. T. F. ( 1999; ). Bacterial DNA methyltransferases. In S-adenosylmethionine-Dependent Methyltransferases: Structure and Function , pp. 283-340. Edited by X. Cheng & R. M. Blumenthal. River Edge, NJ:World Scientific Publishing.
37. Dryden, D. T. F., Murray, N. E. & Rao, D. N. ( 2001; ). Nucleoside triphosphate-dependent restriction enzymes. Nucleic Acids Res 29, 3728-3741.[CrossRef]
    [Google Scholar]
38. Dybvig, K., Sitaraman, R. & French, C. T. ( 1998; ). A family of phase-variable restriction enzymes with differing specificities generated by high-frequency gene rearrangements. Proc Natl Acad Sci USA 95, 13923-13928.[CrossRef]
    [Google Scholar]
39. Eddy, S. R. & Gold, L. ( 1992; ). The DNA restriction endonuclease of Escherichia coli B. J Biol Chem 260, 5729-5738.
    [Google Scholar]
40. Efimova, E. P., Delver, E. P. & Belogurov, A. A. ( 1988a; ). Alleviation of type I restriction in adenine methylase (dam) mutants of Escherichia coli. Mol Gen Genet 214, 313-316.[CrossRef]
    [Google Scholar]
41. Efimova, E. P., Delver, E. P. & Belogurov, A. A. ( 1988b; ). 2-Aminopurine and 5-bromouracil induce alleviation of type I restriction in Escherichia coli: mismatches function as inducing signals? Mol Gen Genet 214, 317-320.[CrossRef]
    [Google Scholar]
42. Fuller-Pace, F. V., Bullas, L. R., Delius, H. & Murray, N. E. ( 1984; ). Genetic recombination can generate altered restriction specificity. Proc Natl Acad Sci USA 81, 6095-6099.[CrossRef]
    [Google Scholar]
43. Gann, A. A., Campbell, A. J., Collins, J. F., Coulson, A. F. & Murray, N. E. ( 1987; ). Reassortment of DNA recognition domains and the evolution of new specificities. Mol Microbiol 1, 13-22.[CrossRef]
    [Google Scholar]
44. Garcia, L. R. & Molineux, I. J. ( 1999; ). Translocation and specific cleavage of bacteriophage T7 DNA in vivo by EcoKI. Proc Natl Acad Sci USA 96, 12430-12435.[CrossRef]
    [Google Scholar]
45. Glover, S. W. & Colson, S. ( 1965; ). The breakdown of the restriction mechanism in zygotes of Escherichia coli. Genet Res 6, 153-155.[CrossRef]
    [Google Scholar]
46. Glover, S. W., Firman, K., Watson, G. & Price, C. ( 1983; ). The alternative expression of two restriction and modification systems. Mol Gen Genetics 190, 65-69.[CrossRef]
    [Google Scholar]
47. Gorbalenya, A. E. & Koonin, E. V. ( 1991; ). Endonuclease (R) subunits of type-I and type-III restriction-modification enzymes contain a helicase-like domain. FEBS Lett 291, 277-281.[CrossRef]
    [Google Scholar]
48. Gottesman, S. ( 1999; ). Regulation by proteolysis: developmental switches. Curr Opin Microbiol 2, 142-147.[CrossRef]
    [Google Scholar]
49. Gough, J. A. & Murray, N. E. ( 1983; ). Sequence diversity among related genes for recognition of specific targets in DNA molecules. J Mol Biol 166, 1-19.[CrossRef]
    [Google Scholar]
50. Gubler, M., Braguglia, D., Meyer, J., Piekarowicz, A. & Bickle, T. A. ( 1992; ). Recombination of constant and variable modules alters DNA sequence recognition by type IC restriction-modification enzymes. EMBO J 11, 233-240.
    [Google Scholar]
51. Hall, M. C. & Matson, S. W. ( 1999; ). Helicase motifs: the engine that powers DNA unwinding. Mol Microbiol 34, 867-877.[CrossRef]
    [Google Scholar]
52. Handa, N., Ichige, A., Kusano, K. & Kobayashi, I. ( 2000; ). Cellular responses to postsegrational killing by restriction-modification genes. J Bacteriol 182, 2218-2229.[CrossRef]
    [Google Scholar]
53. Ives, C. L., Nathan, P. D. & Brooks, J. E. ( 1992; ). Regulation of the BamHI restriction-modification system by a small intergenic open reading frame, bamHIC, in both Escherichia coli and Bacillus subtilis. J Bacteriol 174, 7194-7201.
    [Google Scholar]
54. Ives, C. L., Sohail, A. & Brooks, J. E. ( 1995; ). The regulatory C proteins from different restriction-modification systems can cross-complement. J Bacteriol 177, 6313-6315.
    [Google Scholar]
55. Janscak, P., MacWilliams, M. P., Sandmeier, U., Nagaraja, V. & Bickle, T. A. ( 1999a; ). DNA translocation blockage, a general mechanism of cleavage site selection by type I restriction enzymes. EMBO J 18, 2638-2647.[CrossRef]
    [Google Scholar]
56. Janscak, P., Sandmeier, U. & Bickle, T. A. ( 1999b; ). Single amino acid substitutions in the HsdR subunit of the type IB restriction enzyme EcoAI uncouple the DNA translocation and DNA cleavage activities of the enzyme. Nucleic Acids Res 27, 2638-2643.[CrossRef]
    [Google Scholar]
57. Kannan, P., Cowan, G. M., Daniel, A. S., Gann, A. A. & Murray, N. E. ( 1989; ). Conservation of organization in the specificity polypeptides of two families of type I restriction enzymes. J Mol Biol 209, 335-344.[CrossRef]
    [Google Scholar]
58. King, G. & Murray, N. E. ( 1994; ). Restriction enzymes in cells, not Eppendorfs. Trends Microbiol 2, 465-469.[CrossRef]
    [Google Scholar]
59. Kobayashi, I. ( 1998; ). Selfishness and death: raison d’etre of restriction, recombination and mitochondria. Trends Genet 14, 368-374.[CrossRef]
    [Google Scholar]
60. Kobayashi, I. ( 2001; ). Behaviour of restriction-modification systems as selfish mobile elements and its relationship with genome evolution. Nucleic Acids Res 29, 3742-3756.[CrossRef]
    [Google Scholar]
61. Kong, H., Lin, L.-F., Porter, N., Stickel, S., Byrd, D., Posfai, J. & Roberts, R. J. ( 2000; ). Functional analysis of putative restriction-modification system genes in the Helicobacter pylori J99 genome. Nucleic Acids Res 28, 3216-3223.[CrossRef]
    [Google Scholar]
62. Köppen, A., Krobitsch, S., Thoms, B. & Wackernagel, W. ( 1995; ). Interaction with the recombination hot spot χ in vivo converts the RecBCD enzyme of Escherichia coli into a χ-independent recombinase by inactivation of the RecD subunit. Proc Natl Acad Sci USA 92, 6249-6253.[CrossRef]
    [Google Scholar]
63. Kowalczykowski, S. C., Dixon, D. A., Eggleston, A. K., Lauder, S. D. & Rehrauer, W. M. ( 1994; ). Biochemistry of homologous recombination in Escherichia coli. Microbiol Rev 58, 401-465.
    [Google Scholar]
64. Kulik, E. M. & Bickle, T. A. ( 1996; ). Regulation of the activity of the type IC EcoR124I restriction enzyme. J Mol Biol 264, 891-906.[CrossRef]
    [Google Scholar]
65. Kuzminov, A. ( 1999; ). Recombinational repair of DNA damage in Escherichia coli and bacteriophage lambda. Microbiol Mol Biol Rev 63, 751-813.
    [Google Scholar]
66. Kuzminov, A., Schabtach, E. & Stahl, F. W. ( 1994; ). χ sites in combination with RecA protein increase the survival of linear DNA in Escherichia coli by inactivating ExoV activity of RecBCD nuclease. EMBO J 13, 2764-2776.
    [Google Scholar]
67. Lanio, T., Jeltsch, A. & Pingoud, A. ( 2000; ). On the possibilities and limitations of rational protein design to expand the specificity of restriction enzymes: a case study employing EcoRV as the target. Protein Enz 13, 275-281.[CrossRef]
    [Google Scholar]
68. Lautenberger, J. A. & Linn, S. ( 1972; ). The deoxyribonucleic acid modification and restriction enzymes of Escherichia coli B. I. Purification, subunit structure, and catalytic properties of the modification methylase. J Biol Chem 247, 6176-6182.
    [Google Scholar]
69. Linn, S. & Arber, W. ( 1968; ). Host specificity of DNA produced by Escherichia coli. X. In vitro restriction of phage fd replication form. Proc Natl Acad Sci USA 59, 1300.[CrossRef]
    [Google Scholar]
70. Loenen, W. A., Daniel, A. S., Braymer, H. D. & Murray, N. E. ( 1987; ). Organization and sequence of the hsd genes of Escherichia coli K-12. J Mol Biol 198, 159-170.[CrossRef]
    [Google Scholar]
71. McCorquodale, J. D. & Warner, H. R. ( 1988; ). Bacteriophage T5 and related phages. In The Bacteriophages , pp. 439-476. Edited by R. Calendar. New York:Plenum.
72. McKane, M. & Milkman, R. ( 1995; ). Transduction, restriction and recombination patterns in Escherichia coli. Genetics 139, 35-43.
    [Google Scholar]
73. Makovets, S., Titheradge, A. J. B. & Murray, N. E. ( 1998; ). ClpX and ClpP are essential for the efficient acquisition of genes specifying type IA and IB restriction systems. Mol Microbiol 28, 25-35.
    [Google Scholar]
74. Makovets, S., Doronina, V. A. & Murray, N. E. ( 1999; ). Regulation of endonuclease activity by proteolysis prevents breakage of unmodified bacterial chromosomes by type I restriction enzymes. Proc Natl Acad Sci USA 96, 9757-9762.[CrossRef]
    [Google Scholar]
75. Matic, I., Taddei, F. & Radman, M. ( 1996; ). Genetic barriers among bacteria. Trends Microbiol 4, 69-72.[CrossRef]
    [Google Scholar]
76. Meisel, A., Mackeldanz, P., Bickle, T. A., Krüger, D. V. & Schroeder, C. ( 1995; ). Type III restriction endonucleases translocate DNA in a reaction driven by recognition site-specific ATP hydrolysis. EMBO J 14, 2958-2966.
    [Google Scholar]
77. Meister, J., MacWilliams, M., Hubner, P., Jutte, H., Skrzypek, E., Piekarowicz, A. & Bickle, T. A. ( 1993; ). Macroevolution by transposition: drastic modification of DNA recognition by a type I restriction enzyme following Tn5 transposition. EMBO J 12, 4585-4591.
    [Google Scholar]
78. Meselson, M. & Yuan, R. ( 1968; ). DNA restriction enzyme from E. coli. Nature 217, 1110-1114.[CrossRef]
    [Google Scholar]
79. Milkman, R., Raleigh, E. A., McKane, M., Cryderman, D., Bilodeau, P. & McWeeny, K. ( 1999; ). Molecular evolution of the Escherichia coli chromosome. V. Recombination patterns among strains of diverse origin. Genetics 153, 539-554.
    [Google Scholar]
80. Murray, N. E. ( 2000; ). Type I restriction systems: sophisticated molecular machines (a legacy of Bertani and Weigle). Microbiol Mol Biol Rev 64, 412-434.[CrossRef]
    [Google Scholar]
81. Murray, N. E., Gough, J. A., Suri, B. & Bickle, T. A. ( 1982; ). Structural homologies among type I restriction–modification systems. EMBO J 1, 535-539.
    [Google Scholar]
82. Murray, N. E., Daniel, A. S., Cowan, G. M. & Sharp, P. M. ( 1993; ). Conservation of motifs within the unusually variable polypeptide sequences of type I restriction and modification enzymes. Mol Microbiol 9, 133-143.[CrossRef]
    [Google Scholar]
83. Myers, R. S. & Stahl, F. W. ( 1994; ). χ and the RecBCD enzyme of Escherichia coli. Annu Rev Genet 28, 49-70.[CrossRef]
    [Google Scholar]
84. Myers, R. S., Kuzminov, A. & Stahl, F. W. ( 1995; ). The recombination hot spot χ activates RecBCD recombination by converting Escherichia coli to a recD mutant phenocopy. Proc Natl Acad Sci USA 92, 6244-6248.[CrossRef]
    [Google Scholar]
85. Nagaraja, V., Shepherd, J. C. & Bickle, T. A. ( 1985; ). A hybrid recognition sequence in a recombinant restriction enzyme and the evolution of DNA sequence specificity. Nature 316, 371-372.[CrossRef]
    [Google Scholar]
86. Naito, T., Kusano, K. & Kobayashi, I. ( 1995; ). Selfish behaviour of restriction-modification systems. Science 267, 897-899.[CrossRef]
    [Google Scholar]
87. O’Neill, M., Chen, A. & Murray, N. E. ( 1997; ). The restriction-modification genes of Escherichia coli K-12 may not be selfish: they do not resist loss and are readily replaced by alleles conferring different specificities. Proc Natl Acad Sci USA 94, 14596-14601.[CrossRef]
    [Google Scholar]
88. O’Neill, M., Powell, L. & Murray, N. E. ( 2001; ). Target recognition by EcoKI: the recognition domain is robust and restriction-deficiency commonly results from the proteolytic control of enzyme activity. J Mol Biol 307, 951-963.[CrossRef]
    [Google Scholar]
89. Perna, N. T., Plunkett, G., III, Burland, V. & 25 other authors ( 2001; ). Genome sequence of enterohaemorrhagic Escherichia coli O157 : H7. Nature 409, 529–533.[CrossRef]
    [Google Scholar]
90. Pilarski, L. M. & Egan, J. B. ( 1973; ). Role of DNA topology in transcription of coliphage λ in vivo: M DNA topology protects the template from exonuclease attack. J Mol Biol 76, 257-266.[CrossRef]
    [Google Scholar]
91. Pingoud, A. & Jeltsch, A. ( 2001; ). Structure and function of type II restriction endonucleases. Nucleic Acids Res 29, 3705-3727.[CrossRef]
    [Google Scholar]
92. Pittard, J. ( 1964; ). Effect of phage-controlled restriction on genetic linkage in bacterial crosses. J Bacteriol 87, 1256-1257.
    [Google Scholar]
93. Ponticelli, A. S., Schultz, D. W., Taylor, A. F. & Smith, G. R. ( 1985; ). Chi-dependent DNA strand cleavage by RecBC enzyme. Cell 41, 145-151.[CrossRef]
    [Google Scholar]
94. Powell, L. M., Dryden, D. T. & Murray, N. E. ( 1998; ). Sequence-specific DNA binding by EcoKI, a type IA DNA restriction enzyme. J Mol Biol 283, 963-976.[CrossRef]
    [Google Scholar]
95. Prakash-Cheng, A. & Ryu, J. ( 1993; ). Delayed expression of in vivo restriction activity following conjugal transfer of Escherichia coli hsdK (restriction-modification) genes. J Bacteriol 175, 4905-4906.
    [Google Scholar]
96. Prakash-Cheng, A., Chung, S. S. & Ryu, J. ( 1993; ). The expression and regulation of hsdK genes after conjugative transfer. Mol Gen Genet 241, 491-496.
    [Google Scholar]
97. Price, C. & Bickle, T. A. ( 1986; ). A possible role for DNA restriction in bacterial evolution. Microbiol Sci 3, 296-299.
    [Google Scholar]
98. Price, C., Pripfl, T. & Bickle, T. A. ( 1987; ). EcoR124 and EcoR124/3: the first members of a new family of type I restriction and modification systems. Eur J Biochem 167, 111-115.[CrossRef]
    [Google Scholar]
99. Price, C., Lingner, J., Bickle, T. A., Firman, K. & Glover, S. W. ( 1989; ). Basis for changes in DNA recognition by the EcoR124 and EcoR124/3 type I DNA restriction and modification enzymes. J Mol Biol 205, 115-125.[CrossRef]
    [Google Scholar]
100. Radding, C. M. ( 1973; ). Molecular mechanisms in genetic recombination. Annu Rev Genet 7, 87-111.[CrossRef]
     [Google Scholar]
101. Raleigh, E. A. ( 1992; ). Organization and function of the mcrBC genes of Escherichia coli K-12. Mol Microbiol 6, 1079-1086.[CrossRef]
     [Google Scholar]
102. Raleigh, E. A. & Brooks, J. E. ( 1998; ). Restriction–modification systems; where they are and what they do. In Bacterial Genomes: Physical Structure and Analysis , pp. 78-92. Edited by F. J. de Bruijn, J. R. Lupski & G. M. Weinstock. New York:Chapman & Hall.
103. Rao, D. N., Saga, S. & Krishnamurthy, V. ( 2000; ). The ATP-dependent restriction enzymes. Prog Nucleic Acids Res Mol Biol 64, 1-63.
     [Google Scholar]
104. Read, T. D., Thomas, A. T. & Wilkins, B. M. ( 1992; ). Evasion of type I and type II DNA restriction systems by IncI1 plasmid ColIb-P9 during transfer by bacterial conjugation. Mol Microbiol 6, 1933-1941.[CrossRef]
     [Google Scholar]
105. Redaschi, N. & Bickle, T. A. (1996). DNA restriction and modification systems. In Escherichia coli and Salmonella: Cellular and Molecular Biology, 2nd edn, pp. 773–781. Edited by F. C. Neidhardt and others. Washington, DC: American Society for Microbiology.
106. Roberts, R. J. & Halford, S. E. ( 1993; ). Type II endonucleases. In Nucleases , pp. 35-88. Edited by S. M. Linn, R. S. Lloyd & R. J. Roberts. Cold Spring Harbor, NY:Cold Spring Harbor Press.
107. Roberts, R. J. & Macelis, D. ( 2000; ). REBASE – restriction enzymes and methylases. Nucleic Acids Res 28, 306-307.[CrossRef]
     [Google Scholar]
108. Salaj-Šmic, E., Maršic, N., Trgovcevic, Z. & Lloyd, R. G. ( 1997; ). Modulation of EcoKI restriction in vivo: role of the λGam protein and plasmic metabolism. J Bacteriol 179, 1852-1856.
     [Google Scholar]
109. Sharp, P. M., Kelleher, J. E., Daniel, A. S., Cowan, G. M. & Murray, N. E. ( 1992; ). Roles of selection and recombination in the evolution of type I restriction-modification systems in enterobacteria. Proc Natl Acad Sci USA 89, 9836-9840.[CrossRef]
     [Google Scholar]
110. Simmon, V. F. & Lederberg, S. ( 1972; ). Degradation of bacteriophage lambda deoxyribonucleic acid after restriction by Escherichia coli K-12. J Bacteriol 112, 161-169.
     [Google Scholar]
111. Smith, G. R. ( 2001; ). Homologous recombination near and far from DNA breaks: alternative roles and contrasting views. Annu Rev Genetics 35, 243-274.[CrossRef]
     [Google Scholar]
112. Smith, J. D., Arber, W. & Kuhnlein, U. ( 1972; ). Host specificity of DNA produced by Escherichia coli. XIV. The role of nucleotide methylation in in vivo B-specific modification. J Mol Biol 63, 1-8.[CrossRef]
     [Google Scholar]
113. Smith, G. R., Amundsen, S. K., Dabert, P. & Taylor, A. F. ( 1995; ). The initiation and control of homologous recombination in Escherichia coli. Philos Trans R Soc Lond B Biol Sci 347, 13-20.[CrossRef]
     [Google Scholar]
114. Stahl, F. W., Stahl, M. M., Malone, R. E. & Craseman, J. M. ( 1980; ). Directionality and nonreciprocality of Chi-stimulated recombination in phage lambda. Genetics 94, 235-248.
     [Google Scholar]
115. Stahl, M. M., Kobayashi, I., Stahl, F. W. & Huntingdon, S. K. ( 1983; ). Activation of Chi, a recombinator, by the action of endonuclease at a distant site. Proc Natl Acad Sci USA 80, 2310-2313.[CrossRef]
     [Google Scholar]
116. Studier, F. W. & Bandyopadhyay, P. K. ( 1988; ). Model for how type I restriction enzymes select cleavage sites in DNA. Proc Natl Acad Sci USA 85, 4677-4681.[CrossRef]
     [Google Scholar]
117. Suri, B. & Bickle, T. A. ( 1985; ). EcoA: the first member of a new family of type I restriction modification systems: gene organization and enzymic activities. J Mol Biol 186, 77-85.[CrossRef]
     [Google Scholar]
118. Szczelkun, M. D. (2000). How do proteins move along DNA? Lessons from type I and type III restriction endonucleases. In Essays in Biochemistry, vol. 35. Edited by G. Banting & S. J. Higgins. London: Portland Press.
119. Tao, T. & Blumenthal, R. M. ( 1992; ). Sequence and characterization of pvuIIR, the PvuII endonuclease gene, and of pvuIIC, its regulatory gene. J Bacteriol 174, 3395-3398.
     [Google Scholar]
120. Tao, T., Bourne, J. C. & Blumenthal, R. M. ( 1991; ). A family of regulatory genes associated with type II restriction-modification systems. J Bacteriol 173, 1367-1375.
     [Google Scholar]
121. Taylor, A. F. & Smith, G. R. ( 1990; ). Action of RecBCD enzyme on cruciform DNA. J Mol Biol 211, 117-134.[CrossRef]
     [Google Scholar]
122. Taylor, A. F. & Smith, G. R. ( 1999; ). Regulation of homologous recombination: Chi inactivates RecBCD enzyme by disassembly of the three subunits. Genes Dev 13, 890-900.[CrossRef]
     [Google Scholar]
123. Taylor, A. F., Schultz, D. W., Ponticelli, A. S. & Smith, G. R. ( 1985; ). RecBC enzyme nicking at Chi sites during DNA unwinding: location and orientation dependence of cutting. Cell 41, 153-163.[CrossRef]
     [Google Scholar]
124. Taylor, I., Patel, J., Firman, K. & Kneale, G. ( 1992; ). Purification and biochemical characteristation of the EcoR124 type I modification methylase. Nucleic Acids Res 20, 179-186.[CrossRef]
     [Google Scholar]
125. Taylor, I., Watts, D. & Kneale, G. ( 1993; ). Substrate recognition and selectivity in the type IC DNA modification methylase M EcoR124I. Nucleic Acids Res 21, 4929-4935.[CrossRef]
     [Google Scholar]
126. Telander-Muskavitch, K. M. & Linn, S. ( 1981; ). RecBC-like enzymes: exonuclease V deoxyribonucleases. Enzymes 14A, 233-250.
     [Google Scholar]
127. Thaler, D. S., Stahl, M. M. & Stahl, F. W. ( 1987; ). Tests of the double-strand-break repair model for Red-mediated recombination of phage λ and plasmid dv. Genetics 116, 501-511.
     [Google Scholar]
128. Thoms, B. & Wackernagel, W. ( 1984; ). Genetic control of damage-inducible restriction alleviation in Escherichia coli K12: an SOS function not repressed by lexA. Mol Gen Genet 197, 297-303.[CrossRef]
     [Google Scholar]
129. Thorpe, P. H., Ternent, D. & Murray, N. E. ( 1997; ). The specificity of StySKI, a type I restriction enzyme, implies a structure with rotational symmetry. Nucleic Acids Res 25, 1694-1700.[CrossRef]
     [Google Scholar]
130. Titheradge, A. J. B., Ternent, D. & Murray, N. E. ( 1996; ). A third family of allelic hsd genes in Salmonella enterica: sequence comparisons with related proteins identify conserved regions implicated in restriction of DNA. Mol Microbiol 22, 437-447.[CrossRef]
     [Google Scholar]
131. Titheradge, A. J. B., King, J., Ryu, J. & Murray, N. E. ( 2001; ). Families of restriction enzymes: an analysis prompted by molecular and genetic data for type ID restriction and modification systems. Nucleic Acids Res 29, 4195-4205.[CrossRef]
     [Google Scholar]
132. Tyndall, C., Meister, J. & Bickle, T. A. ( 1994; ). The Escherichia coli prr region encodes a functional type IC DNA restriction system closely integrated with an anticodon nuclease gene. J Mol Biol 237, 266-274.[CrossRef]
     [Google Scholar]
133. Willcock, D. F., Dryden, D. T. & Murray, N. E. ( 1994; ). A mutational analysis of the two motifs common to adenine methyltransferases. EMBO J 13, 3902-3908.
     [Google Scholar]
134. Wilson, G. G. & Murray, N. E. ( 1991; ). Restriction and modification systems. Annu Rev Genet 25, 585-627.[CrossRef]
     [Google Scholar]