To be or not to be: Regulation of restriction-modification systems and other toxin-antitoxin systems

Nucleic Acids Research

Volumn 42, Issue 1, 2014, Pages 70-86

  Mruk, Iwona ^a   Kobayashi, Ichizo ^b  

^a UNIVERSITY OF GDA SK   (Poland)

^b UNIVERSITY OF TOKYO   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ANTITOXIN; COMPLEMENTARY RNA; MESSENGER RNA; PROTEIN C; TOXIN; TRANSCRIPTOME;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; BACTERIOPHAGE; CELL MOTILITY; CELLULAR STRESS RESPONSE; DNA METHYLATION; DNA SEQUENCE; ENZYME MODIFICATION; EPIGENETICS; GENE EXPRESSION REGULATION; GENE INTERACTION; GENE SEGREGATION; GENETIC CONSERVATION; MOLECULAR BIOLOGY; NONHUMAN; POPULATION ABUNDANCE; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; RESTRICTION MODIFICATION SYSTEM; REVIEW; SEQUENCE HOMOLOGY; TOXIN ANTITOXIN SYSTEM; TRANSCRIPTION REGULATION; BACTERIAL GENETICS; MICROBIOLOGICAL PHENOMENA AND FUNCTIONS; MOLECULAR EVOLUTION; MOLECULAR INTERACTION; STRUCTURE ACTIVITY RELATION; TOXIN ANALYSIS;

EID: 84888261745     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt711     Document Type: Review

References (210)

1. Engelberg-Kulka, H., Amitai, S., Kolodkin-Gal, I. and Hazan, R. (2006) Bacterial programmed cell death and multicellular behavior in bacteria. PLoS Genet., 2, e135.
2. Hazan, R. and Engelberg-Kulka, H. (2004) Escherichia coli mazEFmediated cell death as a defense mechanism that inhibits the spread of phage P1. Mol. Genet. Genomics, 272, 227-234
3. Kobayashi, I. (2004) Genetic addiction-A principle in symbiosis of genes in a genome. In: Phillips, G. and Funnell, B. (eds), Plasmid Biology. ASM Press, Washington, DC, pp. 105-144
4. Gerdes, K., Rasmussen, P.B. and Molin, S. (1986) Unique type of plasmid maintenance function: Postsegregational killing of plasmid-free cells. Proc. Natl Acad. Sci. USA, 83, 3116-3120
5. Tsilibaris, V., Maenhaut-Michel, G., Mine, N. and Van Melderen, L. (2007) What is the benefit to Escherichia coli of having multiple toxin-Antitoxin systems in its genomëJ. Bacteriol., 189, 6101-6108
6. Szekeres, S., Dauti, M., Wilde, C., Mazel, D. and Rowe- Magnus, D.A. (2007) Chromosomal toxin-Antitoxin loci can diminish large-scale genome reductions in the absence of selection. Mol. Microbiol., 63, 1588-1605
7. Wozniak, R.A. and Waldor, M.K. (2009) A toxin-Antitoxin system promotes the maintenance of an integrative conjugative element. PLoS Genet., 5, e1000439
8. Van Melderen, L. (2010) Toxin-Antitoxin systems: Why so many, what for? Curr. Opin. Microbiol., 13, 781-785
9. Fukuda, E., Kaminska, K.H., Bujnicki, J.M. and Kobayashi, I. (2008) Cell death upon epigenetic genome methylation: A novel function of methyl-specific deoxyribonucleases. Genome Biol., 9, R163
10. Ishikawa, K., Fukuda, E. and Kobayashi, I. (2010) Conflicts targeting epigenetic systems and their resolution by cell death: Novel concepts for methyl-specific and other restriction systems. DNA Res., 17, 325-342
11. Makarova, K.S., Wolf, Y.I. and Koonin, E.V. (2013) Comparative genomics of defense systems in archaea and bacteria. Nucleic Acids Res., 41, 4360-4377
12. Asakura, Y. and Kobayashi, I. (2009) From damaged genome to cell surface: Transcriptome changes during bacterial cell death triggered by loss of a restriction-modification gene complex. Nucleic Acids Res., 37, 3021-3031
13. Ishikawa, K., Handa, N. and Kobayashi, I. (2009) Cleavage of a model DNA replication fork by a Type I restriction endonuclease. Nucleic Acids Res., 37, 3531-3544
14. Yamaguchi, Y. and Inouye, M. (2011) Regulation of growth and death in Escherichia coli by toxin-Antitoxin systems. Nat. Rev. Microbiol., 9, 779-790
15. Kawano, M. (2012) Divergently overlapping cis-encoded antisense RNA regulating toxin-Antitoxin systems from E. coli: Hok/sok, ldr/rdl, symE/symR. RNA Biol., 9, 1520-1527
16. Brantl, S. (2012) Bacterial type I toxin-Antitoxin systems. RNA Biol., 9, 1488-1490
17. Furuta, Y. and Kobayashi, I. (2012) Mobility of DNA sequence recognition domains in DNA methyltransferases suggests epigenetics-driven adaptive evolution. Mob. Genet. Elements, 2, 292-296
18. Vasu, K. and Nagaraja, V. (2013) Diverse functions of restrictionmodification systems in addition to cellular defense. Microbiol. Mol. Biol. Rev., 77, 53-72
19. Fozo, E.M., Hemm, M.R. and Storz, G. (2008) Small toxic proteins and the antisense RNAs that repress them. Microbiol. Mol. Biol. Rev., 72, 579-589
20. Fozo, E.M., Makarova, K.S., Shabalina, S.A., Yutin, N., Koonin, E.V. and Storz, G. (2011) Abundance of type I toxin-Antitoxin systems in bacteria: Searches for new candidates and discovery of novel families. Nucleic Acids Res., 38, 3743-3759
21. Gerdes, K., Christensen, S.K. and Lobner-Olesen, A. (2005) Prokaryotic toxin-Antitoxin stress response loci. Nat. Rev. Microbiol., 3, 371-382
22. Leplae, R., Geeraerts, D., Hallez, R., Guglielmini, J., Dreze, P. and Van Melderen, L. (2011) Diversity of bacterial type II toxinantitoxin systems: A comprehensive search and functional analysis of novel families. Nucleic Acids Res., 39, 5513-5525
23. Fineran, P.C., Blower, T.R., Foulds, I.J., Humphreys, D.P., Lilley, K.S. and Salmond, G.P. (2009) The phage abortive infection system, ToxIN, functions as a protein-RNA toxin-Antitoxin pair. Proc. Natl Acad. Sci. USA, 106, 894-899
24. Blower, T.R., Short, F.L., Rao, F., Mizuguchi, K., Pei, X.Y., Fineran, P.C., Luisi, B.F. and Salmond, G.P. (2012) Identification and classification of bacterial Type III toxin-Antitoxin systems encoded in chromosomal and plasmid genomes. Nucleic Acids Res., 40, 6158-6173
25. Masuda, H., Tan, Q., Awano, N., Wu, K.P. and Inouye, M. (2012) YeeU enhances the bundling of cytoskeletal polymers of MreB and FtsZ, antagonizing the CbtA (YeeV) toxicity in Escherichia coli. Mol. Microbiol., 84, 979-989
26. Wang, X., Lord, D.M., Cheng, H.Y., Osbourne, D.O., Hong, S.H., Sanchez-Torres, V., Quiroga, C., Zheng, K., Herrmann, T., Peti, W. et al. (2012) A new type V toxin-Antitoxin system where mRNA for toxin GhoT is cleaved by antitoxin GhoS. Nat. Chem. Biol., 8, 855-861
27. Zhang, J., Zhang, Y. and Inouye, M. (2003) Characterization of the interactions within the mazEF addiction module of Escherichia coli. J. Biol. Chem., 278, 32300-32306
28. Aizenman, E., Engelberg-Kulka, H. and Glaser, G. (1996) An Escherichia coli chromosomal ''addiction module'' regulated by guanosine [corrected] 3', 5'-bispyrophosphate: A model for programmed bacterial cell death. Proc. Natl Acad. Sci. USA, 93, 6059-6063
29. Liu, M., Zhang, Y., Inouye, M. and Woychik, N.A. (2008) Bacterial addiction module toxin Doc inhibits translation elongation through its association with the 30S ribosomal subunit. Proc. Natl Acad. Sci. USA, 105, 5885-5890
30. Ramage, H.R., Connolly, L.E. and Cox, J.S. (2009) Comprehensive functional analysis of Mycobacterium tuberculosis toxin-Antitoxin systems: Implications for pathogenesis, stress responses, and evolution. PLoS Genet., 5, e1000767
31. Winther, K.S. and Gerdes, K. (2011) Enteric virulence associated protein VapC inhibits translation by cleavage of initiator tRNA. Proc. Natl Acad. Sci. USA, 108, 7403-7407
32. Miallau, L., Faller, M., Chiang, J., Arbing, M., Guo, F., Cascio, D. and Eisenberg, D. (2009) Structure and proposed activity of a member of the VapBC family of toxin-Antitoxin systems. VapBC- 5 from Mycobacterium tuberculosis. J. Biol. Chem., 284, 276-283
33. Simic, M., De Jonge, N., Loris, R., Vesnaver, G. and Lah, J. (2009) Driving forces of gyrase recognition by the addiction toxin CcdB. J. Biol. Chem., 284, 20002-20010
34. Jensen, R.B. and Gerdes, K. (1995) Programmed cell death in bacteria: Proteic plasmid stabilization systems. Mol. Microbiol., 17, 205-210
35. Wilbaux, M., Mine, N., Guerout, A.M., Mazel, D. and Van Melderen, L. (2007) Functional interactions between coexisting toxin-Antitoxin systems of the ccd family in Escherichia coli O157:H7. J. Bacteriol., 189, 2712-2719
36. Couturier, M., Bahassi el, M. and Van Melderen, L. (1998) Bacterial death by DNA gyrase poisoning. Trends Microbiol., 6, 269-275
37. Meinhart, A., Alonso, J.C., Strater, N. and Saenger, W. (2003) Crystal structure of the plasmid maintenance system epsilon/zeta: Functional mechanism of toxin zeta and inactivation by epsilon 2 zeta 2 complex formation. Proc. Natl Acad. Sci. USA, 100, 1661-1666
38. Mutschler, H., Gebhardt, M., Shoeman, R.L. and Meinhart, A. (2011) A novel mechanism of programmed cell death in bacteria by toxin-Antitoxin systems corrupts peptidoglycan synthesis. PLoS Biol., 9, e1001033
39. Mutschler, H. and Meinhart, A. (2011) epsilon/zeta systems: Their role in resistance, virulence, and their potential for antibiotic development. J. Mol. Med. (Berl.), 89, 1183-1194
40. Lioy, V.S., Martin, M.T., Camacho, A.G., Lurz, R., Antelmann, H., Hecker, M., Hitchin, E., Ridge, Y., Wells, J.M. and Alonso, J.C. (2006) pSM19035-encoded zeta toxin induces stasis followed by death in a subpopulation of cells. Microbiology, 152, 2365-2379
41. Hansen, S., Vulic, M., Min, J., Yen, T.J., Schumacher, M.A., Brennan, R.G. and Lewis, K. (2012) Regulation of the Escherichia coli HipBA Toxin-Antitoxin System by Proteolysis. PLoS One, 7, e39185
42. Correia, F.F., D'Onofrio, A., Rejtar, T., Li, L., Karger, B.L., Makarova, K., Koonin, E.V. and Lewis, K. (2006) Kinase activity of overexpressed HipA is required for growth arrest and multidrug tolerance in Escherichia coli. J. Bacteriol., 188, 8360-8367
43. Schumacher, M.A., Piro, K.M., Xu, W., Hansen, S., Lewis, K. and Brennan, R.G. (2009) Molecular mechanisms of HipA-mediated multidrug tolerance and its neutralization by HipB. Science, 323, 396-401
44. Blower, T.R., Fineran, P.C., Johnson, M.J., Toth, I.K., Humphreys, D.P. and Salmond, G.P. (2009) Mutagenesis and functional characterization of the RNA and protein components of the toxIN abortive infection and toxin-Antitoxin locus of Erwinia. J. Bacteriol., 191, 6029-6039
45. Gerdes, K., Thisted, T. and Martinussen, J. (1990) Mechanism of post-segregational killing by the hok/sok system of plasmid R1: Sok antisense RNA regulates formation of a hok mRNA species correlated with killing of plasmid-free cells. Mol. Microbiol., 4, 1807-1818
46. Kawano, M., Oshima, T., Kasai, H. and Mori, H. (2002) Molecular characterization of long direct repeat (LDR) sequences expressing a stable mRNA encoding for a 35-Amino-Acid cell-killing peptide and a cis-encoded small antisense RNA in Escherichia coli. Mol. Microbiol., 45, 333-349
47. Unoson, C. and Wagner, E.G. (2008) A small SOS-induced toxin is targeted against the inner membrane in Escherichia coli. Mol. Microbiol., 70, 258-270
48. Vogel, J., Argaman, L., Wagner, E.G. and Altuvia, S. (2004) The small RNA IstR inhibits synthesis of an SOS-induced toxic peptide. Curr. Biol., 14, 2271-2276
49. Kawano, M., Aravind, L. and Storz, G. (2007) An antisense RNA controls synthesis of an SOS-induced toxin evolved from an antitoxin. Mol. Microbiol., 64, 738-754
50. Fozo, E.M., Kawano, M., Fontaine, F., Kaya, Y., Mendieta, K.S., Jones, K.L., Ocampo, A., Rudd, K.E. and Storz, G. (2008) Repression of small toxic protein synthesis by the Sib and OhsC small RNAs. Mol. Microbiol., 70, 1076-1093
51. Mok, W.W., Patel, N.H. and Li, Y. (2010) Decoding toxicity: Deducing the sequence requirements of IbsC, a type I toxin in Escherichia coli. J. Biol. Chem., 285, 41627-41636
52. Silvaggi, J.M., Perkins, J.B. and Losick, R. (2005) Small untranslated RNA antitoxin in Bacillus subtilis. J. Bacteriol., 187, 6641-6650
53. Silvaggi, J.M., Perkins, J.B. and Losick, R. (2006) Genes for small, noncoding RNAs under sporulation control in Bacillus subtilis. J. Bacteriol., 188, 532-541
54. Shokeen, S., Greenfield, T.J., Ehli, E.A., Rasmussen, J., Perrault, B.E. and Weaver, K.E. (2009) An intramolecular upstream helix ensures the stability of a toxin-encoding RNA in Enterococcus faecalis. J. Bacteriol., 191, 1528-1536
55. Greenfield, T.J., Ehli, E., Kirshenmann, T., Franch, T., Gerdes, K. and Weaver, K.E. (2000) The antisense RNA of the par locus of pAD1 regulates the expression of a 33-Amino-Acid toxic peptide by an unusual mechanism. Mol. Microbiol., 37, 652-660
56. Greenfield, T.J., Franch, T., Gerdes, K. and Weaver, K.E. (2001) Antisense RNA regulation of the par post-segregational killing system: Structural analysis and mechanism of binding of the antisense RNA, RNAII and its target, RNAI. Mol. Microbiol., 42, 527-537
57. Greenfield, T.J. and Weaver, K.E. (2000) Antisense RNA regulation of the pAD1 par post-segregational killing system requires interaction at the 5' and 3' ends of the RNAs. Mol. Microbiol., 37, 661-670
58. Weaver, K.E., Weaver, D.M., Wells, C.L., Waters, C.M., Gardner, M.E. and Ehli, E.A. (2003) Enterococcus faecalis plasmid pAD1-encoded Fst toxin affects membrane permeability and alters cellular responses to lantibiotics. J. Bacteriol., 185, 2169-2177
59. Nielsen, A.K., Thorsted, P., Thisted, T., Wagner, E.G. and Gerdes, K. (1991) The rifampicin-inducible genes srnB from F and pnd from R483 are regulated by antisense RNAs and mediate plasmid maintenance by killing of plasmid-free segregants. Mol. Microbiol., 5, 1961-1973
60. Jahn, N., Preis, H., Wiedemann, C. and Brantl, S. (2012) BsrG/SR4 from Bacillus subtilis- The first temperature-dependent type I toxin-Antitoxin system. Mol. Microbiol., 83, 579-598
61. Guglielmini, J. and Van Melderen, L. (2011) Bacterial toxinantitoxin systems: Translation inhibitors everywhere. Mob. Genet. Elements, 1, 283-290
62. Roberts, R.J., Belfort, M., Bestor, T., Bhagwat, A.S., Bickle, T.A., Bitinaite, J., Blumenthal, R.M., Degtyarev, S., Dryden, D.T., Dybvig, K. et al. (2003) A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes. Nucleic Acids Res., 31, 1805-1812
63. O'Neill, M., Chen, A. and Murray, N.E. (1997) The restrictionmodification 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
64. Furuta, Y., Kawai, M., Uchiyama, I. and Kobayashi, I. (2011) Domain movement within a gene: A novel evolutionary mechanism for protein diversification. PLoS One, 6, e18819.
65. Murray, N.E. (2000) Type I restriction systems: Sophisticated molecular machines (a legacy of Bertani and Weigle). Microbiol. Mol. Biol. Rev., 64, 412-434
66. Raghavendra, N.K., Bheemanaik, S. and Rao, D.N. (2012) Mechanistic insights into type III restriction enzymes. Front. Biosci., 17, 1094-1107
67. Ershova, A.S., Karyagina, A.S., Vasiliev, M.O., Lyashchuk, A.M., Lunin, V.G., Spirin, S.A. and Alexeevski, A.V. (2012) Solitary restriction endonucleases in prokaryotic genomes. Nucleic Acids Res., 40, 10107-10115
68. Kobayashi, I. (2004) Restriction-modification systems as minimal forms of life. In: Pingoud, A. (ed.), Restriction Endonucleases. Springer, Berlin, pp. 19-62
69. Furuta, Y. and Kobayashi, I. (2012) Restriction-modification systems as mobile epigenetic elements. In: Roberts, A.P. and Mullany, P. (eds), Bacterial Integrative Mobile Genetic Elements. Landes Bioscience, Austin, TX, USA
70. Makarova, K.S., Wolf, Y.I., Snir, S. and Koonin, E.V. (2011) Defense islands in bacterial and archaeal genomes and prediction of novel defense systems. J. Bacteriol., 193, 6039-6056
71. Anantharaman, V. and Aravind, L. (2003) New connections in the prokaryotic toxin-Antitoxin network: Relationship with the eukaryotic nonsense-mediated RNA decay system. Genome Biol., 4, R81
72. Pandey, D.P. and Gerdes, K. (2005) Toxin-Antitoxin loci are highly abundant in free-living but lost from host-Associated prokaryotes. Nucleic Acids Res., 33, 966-976
73. Hayes, F. and Van Melderen, L. (2011) Toxins-Antitoxins: Diversity, evolution and function. Crit. Rev. Biochem. Mol. Biol., 46, 386-408
74. Makarova, K.S., Wolf, Y.I. and Koonin, E.V. (2009) Comprehensive comparative-genomic analysis of type 2 toxinantitoxin systems and related mobile stress response systems in prokaryotes. Biol. Direct., 4, 19
75. Kobayashi, I. (2001) Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution. Nucleic Acids Res., 29, 3742-3756
76. Jeltsch, A. and Pingoud, A. (1996) Horizontal gene transfer contributes to the wide distribution and evolution of type II restriction-modification systems. J. Mol. Evol., 42, 91-96
77. Kobayashi, I., Nobusato, A., Kobayashi-Takahashi, N. and Uchiyama, I. (1999) Shaping the genome-restriction-modification systems as mobile genetic elements. Curr. Opin. Genet. Dev., 9, 649-656
78. Roberts, R.J., Vincze, T., Posfai, J. and Macelis, D. (2010) REBASE-A database for DNA restriction and modification: Enzymes, genes and genomes. Nucleic Acids Res., 38, D234-D236
79. Shao, Y., Harrison, E.M., Bi, D., Tai, C., He, X., Ou, H.Y., Rajakumar, K. and Deng, Z. (2011) TADB: A web-based resource for Type 2 toxin-Antitoxin loci in bacteria and archaea. Nucleic Acids Res., 39, D606-D611
80. Guglielmini, J., Szpirer, C. and Milinkovitch, M.C. (2008) Automated discovery and phylogenetic analysis of new toxinantitoxin systems. BMC Microbiol., 8, 104
81. Furuta, Y., Abe, K. and Kobayashi, I. (2010) Genome comparison and context analysis reveals putative mobile forms of restrictionmodification systems and related rearrangements. Nucleic Acids Res., 38, 2428-2443
82. Nobusato, A., Uchiyama, I., Ohashi, S. and Kobayashi, I. (2000) Insertion with long target duplication: A mechanism for gene mobility suggested from comparison of two related bacterial genomes. Gene, 259, 99-108
83. Furuta, Y., Kawai, M., Yahara, K., Takahashi, N., Handa, N., Tsuru, T., Oshima, K., Yoshida, M., Azuma, T., Hattori, M. et al. (2011) Birth and death of genes linked to chromosomal inversion. Proc. Natl Acad. Sci. USA, 108, 1501-1506
84. Furuta, Y. and Kobayashi, I. (2012) Movement of DNA sequence recognition domains between non-orthologous proteins. Nucleic Acids Res., 40, 9218-9232
85. Hayes, F. (2003) Toxins-Antitoxins: Plasmid maintenance, programmed cell death, and cell cycle arrest. Science, 301, 1496-1499
86. Black, D.S., Irwin, B. and Moyed, H.S. (1994) Autoregulation of hip, an operon that affects lethality due to inhibition of peptidoglycan or DNA synthesis. J. Bacteriol., 176, 4081-4091
87. Black, D.S., Kelly, A.J., Mardis, M.J. and Moyed, H.S. (1991) Structure and organization of hip, an operon that affects lethality due to inhibition of peptidoglycan or DNA synthesis. J. Bacteriol., 173, 5732-5739
88. Bordes, P., Cirinesi, A.M., Ummels, R., Sala, A., Sakr, S., Bitter, W. and Genevaux, P. (2011) SecB-like chaperone controls a toxinantitoxin stress-responsive system in Mycobacterium tuberculosis. Proc. Natl Acad. Sci. USA, 108, 8438-8443
89. Naito, T., Kusano, K. and Kobayashi, I. (1995) Selfish behavior of restriction-modification systems. Science, 267, 897-899
90. Ichige, A. and Kobayashi, I. (2005) Stability of EcoRI restrictionmodification enzymes in vivo differentiates the EcoRI restrictionmodification system from other postsegregational cell killing systems. J. Bacteriol., 187, 6612-6621
91. Ohno, S., Handa, N., Watanabe-Matsui, M., Takahashi, N. and Kobayashi, I. (2008) Maintenance forced by a restrictionmodification system can be modulated by a region in its modification enzyme not essential for methyltransferase activity. J. Bacteriol., 190, 2039-2049
92. Pedersen, K., Christensen, S.K. and Gerdes, K. (2002) Rapid induction and reversal of a bacteriostatic condition by controlled expression of toxins and antitoxins. Mol. Microbiol., 45, 501-510
93. Neubauer, C., Gao, Y.G., Andersen, K.R., Dunham, C.M., Kelley, A.C., Hentschel, J., Gerdes, K., Ramakrishnan, V. and Brodersen, D.E. (2009) The structural basis for mRNA recognition and cleavage by the ribosome-dependent endonuclease RelE. Cell, 139, 1084-1095
94. Yamaguchi, Y. and Inouye, M. (2009) mRNA interferases, sequence-specific endoribonucleases from the toxin-Antitoxin systems. Prog. Mol. Biol. Transl. Sci., 85, 467-500
95. Agarwal, S., Mishra, N.K., Bhatnagar, S. and Bhatnagar, R. (2010) PemK toxin of Bacillus anthracis is a ribonuclease: An insight into its active site, structure, and function. J. Biol. Chem., 285, 7254-7270
96. Jiang, Y., Pogliano, J., Helinski, D.R. and Konieczny, I. (2002) ParE toxin encoded by the broad-host-range plasmid RK2 is an inhibitor of Escherichia coli gyrase. Mol. Microbiol., 44, 971-979
97. Lioy, V.S., Machon, C., Tabone, M., Gonzalez-Pastor, J.E., Daugelavicius, R., Ayora, S. and Alonso, J.C. (2012) The zeta toxin induces a set of protective responses and dormancy. PLoS One, 7, e30282
98. Yamamoto, S., Kiyokawa, K., Tanaka, K., Moriguchi, K. and Suzuki, K. (2009) Novel toxin-Antitoxin system composed of serine protease and AAA-ATPase homologues determines the high level of stability and incompatibility of the tumor-inducing plasmid pTiC58. J. Bacteriol., 191, 4656-4666
99. Yamaguchi, Y., Park, J.H. and Inouye, M. (2011) Toxin-Antitoxin systems in bacteria and archaea. Annu. Rev. Genet., 45, 61-79
100. Wagner, E.G. and Unoson, C. (2012) The toxin-Antitoxin system tisB-istR1: Expression, regulation, and biological role in persister phenotypes. RNA Biol., 9, 1513-1519
101. Gurnev, P.A., Ortenberg, R., Dorr, T., Lewis, K. and Bezrukov, S.M. (2012) Persister-promoting bacterial toxin TisB produces anion-selective pores in planar lipid bilayers. FEBS Lett., 586, 2529-2534
102. Patel, S. and Weaver, K.E. (2006) Addiction toxin Fst has unique effects on chromosome segregation and cell division in Enterococcus faecalis and Bacillus subtilis. J. Bacteriol., 188, 5374-5384
103. Motiejunaite, R., Armalyte, J., Markuckas, A. and Suziedeliene, E. (2007) Escherichia coli dinJ-yafQ genes act as a toxin-Antitoxin module. FEMS Microbiol. Lett., 268, 112-119
104. Singletary, L.A., Gibson, J.L., Tanner, E.J., McKenzie, G.J., Lee, P.L., Gonzalez, C. and Rosenberg, S.M. (2009) An SOSregulated type 2 toxin-Antitoxin system. J. Bacteriol., 191, 7456-7465
105. Hallez, R., Geeraerts, D., Sterckx, Y., Mine, N., Loris, R. and Van Melderen, L. (2010) New toxins homologous to ParE belonging to three-component toxin-Antitoxin systems in Escherichia coli O157:H7. Mol. Microbiol., 76, 719-732
106. Gerdes, K. and Wagner, E.G. (2007) RNA antitoxins. Curr. Opin. Microbiol., 10, 117-124
107. Murray, I.A., Stickel, S.K. and Roberts, R.J. (2010) Sequencespecific cleavage of RNA by Type II restriction enzymes. Nucleic Acids Res., 38, 8257-8268
108. Handa, N., Ichige, A., Kusano, K. and Kobayashi, I. (2000) Cellular responses to postsegregational killing by restrictionmodification genes. J. Bacteriol., 182, 2218-2229
109. Kamphuis, M.B., Monti, M.C., van den Heuvel, R.H., Santos- Sierra, S., Folkers, G.E., Lemonnier, M., Diaz-Orejas, R., Heck, A.J. and Boelens, R. (2007) Interactions between the toxin Kid of the bacterial parD system and the antitoxins Kis and MazE. Proteins, 67, 219-231
110. Garcia-Pino, A., Balasubramanian, S., Wyns, L., Gazit, E., De Greve, H., Magnuson, R.D., Charlier, D., van Nuland, N.A. and Loris, R. (2010) Allostery and intrinsic disorder mediate transcription regulation by conditional cooperativity. Cell, 142, 101-111.
111. Wang, X., Kim, Y., Hong, S.H., Ma, Q., Brown, B.L., Pu, M., Tarone, A.M., Benedik, M.J., Peti, W., Page, R. et al. (2011) Antitoxin MqsA helps mediate the bacterial general stress response. Nat. Chem. Biol., 7, 359-366
112. Hu, Y., Benedik, M.J. and Wood, T.K. (2011) Antitoxin DinJ influences the general stress response through transcript stabilizer CspE. Environ. Microbiol., 14, 669-679
113. Kim, Y., Wang, X., Zhang, X.S., Grigoriu, S., Page, R., Peti, W. and Wood, T.K. (2010) Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD. Environ. Microbiol., 12, 1105-1121
114. Srikhanta, Y.N., Fox, K.L. and Jennings, M.P. (2010) The phasevarion: Phase variation of type III DNA methyltransferases controls coordinated switching in multiple genes. Nat. Rev. Microbiol., 8, 196-206
115. Srikhanta, Y.N., Gorrell, R.J., Steen, J.A., Gawthorne, J.A., Kwok, T., Grimmond, S.M., Robins-Browne, R.M. and Jennings, M.P. (2011) Phasevarion mediated epigenetic gene regulation in Helicobacter pylori. PLoS One, 6, e27569
116. Jeltsch, A. (2002) Beyond Watson and Crick: DNA methylation and molecular enzymology of DNA methyltransferases. Chembiochem, 3, 274-293
117. Marinus, M.G. (1987) DNA methylation in Escherichia coli. Annu. Rev. Genet., 21, 113-131
118. Wion, D. and Casadesus, J. (2006) N6-methyl-Adenine: An epigenetic signal for DNA-protein interactions. Nat. Rev. Microbiol., 4, 183-192
119. Collier, J., McAdams, H.H. and Shapiro, L. (2007) A DNA methylation ratchet governs progression through a bacterial cell cycle. Proc. Natl Acad. Sci. USA, 104, 17111-17116
120. Kahramanoglou, C., Prieto, A.I., Khedkar, S., Haase, B., Gupta, A., Benes, V., Fraser, G.M., Luscombe, N.M. and Seshasayee, A.S. (2012) Genomics of DNA cytosine methylation in Escherichia coli reveals its role in stationary phase transcription. Nat. Commun., 3, 886
121. Handa, N. and Kobayashi, I. (2005) Type III restriction is alleviated by bacteriophage (RecE) homologous recombination function but enhanced by bacterial (RecBCD) function. J. Bacteriol., 187, 7362-7373
122. Bair, C.L. and Black, L.W. (2007) A type IV modification dependent restriction nuclease that targets glucosylated hydroxymethyl cytosine modified DNAs. J. Mol. Biol., 366, 768-778
123. Terns, M.P. and Terns, R.M. (2011) CRISPR-based adaptive immune systems. Curr. Opin. Microbiol., 14, 321-327
124. Labrie, S.J., Samson, J.E. and Moineau, S. (2010) Bacteriophage resistance mechanisms. Nat. Rev. Microbiol., 8, 317-327
125. Fukuyo, M., Sasaki, A. and Kobayashi, I. (2012) Success of a suicidal defense strategy against infection in a structured habitat. Sci. Rep., 2, 238
126. Otsuka, Y. and Yonesaki, T. (2012) Dmd of bacteriophage T4 functions as an antitoxin against Escherichia coli LsoA and RnlA toxins. Mol. Microbiol., 83, 669-681
127. Pecota, D.C. and Wood, T.K. (1996) Exclusion of T4 phage by the hok/sok killer locus from plasmid R1. J. Bacteriol., 178, 2044-2050
128. Mochizuki, A., Yahara, K., Kobayashi, I. and Iwasa, Y. (2006) Genetic addiction: Selfish gene's strategy for symbiosis in the genome. Genetics, 172, 1309-1323
129. Cooper, T.F., Paixao, T. and Heinemann, J.A. (2010) Within-host competition selects for plasmid-encoded toxin-Antitoxin systems. Proc. Biol. Sci., 277, 3149-3155
130. Cooper, T.F. and Heinemann, J.A. (2000) Postsegregational killing does not increase plasmid stability but acts to mediate the exclusion of competing plasmids. Proc. Natl Acad. Sci. USA, 97, 12643-12648
131. Handa, N., Nakayama, Y., Sadykov, M. and Kobayashi, I. (2001) Experimental genome evolution: Large-scale genome rearrangements associated with resistance to replacement of a chromosomal restriction-modification gene complex. Mol. Microbiol., 40, 932-940
132. Sadykov, M., Asami, Y., Niki, H., Handa, N., Itaya, M., Tanokura, M. and Kobayashi, I. (2003) Multiplication of a restriction-modification gene complex. Mol. Microbiol., 48, 417-427
133. Yahara, K., Kawai, M., Furuta, Y., Takahashi, N., Handa, N., Tsuru, T., Oshima, K., Yoshida, M., Azuma, T., Hattori, M. et al. (2012) Genome-wide survey of mutual homologous recombination in a highly sexual bacterial species. Genome Biol. Evol., 4, 628-640
134. Vazquez-Laslop, N., Lee, H. and Neyfakh, A.A. (2006) Increased persistence in Escherichia coli caused by controlled expression of toxins or other unrelated proteins. J. Bacteriol., 188, 3494-3497
135. Dorr, T., Vulic, M. and Lewis, K. (2010) Ciprofloxacin causes persister formation by inducing the TisB toxin in Escherichia coli. PLoS Biol., 8, e1000317
136. Korch, S.B., Henderson, T.A. and Hill, T.M. (2003) Characterization of the hipA7 allele of Escherichia coli and evidence that high persistence is governed by (p)ppGpp synthesis. Mol. Microbiol., 50, 1199-1213
137. Bokinsky, G., Baidoo, E.E., Akella, S., Burd, H., Weaver, D., Alonso-Gutierrez, J., Garcia-Martin, H., Lee, T.S. and Keasling, J.D. (2013) HipA-Triggered growth arrest and betalactam tolerance in Escherichia coli is mediated by RelAdependent ppGpp synthesis. J. Bacteriol., 195, 3173-3182
138. Georgiades, K. and Raoult, D. (2011) Genomes of the most dangerous epidemic bacteria have a virulence repertoire characterized by fewer genes but more toxin-Antitoxin modules. PLoS One, 6, e17962
139. Daines, D.A., Jarisch, J. and Smith, A.L. (2004) Identification and characterization of a nontypeable Haemophilus influenzae putative toxin-Antitoxin locus. BMC Microbiol., 4, 30
140. Norton, J.P. and Mulvey, M.A. (2012) Toxin-Antitoxin systems are important for niche-specific colonization and stress resistance of uropathogenic Escherichia coli. PLoS Pathog., 8, e1002954
141. Nariya, H. and Inouye, M. (2008) MazF, an mRNA interferase, mediates programmed cell death during multicellular Myxococcus development. Cell, 132, 55-66
142. Boynton, T.O., McMurry, J.L. and Shimkets, L.J. (2013) Characterization of Myxococcus xanthus MazF and implications for a new point of regulation. Mol. Microbiol., 87, 1267-1276
143. Srikhanta, Y.N., Maguire, T.L., Stacey, K.J., Grimmond, S.M. and Jennings, M.P. (2005) The phasevarion: A genetic system controlling coordinated, random switching of expression of multiple genes. Proc. Natl Acad. Sci. USA, 102, 5547-5551
144. Kusano, K., Naito, T., Handa, N. and Kobayashi, I. (1995) Restriction-modification systems as genomic parasites in competition for specific sequences. Proc. Natl Acad. Sci. USA, 92, 11095-11099
145. Chinen, A., Naito, Y., Handa, N. and Kobayashi, I. (2000) Evolution of sequence recognition by restriction-modification enzymes: Selective pressure for specificity decrease. Mol. Biol. Evol., 17, 1610-1619.
146. Takahashi, N., Naito, Y., Handa, N. and Kobayashi, I. (2002) A DNA methyltransferase can protect the genome from postdisturbance attack by a restriction-modification gene complex. J. Bacteriol., 184, 6100-6108.
147. Saavedra De Bast, M., Mine, N. and Van Melderen, L. (2008) Chromosomal toxin-Antitoxin systems may act as antiaddiction modules. J. Bacteriol., 190, 4603-4609.
148. Smith, A.B., Lopez-Villarejo, J., Diago-Navarro, E., Mitchenall, L.A., Barendregt, A., Heck, A.J., Lemonnier, M., Maxwell, A. and Diaz-Orejas, R. (2012) A Common Origin for the Bacterial Toxin-Antitoxin Systems parD and ccd, Suggested by Analyses of Toxin/Target and Toxin/Antitoxin Interactions. PLoS One, 7, e46499.
149. Wang, X., Lord, D.M., Hong, S.H., Peti, W., Benedik, M.J., Page, R. and Wood, T.K. (2013) Type II toxin/antitoxin MqsR/MqsA controls type V toxin/antitoxin GhoT/GhoS. Environ. Microbiol., 15, 1734-1744.
150. Koga, M., Otsuka, Y., Lemire, S. and Yonesaki, T. (2011) Escherichia coli rnlA and rnlB compose a novel toxin-Antitoxin system. Genetics, 187, 123-130.
151. Kasari, V., Mets, T., Tenson, T. and Kaldalu, N. (2013) Transcriptional cross-Activation between toxin-Antitoxin systems of Escherichia coli. BMC Microbiol., 13, 45.
152. Nakayama, Y. and Kobayashi, I. (1998) Restriction-modification gene complexes as selfish gene entities: Roles of a regulatory system in their establishment, maintenance, and apoptotic mutual exclusion. Proc. Natl Acad. Sci. USA, 95, 6442-6447.
153. Mruk, I. and Blumenthal, R.M. (2008) Real-Time kinetics of restriction-modification gene expression after entry into a new host cell. Nucleic Acids Res., 36, 2581-2593.
154. Mruk, I., Rajesh, P. and Blumenthal, R.M. (2007) Regulatory circuit based on autogenous activation-repression: Roles of C-boxes and spacer sequences in control of the PvuII restrictionmodification system. Nucleic Acids Res., 35, 6935-6952.
155. Mruk, I. and Blumenthal, R.M. (2009) Tuning the relative affinities for activating and repressing operators of a temporally regulated restriction-modification system. Nucleic Acids Res., 37, 983-998.
156. Bogdanova, E., Djordjevic, M., Papapanagiotou, I., Heyduk, T., Kneale, G. and Severinov, K. (2008) Transcription regulation of the type II restriction-modification system AhdI. Nucleic Acids Res., 36, 1429-1442.
157. Nagornykh, M., Zakharova, M., Protsenko, A., Bogdanova, E., Solonin, A.S. and Severinov, K. (2011) Regulation of gene expression in restriction- modification system Eco29kI. Nucleic Acids Res., 39, 4653-4663.
158. Tao, T., Bourne, J.C. and Blumenthal, R.M. (1991) A family of regulatory genes associated with type II restriction-modification systems. J. Bacteriol., 173, 1367-1375.
159. Sorokin, V., Severinov, K. and Gelfand, M.S. (2010) Large-scale identification and analysis of C-proteins. Methods Mol. Biol., 674, 269-282.
160. Knowle, D., Lintner, R.E., Touma, Y.M. and Blumenthal, R.M. (2005) Nature of the promoter activated by C.PvuII, an unusual regulatory protein conserved among restriction-modification systems. J. Bacteriol., 187, 488-497.
161. Vijesurier, R.M., Carlock, L., Blumenthal, R.M. and Dunbar, J.C. (2000) Role and mechanism of action of C. PvuII, a regulatory protein conserved among restriction-modification systems. J. Bacteriol., 182, 477-487.
162. Bogdanova, E., Zakharova, M., Streeter, S., Taylor, J., Heyduk, T., Kneale, G. and Severinov, K. (2009) Transcription regulation of restriction-modification system Esp1396I. Nucleic Acids Res., 37, 3354-3366.
163. Williams, K., Savageau, M.A. and Blumenthal, R.M. (2013) A bistable hysteretic switch in an activator-repressor regulated restriction-modification system. Nucleic Acids Res., 41, 6045-6057.
164. McGeehan, J.E., Papapanagiotou, I., Streeter, S.D. and Kneale, G.G. (2006) Cooperative binding of the C.AhdI controller protein to the C/R promoter and its role in endonuclease gene expression. J. Mol. Biol., 358, 523-531.
165. de la Hoz, A.B., Pratto, F., Misselwitz, R., Speck, C., Weihofen, W., Welfle, K., Saenger, W., Welfle, H. and Alonso, J.C. (2004) Recognition of DNA by omega protein from the broad-host range Streptococcus pyogenes plasmid pSM19035: Analysis of binding to operator DNA with one to four heptad repeats. Nucleic Acids Res., 32, 3136-3147.
166. Weihofen, W.A., Cicek, A., Pratto, F., Alonso, J.C. and Saenger, W. (2006) Structures of omega repressors bound to direct and inverted DNA repeats explain modulation of transcription. Nucleic Acids Res., 34, 1450-1458.
167. de la Hoz, A.B., Ayora, S., Sitkiewicz, I., Fernandez, S., Pankiewicz, R., Alonso, J.C. and Ceglowski, P. (2000) Plasmid copy-number control and better-Than-random segregation genes of pSM19035 share a common regulator. Proc. Natl Acad. Sci. USA, 97, 728-733.
168. Cesnaviciene, E., Mitkaite, G., Stankevicius, K., Janulaitis, A. and Lubys, A. (2003) Esp1396I restriction-modification system: Structural organization and mode of regulation. Nucleic Acids Res., 31, 743-749.
169. Som, S. and Friedman, S. (1994) Regulation of EcoRII methyltransferase: Effect of mutations on gene expression and in vitro binding to the promoter region. Nucleic Acids Res., 22, 5347-5353.
170. Karyagina, A., Shilov, I., Tashlitskii, V., Khodoun, M., Vasil'ev, S., Lau, P.C. and Nikolskaya, I. (1997) Specific binding of ssoII DNA methyltransferase to its promoter region provides the regulation of sso II restriction-modification gene expression. Nucleic Acids Res., 25, 2114-2120.
171. Fedotova, E.A., Protsenko, A.S., Zakharova, M.V., Lavrova, N.V., Alekseevsky, A.V., Oretskaya, T.S., Karyagina, A.S., Solonin, A.S. and Kubareva, E.A. (2009) SsoII-like DNA-methyltransferase Ecl18kI: Interaction between regulatory and methylating functions. Biochemistry (Mosc.), 74, 85-91.
172. Butler, D. and Fitzgerald, G.F. (2001) Transcriptional analysis and regulation of expression of the ScrFI restriction-modification system of Lactococcus lactis subsp. cremoris UC503. J. Bacteriol., 183, 4668-4673.
173. Som, S. and Friedman, S. (1997) Characterization of the intergenic region which regulates the MspI restrictionmodification system. J. Bacteriol., 179, 964-967.
174. Beletskaya, I.V., Zakharova, M.V., Shlyapnikov, M.G., Semenova, L.M. and Solonin, A.S. (2000) DNA methylation at the CfrBI site is involved in expression control in the CfrBI restriction-modification system. Nucleic Acids Res., 28, 3817-3822.
175. Christensen, L.L. and Josephsen, J. (2004) The methyltransferase from the LlaDII restriction-modification system influences the level of expression of its own gene. J. Bacteriol., 186, 287-295.
176. Protsenko, A., Zakharova, M., Nagornykh, M., Solonin, A. and Severinov, K. (2009) Transcription regulation of restrictionmodification system Ecl18kI. Nucleic Acids Res., 37, 5322-5330.
177. Marianovsky, I., Aizenman, E., Engelberg-Kulka, H. and Glaser, G. (2001) The regulation of the Escherichia coli mazEF promoter involves an unusual alternating palindrome. J. Biol. Chem., 276, 5975-5984.
178. Chan, W.T., Nieto, C., Harikrishna, J.A., Khoo, S.K., Othman, R.Y., Espinosa, M. and Yeo, C.C. (2011) Genetic regulation of the yefM-yoeB toxin-Antitoxin locus of Streptococcus pneumoniae. J. Bacteriol., 193, 4612-4625.
179. Kedzierska, B., Lian, L.Y. and Hayes, F. (2007) Toxin-Antitoxin regulation: Bimodal interaction of YefM-YoeB with paired DNA palindromes exerts transcriptional autorepression. Nucleic Acids Res., 35, 325-339.
180. Afif, H., Allali, N., Couturier, M. and Van Melderen, L. (2001) The ratio between CcdA and CcdB modulates the transcriptional repression of the ccd poison-Antidote system. Mol. Microbiol., 41, 73-82.
181. Salmon, M.A., Van Melderen, L., Bernard, P. and Couturier, M. (1994) The antidote and autoregulatory functions of the F plasmid CcdA protein: A genetic and biochemical survey. Mol. Gen. Genet., 244, 530-538.
182. Magnuson, R. and Yarmolinsky, M.B. (1998) Corepression of the P1 addiction operon by Phd and Doc. J. Bacteriol., 180, 6342-6351.
183. Li, G.Y., Zhang, Y., Inouye, M. and Ikura, M. (2008) Structural mechanism of transcriptional autorepression of the Escherichia coli RelB/RelE antitoxin/toxin module. J. Mol. Biol., 380, 107-119.
184. Overgaard, M., Borch, J., Jorgensen, M.G. and Gerdes, K. (2008) Messenger RNA interferase RelE controls relBE transcription by conditional cooperativity. Mol. Microbiol., 69, 841-857.
185. Cataudella, I., Trusina, A., Sneppen, K., Gerdes, K. and Mitarai, N. (2012) Conditional cooperativity in toxin-Antitoxin regulation prevents random toxin activation and promotes fast translational recovery. Nucleic Acids Res., 40, 6424-6434.
186. Gottesman, S. (2005) Micros for microbes: Non-coding regulatory RNAs in bacteria. Trends Genet., 21, 399-404.
187. Majdalani, N., Vanderpool, C.K. and Gottesman, S. (2005) Bacterial small RNA regulators. Crit. Rev. Biochem. Mol. Biol., 40, 93-113.
188. Waters, L.S. and Storz, G. (2009) Regulatory RNAs in bacteria. Cell, 136, 615-628.
189. Fozo, E.M. (2012) New type I toxin-Antitoxin families from ''wild'' and laboratory strains of E. coli: Ibs-Sib, ShoB-OhsC and Zor-Orz. RNA Biol., 9, 1504-1512.
190. Thisted, T. and Gerdes, K. (1992) Mechanism of postsegregational killing by the hok/sok system of plasmid R1. Sok antisense RNA regulates hok gene expression indirectly through the overlapping mok gene. J. Mol. Biol., 223, 41-54.
191. Gerdes, K., Nielsen, A., Thorsted, P. and Wagner, E.G. (1992) Mechanism of killer gene activation. Antisense RNA-dependent RNase III cleavage ensures rapid turn-over of the stable hok, srnB and pndA effector messenger RNAs. J Mol Biol, 226, 637-649.
192. Shokeen, S., Patel, S., Greenfield, T.J., Brinkman, C. and Weaver, K.E. (2008) Translational regulation by an intramolecular stem-loop is required for intermolecular RNA regulation of the par addiction module. J. Bacteriol., 190, 6076-6083.
193. Koyanagi, S. and Levesque, C.M. (2013) Characterization of a Streptococcus mutans Intergenic Region Containing a Small Toxic Peptide and Its cis-Encoded Antisense Small RNA Antitoxin. PLoS One, 8, e54291.
194. Weaver, K.E., Reddy, S.G., Brinkman, C.L., Patel, S., Bayles, K.W. and Endres, J.L. (2009) Identification and characterization of a family of toxin-Antitoxin systems related to the Enterococcus faecalis plasmid pAD1 par addiction module. Microbiology, 155, 2930-2940.
195. Durand, S., Jahn, N., Condon, C. and Brantl, S. (2012) Type I toxin-Antitoxin systems in Bacillus subtilis. RNA Biol., 9, 1491-1497.
196. Liu, Y., Ichige, A. and Kobayashi, I. (2007) Regulation of the EcoRI restriction-modification system: Identification of ecoRIM gene promoters and their upstream negative regulators in the ecoRIR gene. Gene, 400, 140-149.
197. Liu, Y. and Kobayashi, I. (2007) Negative regulation of the EcoRI restriction enzyme gene is associated with intragenic reverse promoters. J. Bacteriol., 189, 6928-6935.
198. Mruk, I., Liu, Y., Ge, L. and Kobayashi, I. (2011) Antisense RNA associated with biological regulation of a restriction-modification system. Nucleic Acids Res., 39, 5622-5632.
199. Pedersen, M. and Hammer, K. (2008) The role of MOR and the CI operator sites on the genetic switch of the temperate bacteriophage TP901-1. J. Mol. Biol., 384, 577-589.
200. Ferrell, J.E. Jr. (2002) Self-perpetuating states in signal transduction: Positive feedback, double-negative feedback and bistability. Curr. Opin. Cell. Biol., 14, 140-148.
201. Dubnau, D. and Losick, R. (2006) Bistability in bacteria. Mol. Microbiol., 61, 564-572.
202. Orlowski, J. and Bujnicki, J.M. (2008) Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses. Nucleic Acids Res., 36, 3552-3569.
203. Ishikawa, K., Watanabe, M., Kuroita, T., Uchiyama, I., Bujnicki, J.M., Kawakami, B., Tanokura, M. and Kobayashi, I. (2005) Discovery of a novel restriction endonuclease by genome comparison and application of a wheat-germ-based cell-free translation assay: PabI (50-GTA/C) from the hyperthermophilic archaeon Pyrococcus abyssi. Nucleic Acids Res., 33, e112.
204. Cheng, X. (1995) Structure and function of DNA methyltransferases. Annu. Rev. Biophys. Biomol. Struct., 24, 293-318.
205. Bujnicki, J.M. (2001) Understanding the evolution of restrictionmodification systems: Clues from sequence and structure comparisons. Acta. Biochim. Pol., 48, 935-967.
206. Miyazono, K., Watanabe, M., Kosinski, J., Ishikawa, K., Kamo, M., Sawasaki, T., Nagata, K., Bujnicki, J.M., Endo, Y., Tanokura, M. et al. (2007) Novel protein fold discovered in the PabI family of restriction enzymes. Nucleic Acids Res., 35, 1908-1918.
207. Dryden, D.T. and Tock, M.R. (2006) DNA mimicry by proteins. Biochem. Soc. Trans., 34, 317-319.
208. Werren, J.H. (2011) Selfish genetic elements, genetic conflict, and evolutionary innovation. Proc. Natl Acad. Sci. USA, 108 (Suppl. 2), 10863-10870.
209. Asakura, Y., Kojima, H. and Kobayashi, I. (2011) Evolutionary genome engineering using a restriction-modification system. Nucleic Acids Res., 39, 9034-9046.
210. Magnuson, R.D. (2007) Hypothetical functions of toxin-Antitoxin systems. J. Bacteriol., 189, 6089-6092