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Type I and Type III Restriction-Modification Enzymes

  • Chapter
DNA Methylation

Part of the book series: Springer Series in Molecular Biology ((SSMOL))

Abstract

DNA methylation is the most ubiquitous form of DNA modification. It has been studied extensively in a wide variety of organisms. Although it generally is believed that DNA methylation is involved in mismatch repair in prokaryotic cells, and in the control of gene expression in eukaryotic cells, the precise nature of its biological functions remains largely unknown. One case in which the role of DNA methylation has been clearly defined is that of host-controlled restriction and modification in bacteria. This biological system consists of two highly specific enzymatic activities: an endonuclease and a DNA methylate. The endonuclease enables a given strain to both recognize and destroy foreign DNA by cutting both DNA strands at a limited number of sites. This function is defined as restriction. Kuhnlein and Arber (1972) showed that methylation at specific sequences protected the DNA from its homologous restriction endonuclease. This function is defined as modification.

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References

  • Arber W: Host controlled modification of bacteriophage. Ann Rev Microbiol 1965; 19: 365–378.

    Article  CAS  Google Scholar 

  • Arber W, Kuhnlein U: Mutationeller Verlust B-Spezifischer Restriktion des Bakteriophagen fd. Pathol Microbiol 1967; 30: 946–952.

    CAS  Google Scholar 

  • Arber W, Wauters-Willems D: The two restriction and modification systems of strain 15T- . Mol Gen Genetics 1970; 108: 203–217.

    Article  CAS  Google Scholar 

  • Bächi B, Reiser J, Pirrotta V: Methylation and cleavage sequences of the EcoP1 restriction-modification enzyme. J Mol Biol 1979; 128: 143–163.

    Article  PubMed  Google Scholar 

  • Bickle TA, Brack C, Yuan R: ATP-induced conformational changes in the restriction endonuclease from Escherichia coli K12. Proc Natl Acad Sci USA 1978; 75: 3099–4103.

    Article  PubMed  CAS  Google Scholar 

  • Bickle TA: The ATP-dependent restriction endonucleases, in Linn SM, Roberts RJ (eds.): Nucleases. Cold Spring Harbor, NY, Cold Spring Harbor Laboratory, 1983; 85–108.

    Google Scholar 

  • Boyer HW: Genetic control of restriction and modification in Escherichia coli. J Bacteriol 1964; 88: 1652–1660.

    CAS  Google Scholar 

  • Boyer HW, Roulland-Dussoix D: A complementation analÿsis of the restriction and modification of DNA in Escherichia coll. J Mol Biol. 1969; 41: 459–472.

    CAS  Google Scholar 

  • Brack C, Eberle H, Bickle TA, Yuan R: Mapping of recognition sites for the restriction endonuclease from Escherichia coli K12 on bacteriophage PM2 DNA. J Mol Biol 1976; 108: 583–593.

    Article  PubMed  CAS  Google Scholar 

  • Brzezinski R, Piekarowicz A: Steps in the reaction mechanism of the Haemophilus influenzae Rf restriction endonuclease. J Mol Biol. 1982; 154: 615–627.

    Article  PubMed  CAS  Google Scholar 

  • Bühler R, Yuan R: Characterization of a restriction enzyme from Escherichia coli K carrying a mutation on the modification subunit. J Biol Chem 1978; 253: 6756–6760.

    PubMed  Google Scholar 

  • Bullas LR, Colson C, Van Pel A: 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 postdam. J Gen Microbiol 1976; 95: 166–172.

    PubMed  CAS  Google Scholar 

  • Burchhardt J K, Weisemann J, Yuan R: Characterization of the DNA methylase activity of the restriction enzyme from Escherichia coli K. J Biol Chem 198la; 256:4024–4032.

    Google Scholar 

  • Burckhardt J, Weisemann J, Hamilton DL, Yuan R: Complexes formed between the restriction endonuclease EcoK and heteroduplex DNA. J Mol Biol 1981b;153:425–440.

    Article  CAS  Google Scholar 

  • Colson C, Colson AM: A new Salmonella typhimurium DNA host specificity. J Gen Microbiol 1971; 69: 345–351.

    PubMed  CAS  Google Scholar 

  • Colson AM, Colson C: Expression of the Escherichia coli K, B and phage P1 DNA host specificities in Salmonella typhimurium. J Gen Microbiol, 1972; 70: 123–128.

    PubMed  CAS  Google Scholar 

  • Dugaiczyk A, Kimball M, Linn S, Goodman HM: Location and nucleotide sequence of the site on SV40 DNA methylated by the EcoB modification methylase. Biochem Biophys Res Commun 1974; 61: 1133–1140.

    Article  PubMed  CAS  Google Scholar 

  • Eskin B, Linn S: The deoxyribonucleic acid modification and restriction enzymes of Escherichia coli B. II. Purification, subunit structure, and catalytic properties of the restriction endonuclease. J Biol Chem 1972b; 247: 6183–6191.

    PubMed  CAS  Google Scholar 

  • Eskin B, Linn S: The deoxyribonucleic acid modification and restriction enzymes of Escherichia coli B. II. Purification, subunit structure, and catalytic properties of the restriction endonuclease. J Biol Chem 1972b; 247: 6183–6191.

    PubMed  CAS  Google Scholar 

  • Glover SW: Functional analysis of host-specificity mutants in Escherichia coli. Genet Res 1970; 15: 237–250.

    CAS  Google Scholar 

  • Gough JA, Murray, NE: Sequence diversity among related genes for recognition of specific targets in DNA molecules. J Mol Biol 1983; 166: 1–19.

    Article  PubMed  CAS  Google Scholar 

  • Haberman A: The bacteriophage P1 restriction endonuclease. J Mol Biol 1974; 89: 545–563.

    Article  PubMed  CAS  Google Scholar 

  • Haberman A, Heywood J, Meselson M: DNA modification methylase activity of Escherichia coli restriction endonucleases K and P. Proc Natl Acad Sci USA 1972; 69: 3138–3141.

    Article  PubMed  CAS  Google Scholar 

  • Hadi SM, Yuan R: Complementation in vitro by mutant restriction enzymes from Escherichia coli K. J Biol Chem 1974; 249: 4580–4586.

    PubMed  CAS  Google Scholar 

  • Hadi SM, Bächi B, Shepherd JCW, Yuan R, Ineichen K, Bickle TA: DNA recognition and cleavage by the EcoP15 restriction endonuclease. J Mol Biol 1979; 134: 655–666.

    Article  PubMed  CAS  Google Scholar 

  • Hadi SM, Bächi B, Iida S, Bickle TA: DNA restriction-modification enzymes of phage P1 and plasmid p15B: subunit functions and structural homologies. J Mol Biol 1983; 165: 19–34.

    Article  PubMed  CAS  Google Scholar 

  • Hattman S: Specificity of the bacteriophage Mu mom +- controlled DNA modification. J Virol 1980; 34: 277–279.

    PubMed  CAS  Google Scholar 

  • Horiuchi K, Zinder ND: Cleavage of bacteriophage fl DNA by the restriction enzyme of Escherichia coli B. Proc Nat Acad Sci USA 1972; 69: 3220–3224.

    Article  PubMed  CAS  Google Scholar 

  • Hubacek J, Glover SW: Complementation analysis of temperature-sensitive host specificity mutations in Escherichia coli. J Mol Biol 1970; 50: 111–127.

    CAS  Google Scholar 

  • Iida S, Meyer B, Bächi B, Stolhammar-Carlemalm M, Schrickel S, Bickle TA, Arber W: DNA restriction-modification genes of phage P1 and plasmid pl5B: Structure and in vitro transcription. J Mol Biol 1983; 165: 1–18.

    Article  PubMed  CAS  Google Scholar 

  • Kan NC, Lautenberger JA, Edgell MH, Hutchinson III CA: The nucleotide sequence recognized by the Escherichia coli K12 restriction and modification enzymes. J Mol Biol 1979; 130: 191–209.

    Article  PubMed  CAS  Google Scholar 

  • Kauc L, Piekarowicz A: Purification and properties of a new restriction endonuclease from Haemophilus influenzae Rf. Eur J Biochem 1978; 92: 417–426.

    Article  PubMed  CAS  Google Scholar 

  • Kuhnlein U, Arber W: The role of nucleotide methylation in in vitro B-specific modification. J Mol Biol 1972; 63: 9–19.

    Article  PubMed  CAS  Google Scholar 

  • Lark C, Arber W: Host specificity of DNA produced by Escherichia coll. Breakdown of cellular DNA upon growth in ethionine of strains with r +14 , r +P1 , or r +N3 restriction phenotypes. J Mol Biol 1970; 52: 337 - 348.

    Article  PubMed  CAS  Google Scholar 

  • Lautenberger JA, Linn S: The deoxyribonucleic acid modification and restriction enzymes of Escherichia toll B. I. Purification, subunit structure, and catalytic properties of the modification methylase. J Biol Chem 1972; 247: 6176–6182.

    PubMed  CAS  Google Scholar 

  • Lautenberger JA, Kan NC, Lackey D, Linn S, Edgell MH, Hutchinson III CA: Recogniton site of Escherichia coli B restriction enzyme on 43XsBI and Simian virus 40 DNAs: An interrupted sequence. Proc Nall Acad Sci USA 1978; 75: 2271–2275.

    Article  CAS  Google Scholar 

  • Linn S, Arber W: In vitro restriction of phage fd replicative form. Proc Natl Acad Sci USA 1968; 59: 1300–1306.

    Article  PubMed  CAS  Google Scholar 

  • Lyons LB, Zinder ND: The genetic map of the filamentous bacteriophage fl. Virology 1972; 49: 45–60.

    Article  PubMed  CAS  Google Scholar 

  • Mark KK, Studier FW: Purification of the gene 0.3 protein of bacteriophage T7, an inhibitor of the DNA restriction system of Escherichia coli. J Biol Chem 1981; 256: 2573–2578.

    CAS  Google Scholar 

  • Meselson M, Yuan R: DNA restriction enzyme from E. coli. Nature 1968; 217: 1111–1113.

    Google Scholar 

  • Meselson, M, Yuan R, Heywood J: Restriction and modification of DNA. Ann Rev Biochem 1972; 41: 447–466.

    Article  PubMed  CAS  Google Scholar 

  • Murray NE, Manduca de Ritis P, Foster L: DNA targets for the Escherichia toll K restriction system analyzed genetically in recombinants between phages 080 and lambda. Mol Gen Genet 1973; 120: 261–281.

    Article  PubMed  CAS  Google Scholar 

  • Murray NE, Gough JA, Suri B, Bickle TA: Structural homologies among Type I restriction-modification systems. The EMBO J 1982; 1: 535–539

    CAS  Google Scholar 

  • Piekarowicz A, Brzezinski R: Cleavage and methylation of DNA by the restriction endonuclease HinfIII isolated from Haemophilus influenzae Rf. J Mol Biol 1980; 144: 415–429.

    Article  PubMed  CAS  Google Scholar 

  • Piekarowicz A, Bickle TA, Shepherd JCW, Ineichen K: The DNA sequence recognized by the Hinflll restriction endonuclease. J Mol Biol 1981; 146: 167–172.

    Article  PubMed  CAS  Google Scholar 

  • Ravetch JV, Horiuchi K, Zinder ND: Nucleotide sequence of the recognition site for the restriction-modification enzyme of Escherichia coli B. Proc Nall Acad Sci USA 1978; 75: 2266–2270.

    Article  CAS  Google Scholar 

  • Reiser J, Yuan R: Purification and properties of the P15 Specific restriction endonuclease from Escherichia coli. J Biol Chem 1977; 252: 451–456.

    CAS  Google Scholar 

  • Roulland-Dussoix D, Boyer H: The Escherichia coli B restriction endonuclease. Biochem Biophys Acta 1969; 195: 219–229.

    PubMed  CAS  Google Scholar 

  • Sain B, Murray NE: The hsd (host specificity) genes of Escherichia coli K12. Mol Gen Genet 1980; 180: 35–46.

    Article  PubMed  CAS  Google Scholar 

  • Sclair M, Edgell MH, Hutchinson, CA III: Mapping of new Escherichia coli K and 15 restriction sites on specific fragments of bacteriophage X174 DNA. J Virol 1973; 11: 278–285.

    Google Scholar 

  • Smith HO, Nathans D: A suggested nomenclaturefor bacterial host-modification and restriction systems and their enzymes. J Mol Biol 1973; 81: 419–423.

    Article  PubMed  CAS  Google Scholar 

  • Smith J, Arber W, and Kühnlein U: Host specificity of DNA produced by Escherichia coli 15. The implication of nucleotide methylation in in vitro B-specific modification. J Mol Biol 1972; 63: 9–19.

    Article  Google Scholar 

  • Spoerel N, Herrlich P: Colivirus T3-coded S-adenosylmethionine hydrolase. Eur J Biochem 1979; 95: 227–233.

    Article  PubMed  CAS  Google Scholar 

  • Spoerel N, Herrlich PA, Bickle TA: A novel bacteriophage defence mechanism: the anti-restriction protein. Nature (London) 1979; 278: 30–34.

    Article  CAS  Google Scholar 

  • Studier FW: Gene 0.3 of bacteriophage T7 acts to overcome the DNA restriction enzyme of the host. J Mol Biol 1975; 94: 283–295.

    Article  PubMed  CAS  Google Scholar 

  • Studier FW, Movva NR: SAMase gene of bacteriophage T3 is responsible for overcoming host restriction. J Virol 1976; 19: 136–145.

    PubMed  CAS  Google Scholar 

  • Suri B, Nagaraja V, Bickle TA: Bacterial DNA modification. Curr Topics Microbiol Immunol (vol 102, in press, 1983).

    Google Scholar 

  • Toussaint A: The DNA modification function of temperate phage Mu-1. Virology 1976; 70: 17–27.

    Article  PubMed  CAS  Google Scholar 

  • van Ormondt H, Lautenberger JA, Linn S, deWaard A: Methylated oligonucleotides derived from bacteriophage fd Rf DNA modified in vitro by E. coli B modification methylase. FEBS Letters 1973; 33: 177–180.

    Article  PubMed  Google Scholar 

  • Vovis GF, Zinder ND: Methylation of fl DNA by a restriction endonuclease from Escherichia coli B. J Mol Biol 1975: 95: 557–568.

    Article  PubMed  CAS  Google Scholar 

  • Vovis GF, Horiuchi K, Hartman N, Zinder ND: Restriction endonuclease B and fl heteroduplex DNA. Nature New Biol 1973; 246: 13–16.

    PubMed  CAS  Google Scholar 

  • Vovis GF, Horiuchi K Zinder ND: Kinetics of methylation by a restriciton endonu- clease from Escherichia coli B. Proc Natl Acad Sci USA 1974; 71: 3810–3813.

    Article  PubMed  CAS  Google Scholar 

  • Yuan R: Structure and mechanism aof multifunctional restriction endonucleases. Ann Rev Biochem. 1981; 50: 285–315.

    Article  PubMed  CAS  Google Scholar 

  • Yuan R, Reiser J: Steps in the reaction mechanism of the Escherichia coli plasmid P15-specific restriction endonuclease. J Mol Biol 1978; 122: 433–445.

    Article  PubMed  CAS  Google Scholar 

  • Yuan R, Heywood J Messelson M: ATP hydrolysis by restriction endonuclease from E. coli K. Nature New Biol 1972; 240: 42–43.

    PubMed  CAS  Google Scholar 

  • Yuan R, Bickle TA, Ebbers W, Brack C: Multiple steps in DNA recognition by restriction endonuclease from E. coli K. Nature 1975; 256: 556–560.

    Article  PubMed  CAS  Google Scholar 

  • Yuan R, Hamilton DL, Hadi SM, Bickle TA: Role of ATP in the cleavage mechanism of the EcoPl5 restriction endonuclease. J Mol Biol 1980: 144: 501–519.

    Article  PubMed  CAS  Google Scholar 

  • Yuan R, Burckhardt J, Weisemann J, Hamilton DL: The mechanism of DNA methylation by the restriction endonuclease from E. coli K. in Usdin E, Borchardt RT, Creveling CR (eds.): Biochemistry of S-adenosylmethionine and related compounds. London, MacMillan Press, Ltd, 1981, pp. 239–247.

    Google Scholar 

  • Zabeau M, Friedman SF, VanMontagu M, Schell J: The ral gene of phage X. I: Identification of a non-essential gene that modulates restriction and modification in E. coli. Mol Gen. Genet 1980; 179: 63–73.

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. NCI-Frederick Cancer Research Facility, P.O. Box B, Frederick, Maryland, 21701, USA

    Robert Yuan & Daniel L. Hamilton

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  1. Robert Yuan
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  2. Daniel L. Hamilton
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Editors and Affiliations

  1. Department of Cellular Biology, The Hebrew University Hadassah Medical School, 91-010, Jerusalem, Israel

    Aharon Razin (Chairman) (Chairman)

  2. Department of Cellular Biochemistry, The Hebrew University Hadassah Medical School, 91-010, Jerusalem, Israel

    Howard Cedar

  3. Beckman Research Institute of the City of Hope, 91010, Duarte, California, USA

    Arthur D. Riggs

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© 1984 Springer-Verlag New York Inc.

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Yuan, R., Hamilton, D.L. (1984). Type I and Type III Restriction-Modification Enzymes. In: Razin, A., Cedar, H., Riggs, A.D. (eds) DNA Methylation. Springer Series in Molecular Biology. Springer, New York, NY. https://doi.org/10.1007/978-1-4613-8519-6_2

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  • DOI: https://doi.org/10.1007/978-1-4613-8519-6_2

  • Publisher Name: Springer, New York, NY

  • Print ISBN: 978-1-4613-8521-9

  • Online ISBN: 978-1-4613-8519-6

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