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Restriction-Modification Systems as Minimal Forms of Life

  • Chapter
Restriction Endonucleases

Part of the book series: Nucleic Acids and Molecular Biology ((NUCLEIC,volume 14))

Abstract

A restriction (R) endonuclease recognizes a specific DNAsequence and introduces a double-strand break (Fig. 1A). A cognate modification (M) enzyme methylates the same sequence and thereby protects it from cleavage. Together, these two enzymes form a restriction-modification system. The genes encoding the restriction endonuclease and the cognate modification enzyme are often tightly linked and can be termed a restriction-modification gene complex. Restriction enzymes will cleave incoming DNA if it has not been modified by a cognate or another appropriate methyltransferase (Fig. 1B). Consequently, it is widely believed that restriction-modification systems have been maintained by bacteria because they serve to defend the cells from infection by viral, plasmid, and other foreign DNAs(cellular defensehypothesis).

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References

  • Akopyants NS, Fradkov A, Diatchenko L, Hill JE, Siebert PD, Lukyanov SA, Sverdlov ED, Berg DE (1998) PCR-based subtractive hybridization and differences in gene content among strains of Helicobacter pylori. Proc Natl Acad Sci USA95:13108–13113

    Article  PubMed  CAS  Google Scholar 

  • Alm RA, Ling LS, Moir DT, King BL, Brown ED, Doig PC, Smith DR, Noonan B, Guild BC, delonge BL, Carmel G, Tummino PJ, Caruso A, Uria-Nickelsen M, Mills DM, Ives C, Gibson R, Merberg D, Mills SD, Jiang Q, Taylor DE, Vovis GF, Trust TJ (1999) Genomicsequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori. Nature 397:176–180

    Article  PubMed  CAS  Google Scholar 

  • Alvarez MA, Chater KF, Rodicio MR (1993) Complex transcription of an operon encoding the SalI restriction-modification system of Streptomyces albus G. Mol Microbiol 8:243–252

    Article  PubMed  CAS  Google Scholar 

  • Anton BP, Heiter DF, Benner JS, Hess EJ, Greenough L, Moran LS, Slatko BE, Brooks JE (1997) Cloning and characterization of the BglII restriction-modification system reveals a possible evolutionary footprint. Gene 187:19–27

    Article  PubMed  CAS  Google Scholar 

  • Aras RA, Takata T, Ando T, van der Ende A, Blaser MJ (2001) Regulation of the Hpyll restriction-modification system of Helicobacter pylori by gene deletion and horizontal reconstitution. Mol Microbiol 42:369–382

    Article  PubMed  CAS  Google Scholar 

  • Arber W (1993) Evolution of prokaryotic genomes. Gene 135:49–56

    Article  PubMed  CAS  Google Scholar 

  • Arnold DA, Handa N, Kobayashi I, Kowakzykowski SC (2000) A novel, 11-nucleotide variant of chi, chi*: one of a class of sequences defining the E. coli recombination hotspot, chi. J Mol Biol 300:469–479

    Article  PubMed  CAS  Google Scholar 

  • Bart A, Dankert J, van der Ende A (1999) Operator sequences for the regulatory proteins of restriction modification systems. Mol Microbiol 31:1277–1278

    Article  PubMed  CAS  Google Scholar 

  • Beletskaya IV, Zakharova MV, Shlyapnikov MG, Semenova LM, Solonin AS (2000) DNA methylation at the CfrBI site is involved in expression control in the CfrBI restrictionmodification system. Nucleic Acids Res 28:3817–3822

    Article  PubMed  CAS  Google Scholar 

  • Bickle TA, Kruger DH (1993) Biology of DNA restriction. Microbiol Rev 57:434–450

    PubMed  CAS  Google Scholar 

  • Bujnicki JM (2000) Phylogeny of the restriction endonuclease-like superfamily inferred from comparison of protein structures. J Mol Evol 50:39–44

    PubMed  CAS  Google Scholar 

  • Bujnicki JM (2001) Understanding the evolution of restriction-modification systems: clues from sequence and structure comparisons. Acta Biochim Pol 48:935–967

    PubMed  CAS  Google Scholar 

  • Burrus V, Bontemps C, Decaris B, Guedon G (2001) Characterization of a novel type II restriction-modification system, Sth368I, encoded by the integrative element ICEStl of Streptococcus thermophilus CNRZ368. Appl Environ Microbiol 67: 1522–1528

    Article  PubMed  CAS  Google Scholar 

  • Butler D, Fitzgerald GF (2001) Transcriptional analysis and regulation of expression of the ScrFI restriction-modification system of Lactococcus lactis subsp. cremoris UC503. J Bacteriol 183:4668–4673

    Article  PubMed  CAS  Google Scholar 

  • Cesnaviciene E, Mitkaite G, Stankevicius K, Janulaitis A, Lubys A (2003) Esp1396I restriction-modification system: structural organization and mode of regulation. Nucleic Acids Res 31:743–749

    Article  PubMed  CAS  Google Scholar 

  • Chinen A, Naito Y, Handa N, Kobayashi I (2000a) Evolution of sequence recognition by restriction-modification enzymes: selective pressure for specificity decrease. Mol BioI Evol 17:1610–1619

    Article  CAS  Google Scholar 

  • Chinen A, Uchiyama I, Kobayashi I (2000b) Comparison between Pyrococcus horikoshii and Pyrococcus abyssi genome sequences reveals linkage of restriction-modification genes with large genome polymorphisms. Gene 259:109–121

    Article  PubMed  CAS  Google Scholar 

  • Claus H, Friedrich A, Frosch M, Vogel U (2000) Differential distribution of novel restriction-modification systems in clonal lineages of Neisseria meningitidis. J Bacteriol 182:1296–1303

    Article  PubMed  CAS  Google Scholar 

  • Cromie GA, Leach DR (2001) Recombinational repair of chromosomal DNA doublestrand breaks generated by a restriction endonuclease. Mol Microbiol 41:873–883

    Article  PubMed  CAS  Google Scholar 

  • Dandekar T, Huynen M, Regula JT, Ueberle B, Zimmermann CU, Andrade MA, Doerks T, Sanchez-Pulido L, Snel B, Suyama M, Yuan YP, Herrmann R, Bork P (2000) Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames. Nucleic Acids Res 28:3278–3288

    Article  PubMed  CAS  Google Scholar 

  • Doronina VA, Murray NE (2001) The proteolytic control of restriction activity in Escherichia coli K-12. Mol Microbiol 39:416–428

    Article  PubMed  CAS  Google Scholar 

  • Dybvig K, Sitaraman R, French CT (1998) Afamily of phase-variable restriction enzymes with differing specificities generated by high-frequency gene rearrangements. Proc Natl Acad Sci USA 95:13923–13928

    Article  PubMed  CAS  Google Scholar 

  • Eddy SR, Gold L (1992) Artificial mobile DNA element constructed from the EcoRI endonuclease gene. Proc Natl Acad Sci USA 89:1544–1547

    Article  PubMed  CAS  Google Scholar 

  • el Karoui M, Ehrlich D, Gruss A (1998) Identification of the lactococcal exonuclease/ recombinase and its modulation by the putative Chi sequence. Proc Natl Acad Sci USA 95:626–631

    Article  PubMed  Google Scholar 

  • Friedberg EC, Walker GC, Siede W (1995) DNA repair and mutagenesis. ASM Press, Washington, D.C.

    Google Scholar 

  • Gelfand MS, Koonin EV (1997) Avoidance of palindromic words in bacterial and archaeal genomes: a close connection with restriction enzymes. Nucleic Acids Res 25:2430–2439

    Article  PubMed  CAS  Google Scholar 

  • Gerdes K (2000) Toxin-antitoxin modules may regulate synthesis of macromolecules during nutritional stress. J Bacteriol 182:561–572

    Article  PubMed  CAS  Google Scholar 

  • Gerdes K, Guityaev AP, Franch T, Pedersen K, Mikkelsen ND (1997) Antisense RNA-regulated programmed cell death. Annu Rev Genet 31:1–31

    Article  PubMed  CAS  Google Scholar 

  • Gunn JS, Stein DC (1997) The Neisseria gonorrhoeae S.Ngo VIII restriction/modification system: a type IIs system homologous to the Haemophilus parahaemolyticus HphI restriction/modification system. Nucleic Acids Res 25:4147–4152

    Article  PubMed  CAS  Google Scholar 

  • Haig D (1997) The social gene. In: Krebs J, Davies NB (eds) Behavioural ecology: an evolutionary approach, 4th edn. Blackwell Science, Oxford, pp 284–304

    Google Scholar 

  • Handa N, Ichige A, Kusano K, Kobayashi I (2000) Cellular responses to postsegregational killing by restriction-modification genes. J Bacteriol 182:2218–2229

    Article  PubMed  CAS  Google Scholar 

  • Handa N, Kobayashi I (1999) Post-segregational killing by restriction modification gene complexes: observations of individual cell deaths. Biochimie 81:931–938

    Article  PubMed  CAS  Google Scholar 

  • Handa N, Kobayashi I (2003) Accumulation of large non-circular forms of the chromosome in recombination-defective mutants of Escherichia coli. BMCMol Bioi 4:5

    Article  Google Scholar 

  • Handa N, Nakayama Y, Sadykov M, Kobayashi I (2001) Experimental genome evolution: large-scale genome rearrangements associated with resistance to replacement of a chromosomal restriction modificaiton gene complex. Mol Microbiol 40:932–940

    Article  PubMed  CAS  Google Scholar 

  • Handa N, Ohashi S, Kusano K, Kobayashi I (1997) Chi*, a chi-related 11-mer partially active in an E. coli recC* strain. Genes Cells 2:525–536

    Article  PubMed  CAS  Google Scholar 

  • Hattman S, Wilkinson J, Swinton D, Schlagman S, Macdonald PM, Mosig G (1985) Common evolutionary origin of the phage T4 dam and host Escherichia coli dam DNA-adenine methyltransferase genes. J Bacteriol 164:932–937

    PubMed  CAS  Google Scholar 

  • Heidelberg JF, Eisen JA, Nelson WC, Clayton RA, Gwinn ML, Dodson RJ, Haft DH, Hickey EK, Peterson JD, Umayam L, Gill SR, Nelson KE, Read TD, Tettelin H, Richardson D, Ermolaeva MD, Vamathevan J, Bass S, Qin H, Dragoi I, Sellers P, McDonald L, Utterback T, Fleishmann RD, Nierman WC, White O (2000) DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae. Nature 406:477–483

    Article  PubMed  CAS  Google Scholar 

  • Heitman J, Ivanenko T, Kiss A (1999) DNA nicks inflicted by restriction endonucleases are repaired by a RecA-and RecB-dependent pathway in Escherichia coli. Mol Microbioi 33:1141–1151

    Article  CAS  Google Scholar 

  • Heitman J, Model P (1987) Site-Specific Methylases Induce the SOS DNA Repair Response in Escherichia coli. J Bacteriol 169:3243–3250

    PubMed  CAS  Google Scholar 

  • Heitman J, Model P (1991) SOS induction as an in vivo assay of enzyme-DNA interactions. Gene 103:1–9

    Article  PubMed  CAS  Google Scholar 

  • Heitman J, Zinder ND, Model P (1989) Repair of the Escherichia coli chromosome after in vivo scission the EcoRI endonuclease. Proc Natl Acad Sci USA 86:2281–2285

    Article  PubMed  CAS  Google Scholar 

  • Hendrix RW, Smith MC, Burns RN, Ford ME, Hatfull GF (1999) Evolutionary relationships among diverse bacteriophages and prophages: all the world’s a phage. Proc Natl Acad Sci USA 96:2192–2197

    Article  PubMed  CAS  Google Scholar 

  • Higgins NP (1992) Death and transfiguration among bacteria. Trends Biochem Sci 17:207–211

    Article  PubMed  CAS  Google Scholar 

  • Hurst GD, Werren JH (2001) The role of selfish genetic elements in eukaryotic evolution. Nat Rev Genet 2:597–606

    Article  PubMed  CAS  Google Scholar 

  • Ibanez M, Alvarez I, Rodriguez-Pena JM, Rotger R (1997) A ColEl-type plasmid from Salmonella enteritidis encodes a DNA cytosine methyltransferase. Gene 196:145–158

    Article  PubMed  CAS  Google Scholar 

  • Jaffe A, Ogura T, Hiraga S (1985) Effects of the ccd function of the F plasmid on bacterial growth. J Bacteriol 163:841–849

    PubMed  CAS  Google Scholar 

  • Jamsai D, Nefedov M, Narayanan K, Orford M, Fucharoen S, Williamson R, Ioannou PA (2003) Insertion of common mutations into the human beta-globin locus using GET Recombination and an EcoRI endonuclease counterselection cassette. J Biotechnol 101:1–9

    Article  PubMed  CAS  Google Scholar 

  • Jeltsch A, Kroger M, Pingoud A (1995) Evidence for an evolutionary relationship among type-II restriction endonucleases. Gene 160:7–16

    Article  PubMed  CAS  Google Scholar 

  • Jeltsch A, 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

    Article  PubMed  CAS  Google Scholar 

  • Kamada K, Hanaoka F, Burley SK (2003) Crystal structure of the MazE/MazF complex. Molecular bases of antidote-toxin recognition. Mol Cell 11:875–884

    Article  PubMed  CAS  Google Scholar 

  • Karlin S, Campbell AM, Mrazek J (1998a) Comparative DNA analysis across diverse genomes. Annu Rev Genet 32:185–225

    Article  PubMed  CAS  Google Scholar 

  • Karlin S, Mrazek J, Campbell AM (1998b) Codon usages in different gene classes of the Escherichia coli genome. Mol Microbiol 29:1341–1355

    Article  PubMed  CAS  Google Scholar 

  • Karyagina A, Shilov I, Tashlitskii V, Khodoun M, Vasil’ev S, Lau PC, Nikolskaya I (1997) Specific binding of sso II DNA methyltransferase to its promoter region provides the regulation of sso II restriction-modification gene expression. Nucleic Acids Res 25:2114–2120

    Article  PubMed  CAS  Google Scholar 

  • Kita K, J. Tsuda, K. Okamoto, H. Yanase, Tanaka M (1999) Evidence of horizontal transfer of the EcoO109I restriction-modification gene to Escherichia coli chromosomal DNA. J Bacteriol 181:6822–6827

    PubMed  CAS  Google Scholar 

  • Kita K, Kawakami H, Tanaka H (2003) Evidence for horizontal transfer of the EcoT38I restriction-modification gene to chromosomal DNA by the P2 phage and diversity of defective P2 prophages in Escherichia coli TH38 strains. J Bacteriol 185:2296–2305

    Article  PubMed  CAS  Google Scholar 

  • Kita K, Tsuda J, Nakai SY (2002) C.EcoO109I, a regulatory protein for production of EcoO109I restriction endonuclease, specifically binds to and bends DNA upstream of its translational start site. Nucleic Acids Res 30:3558–3565

    Article  PubMed  CAS  Google Scholar 

  • Kobayashi I (1996) DNA modification and restriction: Selfish behavior of an epigenetic system. In: Russo V, Martienssen R, Riggs A (eds) Epigenetic mechanisms of gene regulation. Cold Spring Harbor Laboratory Press, NewYork, pp 155–172

    Google Scholar 

  • Kobayashi I (1998) Selfishness and death: raison d’ être of restriction, recombination and mitochondria. Trends Genet 14:368–374

    Article  PubMed  CAS  Google Scholar 

  • Kobayashi I (2001) Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution. Nucleic Acids Res 29:3742–3756

    Article  PubMed  CAS  Google Scholar 

  • Kobayashi I (2002) Life cycle of restriction-modification gene complexes, powers in genome evolution. In: Yoshikawa H, Ogasawara N, Satoh N (eds) Genome science: towards a new paradigm? Elsevier. Amsterdam, pp 191–200

    Google Scholar 

  • Kobayashi I Addiction as a principle of symbiosis of genetic elements in the genome restriction enzymes, chromosome and mitochondria. In: Sugiura M (ed) Symbiosis and cellular organelles. Logos, Berlin (in press)

    Google Scholar 

  • Kobayashi I Genetic addiction: a principle of gene symbiosis in a genome. In: Phillips G, Funnell B,(eds) Plasmid Biology. ASMPress, Washington, DC (in press)

    Google Scholar 

  • Kobayashi I, Nobusato A, Kobayashi-Takahashi N, Uchiyama I (1999) Shaping the genome — restriction-modification systems as mobile genetic elements. Curr Opin Genet Dev 9:649–656

    Article  PubMed  CAS  Google Scholar 

  • Kroger M, Blum E, Deppe E, Dusterhoft A, Erdmann D, Kilz S, Meyer-Rogge S, Mostl D (1995) Organization and gene expression within restriction-modification systems of Herpetosiphon giganteus. Gene 157:43–47

    Article  PubMed  CAS  Google Scholar 

  • Kuhn I, Stephenson FH, Boyer HW, Greene PJ (1986) Positive-selection vectors utilizing lethality of the EcoRI endonuclease. Gene 42:253–263

    Article  PubMed  CAS  Google Scholar 

  • Kulakauskas S, Lubys A, Ehrlich SD (1995) DNArestriction-modification systems mediate plasmid maintenance. J Bacterioll 77:3451–3454

    Google Scholar 

  • Kuroda M, Ohta T, Uchiyama I, Baba T, Yuzawa H, Kobayashi I, Cui L, Oguchi A, Aoki K, Nagai Y, Lian J, Ito T, Kanamori M, Matsumaru H, Maruyama A, Murakami H, Hosoyama A, Mizutani-Ui Y, Takahashi NK, Sawano T, Inoue R, Kaito C, Sekimizu K, Hirakawa H, Kuhara S, Goto S, Yabuzaki J, Kanehisa M, Yamashita A, Oshima K, Furuya K, Yoshino C, Shiba T, Hattori M, Ogasawara N, Hayashi H, Hiramatsu K (2001) Whole genome sequencing of meticillin-resistant Staphylococcus aureus. Lancet 357:1225–1240

    Article  PubMed  CAS  Google Scholar 

  • Kusano K, Naito T, Handa N, Kobayashi I (1995) Restriction-modification systems as genomic parasites in competition for specific sequences. Proc Natl Acad Sci USA 92:11095–11099

    Article  PubMed  CAS  Google Scholar 

  • Kusano K, Sakagami K, Yokochi T, Naito T, Tokinaga Y, Ueda E, Kobayashi I (1997) A new type of illegitimate recombination is dependent on restriction and homologous interaction. J Bacteriol 179:5380–5390

    PubMed  CAS  Google Scholar 

  • Lehnherr H, Maguin E, Iafri S, Yarmolinsky MB (1993) Plasmid addiction genes of bacteriophage P1: doc, which causes cell death on curing of prophage, and phd, which prevents host death when prophage is retained. J Mol Biol 233:414–428

    Article  PubMed  CAS  Google Scholar 

  • Levin BR (1988) Frequency-dependent selection in bacterial populations. Philos Trans R Soc Lond (B) 319:459–472

    Google Scholar 

  • Lieb M (1991) Spontaneous mutation at a 5-methylcytosine hotspot is prevented by very short patch (VSP) mismatch repair. Genetics 128:23–27

    PubMed  CAS  Google Scholar 

  • Lin LF, Posfai J, Roberts RJ, Kong H (2001) Comparative genomics of the restrictionmodification systems in Helicobacter pylori. Proc Natl Acad Sci USA 98:2740–2745

    Article  PubMed  CAS  Google Scholar 

  • Lubys A, Jurenaite S, Janulaitis A (1999) Structural organization and regulation of the plasmid-borne type II restriction-modification system Kpn2I from Klebsiella pneumoniae RFL2. Nucleic Acids Res 27:4228–4234

    Article  PubMed  CAS  Google Scholar 

  • Lubys A, Lubiene J, Kulakauskas S, Stankevicius K, Timinskas A, Janulaitis A (1996) Cloning and analysis of the genes encoding the type IIS restriction-modification system HphI from Haemophilus parahaemolyticus. Nucleic Acids Res 24:2760–6

    Article  PubMed  CAS  Google Scholar 

  • Lubys A, Menkevicius S, Timinskas A, Butkus V, Janulaitis A (1994) Cloning and analysis of translational control for genes encoding the Cfr9I restriction-modification system. Gene 141:85–89

    Article  PubMed  CAS  Google Scholar 

  • Makovets S, Doronina VA, Murray NE (1999) Regulation of endonuclease activity by proteolysis prevents breakage of unmodified bacterial chromosomes by type I restriction enzymes. Proc Nat Acad Sci USA 96:9757–9762

    Article  PubMed  CAS  Google Scholar 

  • McKane M, Milkman R (1995) Transduction, restriction and recombination patterns in Escherichia coli. Genetics 139:35–43

    PubMed  CAS  Google Scholar 

  • Meinhart A, Alonso JC, Strater N, Saenger W (2003) Crystal structure of the plasmid maintenance system epsilonlzeta: functional mechanism of toxin zeta and inactivation by epsilon 2 zeta 2 complex formation. Proc Natl Acad Sci USA 100:1661–1666

    Article  PubMed  CAS  Google Scholar 

  • Michel B, Ehrlich SD, Uzest M (1997) DNAdouble-strand breaks caused by replication arrest. EMBO J 16:430–438

    Article  PubMed  CAS  Google Scholar 

  • Miner Z, Hattman S (1988) Molecular cloning, sequencing, and mapping of the bacteriophage T2 dam gene. J Bacteriol 170:5177–184

    PubMed  CAS  Google Scholar 

  • Mol CD, Arvai AS, Begley TJ, Cunningham RP, Tainer JA (2002) Structure and activity of a thermostable thymine-DNA glycosylase: evidence for base twisting to remove mismatched normal DNAbases. J Mol Biol 315:373–384

    Article  PubMed  CAS  Google Scholar 

  • Murray NE (2002) Immigration control of DNA in bacteria: self versus non-self. Microbiology-Sgm 148:3–20

    CAS  Google Scholar 

  • Naito T, Kusano K, Kobayashi I (1995) Selfish behavior of restriction-modification systems. Science 267:897–899

    Article  PubMed  CAS  Google Scholar 

  • Nakayama Y, 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 Nat Acad Sci USA 95:6442–6447

    Article  PubMed  CAS  Google Scholar 

  • Nishino T, Komori K, Ishino Y, Morikawa K (2003) X-ray and biochemical anatomy of an archaeal XPF/Rad1/Mus81 family nuclease. Similarity between Its endonuclease domain and restriction enzymes. Structure (Cambridge) 11:445–457

    Article  CAS  Google Scholar 

  • Nobusato A, Uchiyama I, Kobayashi I (2000a) Diversity of restriction-modification gene homologues in Helicobacter pylori. Gene 259:89–98

    Article  PubMed  CAS  Google Scholar 

  • Nobusato A, Uchiyama I, Ohashi S, Kobayashi I (2000b) Insertion with long target duplication: a mechanism for gene mobility suggested from comparison of two related bacterial genomes. Gene 259:99–108

    Article  PubMed  CAS  Google Scholar 

  • Nolling J, de Vos WM (1992) Characterization of the archaeal, plasmid-encoded type II restriction-modification system MthTI from Methanobacterium thermoformicicum THF: homology to the bacterial NgoPII system from Neisseria gonorrhoeae. J Bacteriol 174: 5719–5726

    PubMed  CAS  Google Scholar 

  • Nolling J, van Eeden FJ, Eggen RI, de Vos WM (1992) Modular organization of related Archaeal plasmids encoding different restriction-modification systems in Methanobacterium thermoformicicum. Nucleic Acids Res 20:6501–6507

    Article  PubMed  CAS  Google Scholar 

  • O’Connor CD, Humphreys GO (1982) Expression of the Eco RI restriction-modification system and the construction of positive-selection cloning vectors. Gene 20:219–229

    Article  PubMed  Google Scholar 

  • O’Neill M, Chen A, Murray NE (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

    Article  PubMed  Google Scholar 

  • O’Sullivan DJ, Klaenhammer TR (1998) Control of expression of LlaI restriction in Lactococcus lactis. Mol Microbiol 27:1009–1020

    Article  PubMed  Google Scholar 

  • Ohshima H, Matsuoka S, Asai K, Sadaie Y (2002) Molecular organization of intrinsic restriction and modification genes BsuM of Bacillus subtilis Marburg. J Bacteriol 184:381–389

    Article  PubMed  CAS  Google Scholar 

  • Pedersen K, Zavialov AV, Pavlov MY, Elf J, Gerdes K, Ehrenberg M (2003) The bacterial toxin RelE displays codon-specific cleavage of mRNAs in the ribosomal A site. Cell 112:131–140

    Article  PubMed  CAS  Google Scholar 

  • 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

    PubMed  CAS  Google Scholar 

  • Price C, Bickle TA (1986) A possible role for DNA restriction in bacterial evolution. Microbiol Sci 3:296–299

    PubMed  CAS  Google Scholar 

  • Rimseliene R, Vaisvila R, Janulaitis A (1995) The eco72IC gene specifies a trans-acting factor which influences expression of both DNA methyltransferase and endonuclease from the Eco72I restriction-modification system. Gene 157:217–219

    Article  PubMed  CAS  Google Scholar 

  • Roberts RJ, Belfort M, Bestor T, Bhagwat AS, Bickle TA, Bitinaite J, Blumenthal RM, Degtyarev S, Dryden DT, Dybvig K, Firman K, Gromova ES, Gumport RI, Halford SE, Hattman S, Heitman J, Hornby DP, Janulaitis A, Jeltsch A, Josephsen J, Kiss A, Klaenhammer TR, Kobayashi I, Kong H, Kruger DH, Lacks S, Marinus MG, Miyahara M, Morgan RD, Murray NE, Nagaraja V, Piekarowicz A, Pingoud A, Raleigh E, Rao DN, Reich N, Repin VE, Selker EU, Shaw PC, Stein DC, Stoddard BL, Szybalski W, Trautner TA, Van Etten JL, Vitor JM, Wilson GG, Xu SY (2003a) A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes. Nucleic Acids Res 31:1805–1812

    Article  PubMed  CAS  Google Scholar 

  • Roberts RJ, Vincze T, Posfai J, Macelis D (2003b) REBASE: restriction enzymes and methyltransferases. Nucleic Acids Res 31:418–420

    Article  PubMed  CAS  Google Scholar 

  • Rocha EP, Danchin A, Viari A (2001) Evolutionary role of restriction/modification systems as revealed by comparative genome analysis. Genome Res 11:946–958

    Article  PubMed  CAS  Google Scholar 

  • Rocha EP, Viari A, Danchin A (1998) Oligonucleotide bias in Bacillus subtilis: general trends and taxonomic comparisons. Nucleic Acids Res 26:2971–2980

    Article  PubMed  CAS  Google Scholar 

  • Rochepeau P, Selinger LB, Hynes MF (1997) Transposon-like structure of a new plasmidencoded restriction-modification system in Rhizobium leguminosarum VF39SM. Mol Gen Genet 256:387–396

    Article  PubMed  CAS  Google Scholar 

  • Rowe-Magnus DA, Guerout A-M, Ploncard P, Dychinco B, Davies J, Mazel D (2001) The evolutionary history of chromosomal super-integrons provides an ancestry for multiresistant integrons. Proc Natl Acad Sci USA 98:652–657

    Article  PubMed  CAS  Google Scholar 

  • Rowe-Magnus DA, Guerout A-M, Biskri L, Bouige P, Mazel D (2003) Comparative analysis of superintegrons: engineering extensive genetic diversity in the Vibrionaceae. Genome Res 13:428–442

    Article  PubMed  CAS  Google Scholar 

  • Sadykov M, Asami Y, Niki H, Handa N, Itaya M, Tanokura M, Kobayashi I (2003) Multiplication of a restriction-modification gene complex. Mol Microbiol 48:417–427

    Article  PubMed  CAS  Google Scholar 

  • Sampath J, Vijayakumar MN (1998) Identification of a DNAcytosine methyltransferase gene in conjugative transposon Tn5252. Plasmid 39:63–76

    Article  PubMed  CAS  Google Scholar 

  • Saunders NJ, Peden JF, Hood DW, Moxon ER (1998) Simple sequence repeats in the Helicobacterpylori genome. Mol Microbiol 27:1091–1098

    Article  PubMed  CAS  Google Scholar 

  • Saunders NJ, Snyder LAS (2002) The minimal mobile element. Microbiology 148:37563760

    Google Scholar 

  • Schiestl RH, Petes TD (1991) Integration of DNA fragments by illegitimate recombination in Saccharomyces cerevisiae. Proc Natl Acad Sci USA 88:7585–7589

    Article  PubMed  CAS  Google Scholar 

  • Schouler C, Gautier M, Ehrlich SD, Chopin MC (1998) Combinational variation of restriction modification specificities in Lactococcus lactis. Mol Microbiol 28:169–178

    Article  PubMed  CAS  Google Scholar 

  • Sekizaki T, Otani Y, Osaki M, Takamatsu D, Shimoji Y (2001) Evidence for horizontal transfer of SsuDATlI restriction-modification genes to the Streptococcus suis genome. J BacterioI 183:500–511

    Article  CAS  Google Scholar 

  • Snyder L (1995) Phage-exclusion enzymes: a bonanza of biochemical and cell biology reagents? Mol Microbiol 15:415–420

    Article  PubMed  CAS  Google Scholar 

  • Som S, Friedman S (1993) Autogenous regulation of the EcoRII methylase gene at the transcriptional level: effect of 5-azacytidine. EMBO J 12:4297–4303

    PubMed  CAS  Google Scholar 

  • Som S, Friedman S (1997) Characterization of the intergenic region which regulates the MspI restriction-modification system. J Bacteriol 179:964–967

    PubMed  CAS  Google Scholar 

  • Sonoda E, Sasaki MS, Buerstedde J-M, Bezzubova O, Shinohara A, Ogawa H, Takata M, Yamaguchi-Iwai Y, Takeda S (1998) Rad51-deficient vertebrate cells accumulate chromosomal breaks prior to cell death. EMBO J 17:598–608

    Article  PubMed  CAS  Google Scholar 

  • Stein DC, Gunn JS, Piekarowicz A (1998) Sequence similarities between the genes encoding the S.NgoI and HaeII restriction/modification systems. Biol Chem 379:575–578

    PubMed  CAS  Google Scholar 

  • Takahashi N, Kobayashi I (1990) Evidence for the double-strand break repair model of bacteriophage I recombination. Proc Natl Acad Sci USA 87:2790–2794

    Article  PubMed  CAS  Google Scholar 

  • Takahashi N, Naito Y, Handa N, Kobayashi I (2002) A DNAmethyltransferase can protect the genome from postdisturbance attack by a restriction-modification gene complex. J BacterioI 184:6100–6108

    Article  CAS  Google Scholar 

  • Tao T, Bourne JC, Blumenthal RM (1991) A family of regulatory genes associated with type II restriction-modification systems. J Bacteriol 173:1367–1375

    PubMed  CAS  Google Scholar 

  • Tian QB, Hayashi T, Murata T, Terawaki Y (1996) Gene product identification and promoter analysis of hig locus of plasmid Rtsl. Biochem Biophys Res Commun 225:679–684

    Article  PubMed  CAS  Google Scholar 

  • Torres B, Iaenecke S, Timmis KN, Garcia JL, Diaz E (2000) A gene containment strategy based on a restriction-modification system. Env Microbiol 2:555–563

    Article  CAS  Google Scholar 

  • Trautner TA, Noyer-Weidner M (1993) Restriction/modification and methylase systems in Bacillus subtilis, related species, and their phages. In: Sonenshein AL, Hoch JA, Losick R (eds) Bacillussubtilis and other gram-positive bacteria: Biochemistry, physiology, and molecular genetics. ASMPress, Washington, DC, pp 539–552

    Google Scholar 

  • Vaisvila R, Vilkaitis G, Janulaitis A (1995) Identification of a gene encoding a DNAinvertase-like enzyme adjacent to the PaeR7I restriction-modification system. Gene 157:81–84

    Article  PubMed  CAS  Google Scholar 

  • Vijesurier RM, Carlock L, Blumenthal RM, Dunbar JC (2000) Role and mechanism of action of C. PvuII, a regulatory protein conserved among restriction-modification systems. J Bacteriol 182:477–487

    Article  PubMed  CAS  Google Scholar 

  • Wilson GG, Murray NE (1991) Restriction and modification systems. Annu Rev Genet 25:585–627

    Article  PubMed  CAS  Google Scholar 

  • XU Q, Morgan RD, Roberts RJ, Blaser MJ (2000) Identification of type II restriction and modification systems in Helicobacter pylori reveals their substantial diversity among strains. Proc Natl Acad Sci USA 97:9671–9676

    Article  PubMed  CAS  Google Scholar 

  • Xu SY, Xiao JP, Ettwiller L, Holden M, Aliotta J, Poh CL, Dalton M, Robinson DP, Petronzio TR, Moran L, Ganatra M, Ware J, Slatko B, Benner J (1998) Cloning and expression of the ApaLI, Nspl, NspHI, Sad, Seal, and Sapl restriction-modification systems in Escherichia coli. Mol Gen Genet 260:226–231

    Article  PubMed  CAS  Google Scholar 

  • Yarmolinsky MB (1995) Programmed cell death in bacterial populations. Science 267:836–837

    Article  PubMed  CAS  Google Scholar 

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Kobayashi, I. (2004). Restriction-Modification Systems as Minimal Forms of Life. In: Pingoud, A.M. (eds) Restriction Endonucleases. Nucleic Acids and Molecular Biology, vol 14. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-18851-0_2

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  • DOI: https://doi.org/10.1007/978-3-642-18851-0_2

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