Diversity of DNA methyltransferases that recognize asymmetric target sequences

References

• Abdurashitov MA, Kileva EV, Shinkarenko NM, Shevchenko AV, Dedkov VS and Degtyarev S. 1996. BstF5I, an unusual isoschizomer of FokI. Gene 172: 49–51.
   Google Scholar
• Ahmad I and Rao DN. 1994. Interaction of EcoP15I DNA methyltransferase with oligonucleotides containing the asymmetric sequence 5′-CAGCAG-3′. J Mol Biol 242:378–388.
   Google Scholar
• Ahmad I and Rao DN. 1996a. Chemistry and biology of DNA methyltransferases. Crit Rev Biochem Mol Biol 31:361–380.
   Web of Science ®Google Scholar
• Ahmad I and Rao DN. 1996b. Functional analysis of conserved motifs in EcoP15I DNA methyltransferase. J Mol Biol 259: 229–40.
   Google Scholar
• Ahmad I, Krishnamurthy V, Rao DN. 1995. DNA recognition by the EcoP15I and EcoPI modification methyltransferases. Gene 157:143–147.
   Google Scholar
• Allan BW and Reich NO. 1996. Targeted base stacking disruption by the EcoRI DNA methyltransferase. Biochemistry 35:14757–14762.
   Google Scholar
• Alm RA, Ling LS, Moir DT, King BL, Brown ED, Doig PC, Smith DR, Noonan B, Guild BC, deJonge 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. Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori. Nature 397:176–180.
   PubMed Web of Science ®Google Scholar
• Alves J, Selent U and Wolfes H. 1995. Accuracy of the EcoRV restriction endonuclease: binding and cleavage studies with oligodeoxynucleotide substrates containing degenerate recognition sequences. Biochemistry 34:11191–11197.
   Google Scholar
• Arber W. 2000. Genetic variation: molecular mechanisms and impact on microbial evolution. FEMS Microbiol Rev 24:1–7.
   PubMed Web of Science ®Google Scholar
• Arber W. 2002. Evolution of prokaryotic genomes. Curr Top Microbiol Immunol 264:1–14.
   Google Scholar
• Baldwin GS, Kelly SM, Price NC, Wilson GW, Connolly BA, Artymiuk PJ and Hornby DP. 1994. Ligand-induced conformational states of the cytosine-specific DNA methyltransferase M.HgaI-2. J Mol Biol 235:545–553.
   Google Scholar
• Barbeyron T, Kean K and Forterre P. 1984. DNA adenine methylation of GATC sequences appeared recently in the Escherichia coli lineage. J Bacteriol 160:586–590.
   PubMedGoogle Scholar
• Bayliss CD, Callaghan MJ and Moxon ER. 2006. High allelic diversity in the methyltransferase gene of a phase variable type III restriction-modification system has implications for the fitness of Haemophilus influenzae. Nucleic Acids Res 34:4046–4059.
   PubMed Web of Science ®Google Scholar
• Bheemanaik S, Chandrashekaran S, Nagaraja V and Rao DN. 2003. Kinetic and catalytic properties of dimeric KpnI DNA methyltransferase. J Biol Chem 278:7863–7874.
   Google Scholar
• Bheemanaik S, Reddy YV and Rao DN. 2006a. Structure, function and mechanism of exocyclic DNA methyltransferases. Biochem J 399:177–190.
   Google Scholar
• Bheemanaik S, Bujnicki JM, Nagaraja V and Rao DN. 2006b. Functional analysis of amino acid residues at the dimerisation interface of KpnI DNA methyltransferase. Biol Chem 387:515–523.
   Google Scholar
• Bickle TA and Kruger DH. 1993. Biology of DNA restriction. Microbiol Rev 57:434–450.
   PubMedGoogle Scholar
• Bist P and Rao DN. 2003. Identification and mutational analysis of Mg2+ binding site in EcoP15I DNA methyltransferase: involvement in target base eversion. J Biol Chem 278:41837–41848.
   Google Scholar
• Bist P, Sistla S, Krishnamurthy V, Acharya A, Chandrakala B and Rao DN. 2001. S-adenosyl-L-methionine is required for DNA cleavage by type III restriction enzymes. J Mol Biol 310:93–109.
   PubMed Web of Science ®Google Scholar
• Bist P, Madhusoodanan UK and Rao DN. 2007. A mutation in the Mod subunit of EcoP15I restriction enzyme converts the DNA methyltransferase to a site-specific endonuclease. J Biol Chem 282:3520–3530.
   Google Scholar
• Bitinaite J, Grigaite R, Maneliene Z, Butkus V and Janulaitis A. 1991. Esp3I – a novel type IIs restriction endonuclease from Hafnia alvei that recognizes the sequence 5′-CGTCTC(N)1/5-3′. Nucleic Acids Res 19:5076.
   Google Scholar
• Bitinaite J, Maneliene Z, Menkevicius S, Klimasauskas S, Butkus V and Janulaitis A. 1992. Alw26I, Eco31I and Esp3I – type IIs methyltransferases modifying cytosine and adenine in complementary strands of the target DNA. Nucleic Acids Res 20:4981–4985.
   Google Scholar
• Bocklage H, Heeger K and Muller-Hill B. 1991. Cloning and characterization of the MboII restriction-modification system. Nucleic Acids Res 19:1007–1013.
   Google Scholar
• Bujnicki JM and Radlinska M. 1999. Molecular evolution of DNA-(cytosine-N4) methyltransferases: evidence for their polyphyletic origin. Nucleic Acids Res 27:4501–4509.
   PubMed Web of Science ®Google Scholar
• Burckhardt J, Weisemann J, Yuan R. 1981a. Characterization of the DNA MTase activity of the restriction enzyme from Escherichia coli K. J Biol Chem 256:4024–4032.
   Google Scholar
• Burckhardt J, Weisemann J, Hamilton DL and Yuan R. 1981b. Complexes formed between the restriction endonuclease EcoK and heteroduplex DNA. J Mol Biol 153:425–440.
   Google Scholar
• Buryanova Y and Shevchuk T. 2005. The use of prokaryotic DNA methyltransferases as experimental and analytical tools in modern biology. Anal Biochem 338:1–11.
   Google Scholar
• Butkus V, Bitinaite J, Kersulyte D and Janulaitis A. 1985. A new restriction endonuclease Eco31I recognizing a non-palindromic sequence. Biochim Biophys Acta 826:208–212.
   Google Scholar
• Carlson K and Kosturko LD. 1998. Endonuclease II of coliphage T4: a recombinase disguised as a restriction endonuclease? Mol Microbiol 27:671–676.
   Google Scholar
• Cerritelli S, Springhorn SS and Lacks SA. 1989. DpnA, a MTase for single-strand DNA in the Dpn II restriction system, and its biological function. Proc Natl Acad Sci USA 86:9223–9227.
   PubMed Web of Science ®Google Scholar
• Cesnaviciene E, Petrusyte M, Kazlauskiene R, Maneliene Z, Timinskas A, Lubys A and Janulaitis A. 2001. Characterization of AloI, a restriction-modification system of a new type. J Mol Biol 314:205–216.
   PubMed Web of Science ®Google Scholar
• Cheng X. 1995. Structure and function of DNA methyltransferases. Annu Rev Biophys Biomol Struct 24:293–318.
   PubMedGoogle Scholar
• Cheng X and Roberts RJ. 2001. AdoMet-dependent methylation, DNA methyltransferases and base flipping. Nucleic Acids Res 29:3784–3795.
   PubMed Web of Science ®Google Scholar
• Cheng X, Kumar S, Posfai J, Pflugrath JW and Roberts RJ. 1993. Crystal structure of the HhaI DNA methyltransferase complexed with S-adenosyl-L-methionine. Cell 74:299–307.
   PubMed Web of Science ®Google Scholar
• Chernov AV, Matvienko NN, Zheleznaya LA and Matvienko NI. 1996. BspLU11III, a bifunctional restriction and modification enzyme from a thermophilic strain Bacillus species LU11. Nucleic Acids Res 23:1213–1214.
   Google Scholar
• Chernukhin VA, Golikova LN, Gonchar DA, Abdurashitov MA, Kashirina YG, Netesova NA and Degtyarev S. 2003. M.BstF5I-2 and M.BstF5I-4 DNA methyltransferases from BstF5I restriction-modification system of Bacillus stearothermophilus F5. Biochemistry (Moscow). 68:967–975.
   Google Scholar
• Cooper LP and Dryden DT. 1994. The domains of a type I DNA methyltransferase. Interactions and role in recognition of DNA methylation. J Mol Biol 236:1011–1021.
   Google Scholar
• De Bolle X, Bayliss CD, Field D, van de Ven T, Saunders NJ, Hood DW and Moxon ER. 2000. The length of a tetranucleotide repeat tract in Haemophilus influenzae determines the phase variation rate of a gene with homology to type III DNA methyltransferases. Mol Microbiol 35:211–222.
   PubMedGoogle Scholar
• Degtyarev S, Netesova NA, Abdurashitov MA and Shevchenko AV. 1997. Primary structure and strand specificity of BstF5I-1 DNA methyltransferase which recognizes 5′-GGATG-3′. Gene 187:217–219.
   Google Scholar
• de la Campa AG, Kale P, Springhorn SS and Lacks SA. 1987. Proteins encoded by the DpnII restriction gene cassette. Two methylases and an endonuclease. J Mol Biol 196:457–469.
   Google Scholar
• de Vries N, Duinsbergen D, Kuipers EJ, Pot RG, Wiesenekker P, Penn CW, van Vliet AH, Vandenbroucke-Grauls CM and Kusters JG. 2002. Transcriptional phase variation of a type III restriction-modification system in Helicobacter pylori. J Bacteriol 184:6615–6623.
   Google Scholar
• Dong A, Zhou L, Zhang X, Stickel S, Roberts RJ and Cheng X. 2004. Structure of the Q237W mutant of HhaI DNA methyltransferase: an insight into protein–protein interactions. Biol Chem 385:373–379.
   Google Scholar
• Dryden DT. 1999. Bacterial DNA methyltransferases, pp. 283–340. In: Cheng, X and Blumenthal, RM, eds, S-Adenosylmethionine-Dependent Methyltransferases: Structures and Functions. Singapore: World Scientific Publishing.
   Google Scholar
• Dryden DT, Cooper LP and Murray NE. 1993. Purification and characterization of the methyltransferase from the type 1 restriction and modification system of Escherichia coli K12. J Biol Chem 268:13228–13236.
   Google Scholar
• Dryden DT, Sturrock SS and Winter M. 1995. Structural modelling of a type I DNA methyltransferase. Nat Struct Biol 2:632–635.
   Google Scholar
• Dryden DT, Cooper LP, Thorpe PH and Byron O. 1997. The in vitro assembly of the EcoKI type I DNA restriction/modification enzyme and its in vivo implications. Biochemistry 36:1065–1076.
   PubMed Web of Science ®Google Scholar
• Dryden DT, Murray NE and Rao DN. 2001. Nucleoside triphosphate-dependent restriction enzymes. Nucleic Acids Res 29:3728–3741.
   PubMed Web of Science ®Google Scholar
• Dubey AK and Roberts RJ. 1992. Sequence-specific DNA binding by the MspI DNA methyltransferase. Nucleic Acids Res 20:3167–3173.
   PubMed Web of Science ®Google Scholar
• Fellinger K, Rothbauer U, Felle M, Langst G and Leonhardt H. 2009. Dimerization of DNA methyltransferase 1 is mediated by its regulatory domain. J Cell Biochem 106:521–528.
   PubMed Web of Science ®Google Scholar
• Fox KL, Dowideit SJ, Erwin AL, Srikhanta YN, Smith AL and Jennings MP. 2007a. Haemophilus influenzae phasevarions have evolved from type III DNA restriction systems into epigenetic regulators of gene expression. Nucleic Acids Res 35:5242–5252.
   PubMed Web of Science ®Google Scholar
• Fox KL, Srikhanta YN and Jennings MP. 2007b. Phase variable type III restriction-modification systems of host-adapted bacterial pathogens. Mol Microbiol 65:1375–1379.
   PubMedGoogle Scholar
• Friedrich T, Fatemi M, Gowhar H, Leishmann O and Jeltsch A. 2000. Specificity of DNA binding and methylation by the M.FokI DNA Methyltransferase. Biochem. Biophys Acta 1480:145–159.
   Google Scholar
• Fuller-Pace FV and Murray NE. 1986. Two DNA recognition domains of the specificity polypeptides of a family of type I restriction enzymes. Proc Natl Acad Sci USA 83:9368–9372.
   Google Scholar
• Furmanek B, Sektas M, Wons E and Kaczorowski T. 2007. Molecular characterization of the DNA methyltransferase M1.NcuI from Neisseria cuniculi ATCC 14688. Res Microbiol 158:164–174.
   Google Scholar
• Furmanek-Blaszk B, Boratynski R, Zolcinska N and Sektas M. 2009. M1.MboII and M2.MboII type IIS methyltransferases: different specificities, the same target. Microbiology 155:1111–1121.
   Google Scholar
• Gann AA, Campbell AJ, Collins JF, Coulson AF and Murray NE. 1987. Reassortment of DNA recognition domains and the evolution of new specificities. Mol Microbiol 1:13–22.
   Google Scholar
• Goedecke K, Pignot M, Goody RS, Scheidig AJ and Weinhold E. 2001. Structure of the N6-adenine DNA methyltransferase M.TaqI in complex with DNA and a cofactor analog. Nat Struct Biol 8:121–125.
   PubMedGoogle Scholar
• Gong W, O′Gara M, Blumenthal RM and Cheng X. 1997. Structure of Pvu II DNA-(cytosine N4) methyltransferase, an example of domain permutation and protein fold assignment. Nucleic Acids Res 25:2702–2715.
   PubMed Web of Science ®Google Scholar
• Gromova ES and Khoroshaev AV. 2003. Prokaryotic DNA methyltransferases: the structure and the mechanism of interaction with DNA. Mol Biol (Moscow) 37:300–314.
   PubMedGoogle Scholar
• Gubler M, Braguglia, D, Meyer J, Piekarowicz A and Bickle TA. 1992. Recombination of constant and variable modules alters DNA sequence recognition by type IC restriction-modification enzymes. EMBO J 11:233–240.
   Google Scholar
• Hadi SM, Bachi B, Iida S and Bickle TA. 1983. DNA restriciton – modification enzymes of phage P1 and plasmid P15B. Subunit functions and structural homologies. J Mol Biol 165:19–34.
   Google Scholar
• Heitman J. 1993. On the origins, structures and functions of restriction-modification enzymes. Genet Eng (NY) 15:57–108.
   PubMedGoogle Scholar
• Holz B, Klimasauskas S, Serva S and Weinhold E. 1998. 2-Aminopurine as a fluorescent probe for DNA base flipping by methyltransferases. Nucleic Acids Res 26:1076–1083.
   PubMed Web of Science ®Google Scholar
• Janscak P and Bickle TA. 1998. The DNA recognition subunit of the type IB restriction-modification enzyme EcoAI tolerates circular permutions of its polypeptide chain. J Mol Biol 284:937–948.
   Google Scholar
• Janulaitis A, Petrusyte M, Maneliene Z, Klimasauskas S and Butkus V. 1992a. Purification and properties of the Eco57I restriction endonuclease and methylase-prototypes of a new class (type IV). Nucleic Acids Res 20:6043–6049.
   PubMed Web of Science ®Google Scholar
• Janulaitis A, Vaisvila R, Timinskas A, Klimasauskas S and Butkus V. 1992b. Cloning and sequence analysis of the genes coding for Eco57I type IV restriction- modification enzymes. Nucleic Acids Res 20:6051–6056.
   Google Scholar
• Jeltsch A. 2002. Beyond Watson and Crick: DNA methylation and molecular enzymology of DNA methyltransferases. Chembiochem 3:274–293.
   PubMed Web of Science ®Google Scholar
• Jeltsch A. 2003. Maintenance of species identity and controlling speciation of bacteria: a new function for restriction/modification systems? Gene 317:13–16.
   PubMedGoogle Scholar
• Jeltsch A, Christ F, Fatemi M and Roth M. 1999. On the substrate specificity of DNA methyltransferases. adenine-N6 DNA methyltransferases also modify cytosine residues at position N4. J Biol Chem 274:19538–19544.
   Google Scholar
• Jeltsch A, Jurkowska RZ, Jurkowski TP, Liebert K, Rathert P and Schlickenrieder M. 2007. Application of DNA methyltransferases in targeted DNA methylation. Appl Microbiol Biotechnol 75:1233–1240.
   Google Scholar
• Jia D, Jurkowska RZ, Zhang X, Jeltsch A and Cheng X. 2007. Structure of Dnmt3a bound to Dnmt3L suggests a model for de novo DNA methylation. Nature 449:248–251.
   PubMed Web of Science ®Google Scholar
• Jois PS, Madhu N and Rao DN. 2008. Role of histidine residues in EcoP15I DNA methyltransferase activity as probed by chemical modification and site-directed mutagenesis. Biochem J 410:543–553.
   Google Scholar
• Jurenaite-Urbanaviciene S, Kazlauskiene R, Urbelyte V, Maneliene Z, Petrusyte M, Lubys A and Janulaitis A. 2001. Characterization of BseMII, a new type IV restriction-modification system, which recognizes the pentanucleotide sequence 5′-CTCAG(N)(10/8). Nucleic Acids Res 29:895–903.
   PubMed Web of Science ®Google Scholar
• Kaczorowski T, Sektas M, Skowron P and Podhajska AJ. 1999. The FokI methyltransferase from Flavobacterium okeanokoites. Purification and characterization of the enzyme and its truncated derivatives. Mol Biotechnol 13:1–15.
   Google Scholar
• Kaszubska W, Webb HK and Gumport RI. 1992. Purification and characterization of the M.RsrI DNA methyltransferase from Escherichia coli. Gene 118:5–11.
   Google Scholar
• Kelleher JE, Daniel AS and Murray NE. 1991. Mutations that confer de novo activity upon a maintenance methyltransferase. J Mol Biol 221:431–440.
   Google Scholar
• Kennaway CK, Obarska-Kosinska A, White JH, Tuszynska I, Cooper LP, Bujnicki JM, Trinick J and Dryden DT. 2009. The structure of M.EcoKI Type I DNA methyltransferase with a DNA mimic antirestriction protein. Nucleic Acids Res 37:762–770.
   Google Scholar
• Klimasauskas S, Timinskas A, Menkevicius S, Butkiene D, Butkus V and Janulaitis A. 1989. Sequence motifs characteristic of DNA[cytosine-N4]methyltransferases: similarity to adenine and cytosine-C5 DNA-methylases. Nucleic Acids Res 17:9823–9832.
   PubMedGoogle Scholar
• Klimasauskas S, Kumar S, Roberts RJ and Cheng X. 1994. HhaI methyltransferase flips its target base out of the DNA helix. Cell 76:357–369.
   PubMed Web of Science ®Google Scholar
• Kneale GG. 1994. A symmetrical model for the domain structure of type I DNA methyltransferases. J Mol Biol 243:1–5.
   Google Scholar
• Kobayashi I. 2004. Restriction-modification systems as minimal forms of life, pp. 19–62. In: Pingoud A., ed., Restriction Endonucleases Berlin: Springer.
   Google Scholar
• Kong H. 1998. Analyzing the functional organization of a novel restriction modification system, the BcgI system. J Mol Biol 279:823–832.
   Google Scholar
• Kong H and Smith CL. 1997. Substrate DNA and cofactor regulate the activities of a multi-functional restriction-modification enzyme, BcgI. Nucleic Acids Res 25:3687–3692.
   Google Scholar
• Kong H, Morgan RD, Maunus RE and Schildkraut I. 1993. A unique restriction endonuclease, BcgI, from Bacillus coagulans. Nucleic Acids Res 21:987–991.
   Google Scholar
• Kong H, Roemer SE, Waite-Rees PA, Benner JS, Wilson GG and Nwankwo DO. 1994. Characterization of BcgI, a new kind of restriction-modification system. J Biol Chem 269:683–690.
   Google Scholar
• Krishnamurthy V and Rao DN. 1994. Interaction of EcoP1 modification methylase with S-adenosyl-L-methionine: a UV-crosslinking study. Biochem Mol Biol Int 32:623–632.
   Google Scholar
• Kriukiene E, Lubiene J, Lagunavicius A and Lubys A. 2005. MnlI – The member of H-N-H subtype of Type IIS restriction endonucleases. Biochim Biophys Acta 1751:194–204.
   Google Scholar
• Kruger DH, Kupper D, Meisel A, Reuter M and Schroeder C. 1995. The significance of distance and orientation of restriction endonuclease recognition sites in viral DNA genomes. FEMS Microbiol Rev 17:177–184.
   PubMedGoogle Scholar
• Kumar S, Cheng X, Klimasauskas S, Mi S, Posfai J, Roberts RJ and Wilson GG. 1994. The DNA (cytosine-5) methyltransferases. Nucleic Acids Res 22:1–10.
   PubMed Web of Science ®Google Scholar
• Labahn J, Granzin J, Schluckebier G, Robinson DP, Jack WE, Schildkraut I and Saenger W. 1994. Three-dimensional structure of the adenine-specific DNA methyltransferase M.Taq I in complex with the cofactor S-adenosylmethionine. Proc Natl Acad Sci USA 91:10957–10961.
   PubMedGoogle Scholar
• Lacks SA, Ayalew S, de la Campa AG and Greenberg B. 2000. Regulation of competence for genetic transformation in Streptococcus pneumonia: expression of dpnA, a late competence gene encoding a DNA methyltransferase of the DpnII restriction system. Mol Microbiol 35:1089–1098.
   PubMedGoogle Scholar
• Landry D, Looney MC, Feehery GR, Slatko BE, Jack WE, Schildkraut I and Wilson GG. 1989. M.FokI methylates adenine in both strands of its asymmetric recognition sequence. Gene 77:1–10.
   Google Scholar
• Lauster R, Trautner TA and Noyer-Weidner M. 1989. Cytosine-specific type II DNA methyltransferases. A conserved enzyme core with variable target-recognizing domains. J Mol Biol 206:305–312.
   Google Scholar
• Lehours P, Dupouy S, Chaineux J, Ruskone-Fourmestraux A, Delchier JC, Morgner A, Megraud F and Menard A. 2007. Genetic diversity of the HpyC1I restriction modification system in Helicobacter pylori. Res Microbiol 158:265–271.
   Google Scholar
• Leismann O, Roth M, Friedrich T, Wende W and Jeltsch A. 1998. The Flavobacterium okeanokoites adenine-N6-specific DNA-methyltransferase M.FokI is a tandem enzyme of two independent domains with very different kinetic properties. Eur J Biochem 251:899–906.
   Google Scholar
• Lepikhov K, Tchernov A, Zheleznaja L, Matvienko N, Walter J and Trautner TA. 2001. Characterization of the type IV restriction modification system BspLU11III from Bacillus sp. LU11. Nucleic Acids Res 29:4691–4698.
   Google Scholar
• Lesser DR, Kurpiewski MR and Jen-Jacobson L. 1990. The energetic basis of specificity in the Eco RI endonuclease–DNA interaction. Science 250:776–786.
   PubMed Web of Science ®Google Scholar
• Lin TL, Shun CT, Chang KC and Wang JT. 2004. Isolation and characterization of a HpyC1I restriction-modification system in Helicobacter pylori. J Biol Chem 279:11156–11162.
   Google Scholar
• Løbner-Olesen A, Skovgaard O and Marinus MG. 2005. Dam methylation: coordinating cellular processes. Curr Opin Microbiol 8:154–160.
   PubMed Web of Science ®Google Scholar
• Looney MC, Moran LS, Jack WE, Feehery GR, Benner JS, Slatko BE and Wilson GG. 1989. Nucleotide sequence of the FokI restriction-modification system: separate strand-specificity domains in the methyltransferase. Gene 80:193–208.
   Google Scholar
• Low DA, Weyand NJ and Mahan MJ. 2001. Roles of DNA adenine methylation in regulating bacterial gene expression and virulence. Infect Immun 69:7197–7204.
   PubMed Web of Science ®Google Scholar
• Lusk JE, Williams RJ and Kennedy EP. 1968. Magnesium and the growth of Escherichia coli. J Biol Chem 243:2618–2624.
   PubMed Web of Science ®Google Scholar
• Malone T, Blumenthal RM and Cheng X. 1995. Structure-guided analysis reveals nine sequence motifs conserved among DNA amino-methyltransferases, and suggests a catalytic mechanism for these enzymes. J Mol Biol 253:618–632.
   PubMed Web of Science ®Google Scholar
• Malygin EG, Evdokimov AA, Zinoviev VV, Ovechkina LG, Lindstrom WM, Reich NO, Schlagman SL and Hattman S. 2001. A dual role for substrate S-adenosyl-L-methionine in the methylation reaction with bacteriophage T4 Dam DNA-[N6-adenine]-methyltransferase. Nucleic Acids Res 29:2361–2369.
   Google Scholar
• Malygin EG, Sclavi B, Zinoviev VV, Evdokimov AA, Hattman S and Buckle M. 2004. Bacteriophage T4Dam DNA-(adenine-N(6)-methyltransferase. Comparison of pre-steady state and single turnover methylation of 40-mer duplexes containing two (un)modified target sites. J Biol Chem 279:50012–50018.
   Google Scholar
• Malygin EG, Evdokimov AA and Hattman S. 2009. Dimeric/oligomeric DNA methyltransferases: an unfinished story. Biol Chem 390:835–844.
   Google Scholar
• Marinus MG and Casadesus J. 2009. Roles of DNA adenine methylation in host-pathogen interactions: mismatch repair, transcriptional regulation, and more. FEMS Microbiol Rev 33:488–503.
   PubMed Web of Science ®Google Scholar
• Marks P, McGeehan J, Wilson G, Errington N and Kneale G. 2003. Purification and characterisation of a novel DNA methyltransferase, M.AhdI. Nucleic Acids Res 31:2803–2810.
   Google Scholar
• McCleland SE and Sczcelkun MD. 2004. The type I and III restriction endonucleases: structural elements in molecular motors that process DNA, pp. 111–135. In: Pingoud A., ed., Restriction Endonucleases, Berlin: Springer.
   Google Scholar
• McClelland M. 1981. The effect of sequence specific DNA methylation on restriction endonuclease cleavage. Nucleic Acids Res 9:5859–5866.
   PubMedGoogle Scholar
• McClelland M, Nelson M and Cantor CR. 1985. Purification of MboII methylase (GAAGmA) from Moraxella bovis: site specific cleavage of DNA at nine and ten base pair sequences. Nucleic Acids Res 13:7171–7182.
   Google Scholar
• McKane M and Milkman R. 1995. Transduction, restriction and recombination patterns in Escherichia coli. Genetics 139:35–43.
   Google Scholar
• Meisel A, Kruger DH and Bickle TA. 1991. M.EcoP15 methylates the second adenine in its recognition sequence. Nucleic Acids Res 19:3997.
   Google Scholar
• Meisel A, Bickle TA, Kruger DH and Schroeder C. 1992. Type III restriction enzymes need two inversely oriented recognition sites for DNA cleavage. Nature 355:467–469.
   PubMed Web of Science ®Google Scholar
• Meisel A, Mackeldanz P, Bickle TA, Kruger DH and Schroeder C. 1995. Type III restriction endonucleases translocate DNA in a reaction driven by recognition site-specific ATP hydrolysis. EMBO J 14:2958–2966.
   PubMed Web of Science ®Google Scholar
• Merkiene E, Vilkaitis G and Klimasauskas S. 1998. A pair of single-strand and double-strand DNA cytosine-N4 methyltransferases from Bacillus centrosporus. Biol Chem 379:569–571.
   Google Scholar
• Mernagh DR and Kneale GG. 1996. High resolution footprinting of a type I methyltransferase reveals a large structural distortion within the DNA recognition site. Nucleic Acids Res 24:4853–4858.
   Google Scholar
• Mernagh DR, Reynolds LA and Kneale GG. 1997. DNA binding and subunit interactions in the type I methyltransferase M.EcoR124I. Nucleic Acids Res 25:987–991.
   Google Scholar
• Modrich P. 1982. Studies on sequence recognition by type II restriction and modification enzymes. CRC Crit Rev Biochem 13:287–323.
   PubMed Web of Science ®Google Scholar
• Morgan RD, Bhatia TK, Lovasco L and Davis TB. 2008. MmeI: a minimal Type II restriction-modification system that only modifies one DNA strand for host protection. Nucleic Acids Res 36:6558–6570.
   Google Scholar
• Morgan RD, Dwinell EA, Bhatia TK, Lang EM and Luyten YA. 2009. The MmeI family: type II restriction-modification enzymes that employ single-strand modification for host protection. Nucleic Acids Res 37:5208–5221.
   PubMed Web of Science ®Google Scholar
• Morita R, Ishikawa H, Nakagawa N, Kuramitsu S and Masui R. 2008. Crystal structure of a putative DNA methylase TTHA0409 from Thermus thermophilus HB8. Proteins 73:259–264.
   Google Scholar
• Mruk I, Cichowicz M and Kaczorowski T. 2003. Characterization of the LlaCI methyltransferase from Lactococcus lactis subsp. cremoris W15 provides new insights into the biology of type II restriction-modification systems. Microbiology 149:3331–3341.
   Google Scholar
• Naito T, Kusano K and Kobayashi I. 1995. Selfish behavior of restriction-modification systems. Science 267:897–899.
   PubMed Web of Science ®Google Scholar
• Nakonieczna J, Kaczorowski T, Obarska-Kosinska A and Bujnicki JM. 2009. Functional analysis of MmeI from methanol utilizer Methylophilus methylotrophus, a subtype IIC restriction-modification enzyme related to type I enzymes. Appl Environ Microbiol 75:212–223.
   Google Scholar
• Neely RK, Daujotyte D, Grazulis S, Magennis SW, Dryden DT, Klimasauskas S and Jones AC. 2005. Time-resolved fluorescence of 2-aminopurine as a probe of base flipping in M.HhaI-DNA complexes. Nucleic Acids Res 33:6953–6960.
   Google Scholar
• Obarska A, Blundell A, Feder M, Vejsadova S, Sisakova E, Weiserova M, Bujnicki JM and Firman K. 2006. Structural model for the multisubunit Type IC restriction-modification DNA methyltransferase M.EcoR124I in complex with DNA. Nucleic Acids Res 34:1992–2005.
   Google Scholar
• Osipiuk J, Walsh MA and Joachimiak A. 2003. Crystal structure of MboIIA methyltransferase. Nucleic Acids Res 31:5440–5448.
   Google Scholar
• Patel J, Taylor I, Dutta CF, Kneale G and Firman K. 1992. High-level expression of the cloned genes encoding the subunits of and intact DNA methyltransferase, M.EcoR124. Gene 112:21–27.
   Google Scholar
• Piekarowicz A, Golaszewska M, Sunday AO, Siwinska M and Stein DC. 1999. The HaeIV restriction modification system of Haemophilus aegyptius is encoded by a single polypeptide. J Mol Biol 293:1055–1065.
   PubMed Web of Science ®Google Scholar
• Pingoud A, Fuxreiter M, Pingoud V and Wende W. 2005. Type II restriction endonucleases: structure and mechanism. Cell Mol Life Sci 62:685–707.
   PubMed Web of Science ®Google Scholar
• Posfai J, Bhagwat AS, Posfai G and Roberts RJ. 1989. Predictive motifs derived from cytosine methyltransferases. Nucleic Acids Res 17:2421–2435.
   PubMed Web of Science ®Google Scholar
• Powell LM and Murray NE. 1995. S-adenosyl methionine alters the DNA contacts of the EcoKI methyltransferase. Nucleic Acids Res 23:967–974.
   Google Scholar
• Powell LM, Connolly BA and Dryden DT. 1998. The DNA binding characteristics of the trimeric EcoKI methyltransferase and its partially assembled dimeric form determined by fluorescence polarisation and DNA footprinting. J Mol Biol 283:947–961.
   Google Scholar
• Powell LM, Lejeune E, Hussain FS, Cronshaw AD, Kelly SM, Price NC and Dryden DT. 2003. Assembly of EcoKI DNA methyltransferase requires the C-terminal region of the HsdM modification subunit. Biophys Chem 103:129–137.
   Google Scholar
• Raleigh EA and Brooks JE. 1998. Restriction modification systems: where they are and what they do. p. 78–92. In F. J. De Bruijn, J. R. Lupski, and G. M. Weinstock (ed.), Bacterial genomes. Chapman & Hall, New York, N.Y.
   Google Scholar
• Rao DN, Page MG and Bickle TA. 1989. Cloning, over-expression and the catalytic properties of the EcoP15 modification methylase from Escherichia coli. J Mol Biol 209:599–606.
   Google Scholar
• Rao DN, Saha S and Krishnamurthy V. 2000. ATP-dependent restriction enzymes. Prog Nucleic Acid Res Mol Biol 64:1–63.
   Google Scholar
• Rechkunova NI, Zinoviev VV, Malygin EG, Gorbunov Yu, A, Popov SG, Nesterenko VF, Buryanov Ya I and Bayev AA. 1987. Dimerization of Eco dam methylase induced by the ODN substrate. Biopolymers Cell (Russian) 3:152–154.
   Google Scholar
• Redaschi N and Bickle TA. 1996. Posttranscriptional regulation of EcoP1I and EcoP15I restriction activity. J Mol Biol 257:790–803.
   Google Scholar
• Reddy YV and Rao DN. 1998. Probing the role of cysteine residues in the EcoP15I DNA methyltransferase. J Biol Chem 273:23866–23876.
   Google Scholar
• Reddy YV and Rao DN. 2000. Binding of EcoP15I DNA methyltransferase to DNA reveals a large structural distortion within the recognition sequence. J Mol Biol 298:597–610.
   Google Scholar
• Reich NO and Mashhoon N. 1993. Presteady state kinetics of an S-adenosylmethionine-dependent enzyme. Evidence for a unique binding orientation requirement for EcoRI DNA methyltransferase. J Biol Chem 268:9191–9193.
   Google Scholar
• Roberts RJ and Cheng X. 1998. Base flipping. Annu Rev Biochem 67:181–198.
   PubMed Web of Science ®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. 2003. A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes. Nucleic Acids Res 31:1805–1812.
   PubMed Web of Science ®Google Scholar
• Roberts RJ, Vincze T, Posfai J and Macelis D. 2007. REBASE – enzymes and genes for DNA restriction and modification. Nucleic Acids Res 35:D269–270.
   Google Scholar
• Ryan KA and Lo RY. 1999. Characterization of a CACAG pentanucleotide repeat in Pasteurella haemolytica and its possible role in modulation of a novel type III restriction-modification system. Nucleic Acids Res 27:1505–1511.
   Google Scholar
• Sapranauskas R, Sasnauskas G, Lagunavicius A, Vilkaitis G, Lubys A and Siksnys V. 2000. Novel subtype of type IIs restriction enzymes. BfiI endonuclease exhibits similarities to the EDTA-resistant nuclease Nuc of Salmonella typhimurium. J Biol Chem 275:30878–30885.
   PubMed Web of Science ®Google Scholar
• Saunders NJ, Jeffries AC, Peden JF, Hood DW, Tettelin H, Rappuoli R and Moxon ER. 2000. Repeat-associated phase variable genes in the complete genome sequence of Neisseria meningitidis strain MC58. Mol Microbiol 37:207–215.
   PubMed Web of Science ®Google Scholar
• Seib KL, Peak IR and Jennings MP. 2002. Phase variable restriction-modification systems in Moraxella catarrhalis. FEMS Immunol Med Microbiol 32:159–165.
   PubMed Web of Science ®Google Scholar
• Serva S, Weinhold E, Roberts RJ and Klimasauskas S. 1998. Chemical display of thymine residues flipped out by DNA methyltransferases. Nucleic Acids Res 26:3473–3479.
   PubMedGoogle Scholar
• Shier VK, Hancey CJ and Benkovic SJ. 2001. Identification of the active oligomeric state of an essential adenine DNA methyltransferase from Caulobacter crescentus. J Biol Chem 276:14744–14751.
   Google Scholar
• Sistla S and Rao DN. 2004. S-Adenosyl-L-methionine-dependent restriction enzymes. Crit Rev Biochem Mol Biol 39:1–19.
   Web of Science ®Google Scholar
• Sistla S, Krishnamurthy V, Rao, DN. 2004. Single-stranded DNA binding and methylation by EcoP1I DNA methyltransferase. Biochem Biophys Res Commun 314:159–165.
   Google Scholar
• Smith DR. 1996. Restriction endonuclease digestion of DNA. In: Basic DNA and RNA protocols. A.J. Harwood (ed) p. 11–15. Humana Press, Totowa, NJ.
   Google Scholar
• Srikhanta YN, Maguire TL, Stacey KJ, Grimmond SM and Jennings MP. 2005. The phasevarion: a genetic system controlling coordinated, random switching of expression of multiple genes. Proc Natl Acad Sci USA 102:5547–5551.
   PubMed Web of Science ®Google Scholar
• Srikhanta YN, Dowideit SJ, Edwards JL, Falsetta ML, Wu HJ, Harrison OB, Fox KL, Seib KL, Maguire TL, Wang AH, Maiden MC, Grimmond SM, Apicella MA and Jennings MP. 2009. Phasevarions mediate random switching of gene expression in pathogenic Neisseria. PLoS Pathog 5:1–22.
   Google Scholar
• Su TJ, Connolly BA, Darlington C, Mallin R and Dryden DT. 2004. Unusual 2-aminopurine fluorescence from a complex of DNA and the EcoKI methyltransferase. Nucleic Acids Res 32:2223–2230.
   Google Scholar
• Su TJ, Tock MR, Egelhaaf SU, Poon WC and Dryden DT. 2005. DNA bending by M.EcoKI methyltransferase is coupled to nucleotide flipping. Nucleic Acids Res 33:3235–3244.
   PubMed Web of Science ®Google Scholar
• Sugisaki H, Kita K and Takanami M. 1989. The FokI restriction-modification system. II. Presence of two domains in FokI methylase responsible for modification of different DNA strands. J Biol Chem 264:5757–5761.
   Google Scholar
• Sugisaki H, Yamamoto K and Takanami M. 1991. The HgaI restriction-modification system contains two cytosine methylase genes responsible for modification of different DNA strands. J Biol Chem 266:13952–13957.
   Google Scholar
• Sunita S, Tkaczuk KL, Purta E, Kasprzak JM, Douthwaite S, Bujnicki JM and Sivaraman J. 2008. Crystal structure of the Escherichia coli 23S rRNA:m5C methyltransferase RlmI (YccW) reveals evolutionary links between RNA modification enzymes. J Mol Biol 383:652–666.
   Google Scholar
• Suri B and Bickle TA. 1985. EcoA: the first member of a new family of type I restriction modification systems. Gene organization and enzymatic activities. J Mol Biol 186:77–85.
   PubMed Web of Science ®Google Scholar
• Suri B, Nagaraja V and Bickle TA. 1984. Bacterial DNA modification. Curr Top Microbiol Immunol 108:1–9.
   Google Scholar
• Svadbina IV, Matvienko NN, Zheleznaya LA and Matvienko NI. 2005. Location of the bases modified by M.BcoKIA and M.BcoKIB methylases in the sequence 5-CTCTTC-3/5-GAAGAG-3. Biochemistry (Moscow) 70:1126–1128.
   Google Scholar
• Taylor I, Patel J, Firman K and Kneale G. 1992. Purification and biochemical characterisation of the EcoR124 type I modification methylase. Nucleic Acids Res 20:179–186.
   PubMed Web of Science ®Google Scholar
• Taylor I, Watts D and Kneale G. 1993. Substrate recognition and selectivity in the type IC DNA modification methylase M.EcoR124I. Nucleic Acids Res 21:4929–4935.
   Google Scholar
• Taylor IA, Webb M and Kneale GG. 1996. Surface labelling of the type I methyltransferase M.EcoR124I reveals lysine residues critical for DNA binding. J Mol Biol 258:62–73.
   Google Scholar
• Thielking V, Alves J, Fliess A, Maass G and Pingoud A. 1990. Accuracy of the EcoRI restriction endonuclease: binding and cleavage studies with oligodeoxynucleotide substrates containing degenerate recognition sequences. Biochemistry 29:4682–4691.
   PubMedGoogle Scholar
• Thomas CB and Gumport RI. 2006. Dimerization of the bacterial RsrI N6-adenine DNA methyltransferase. Nucleic Acids Res 34:806–815.
   Google Scholar
• Tomb JF, White O, Kerlavage AR, Clayton RA, Sutton GG, Fleischmann RD, Ketchum KA, Klenk HP, Gill S, Dougherty BA, Nelson K, Quackenbush J, Zhou L, Kirkness EF, Peterson S, Loftus B, Richardson D, Dodson R, Khalak HG, Glodek A, McKenney K, Fitzegerald LM, Lee N, Adams MD, Hickey EK, Berg DE, Gocayne JD, Utterback TR, Peterson JD, Kelley JM, Cotton MD, Weidman JM, Fujii C, Bowman C, Watthey L, Wallin E, Hayes WS, Borodovsky M, Karp PD, Smith HO, Fraser CM, Venter JC. 1997. The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature 388:539–547.
   PubMed Web of Science ®Google Scholar
• Tucholski J, Zmijewski JW and Podhajska AJ. 1998. Two intertwined methylation activities of the MmeI restriction-modification class-IIS system from Methylophilus methylotrophus. Gene 223:293–302.
   Google Scholar
• Tuzikov FV, Zinoviev VV, Jashina LN, Vavilin VI, Gorbunov Yu A, Popov SG, Buryanov Ya I and Bayev AA. 1986. Application of the small-angle X-ray scattering for the investigation of substrate-induced changes of methylase state. Mol Biol (Moscow) 20:1002–1007.
   Google Scholar
• Van Etten JL. 2003. Unusual life style of giant chlorella viruses. Annu Rev Genet 37:153–195.
   PubMed Web of Science ®Google Scholar
• Vilkaitis G, Dong A, Weinhold E, Cheng X and Klimasauskas S. 2000. Functional roles of the conserved threonine 250 in the target recognition domain of HhaI DNA methyltransferase. J Biol Chem 275:38722–38730.
   PubMed Web of Science ®Google Scholar
• Vilkaitis G, Lubys A, Merkiene E, Timinskas A, Janulaitis A and Klimasauskas S. 2002. Circular permutation of DNA cytosine-N4 methyltransferases: in vivo coexistence in the BcnI system and in vitro probing by hybrid formation. Nucleic Acids Res 30:1547–1557.
   Google Scholar
• Vitkute J, Stankevicius K, Tamulaitiene G, Maneliene Z, Timinskas A, Berg DE and Janulaitis A. 2001. Specificities of eleven different DNA methyltransferases of Helicobacter pylori strain 26695. J Bacteriol 183:443–450.
   Google Scholar
• Webb M, Taylor IA, Firman K and Kneale GG. 1995. Probing the domain structure of the type IC DNA methyltransferase M.EcoR124I by limited proteolysis. J Mol Biol 250:181–190.
   Google Scholar
• Willcock DF, Dryden DT and Murray NE. 1994. A mutational analysis of the two motifs common to adenine methyltransferases. EMBO J 13:3902–3908.
   PubMedGoogle Scholar
• Wion D and Casadesus J. 2006. N6-methyl-adenine: an epigenetic signal for DNA–protein interactions. Nat Rev Microbiol 4:183–192.
   PubMed Web of Science ®Google Scholar
• Xu Q, Morgan RD, Roberts RJ and 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.
   Google Scholar
• Yoo HY, Noshari J and Lapeyre JN. 1987. Subunit and functional size of human placental DNA methyltransferase involved in de novo and maintenance methylation. J Biol Chem 262:8066–8070.
   Google Scholar
• Zylicz-Stachula A, Bujnicki JM and Skowron PM. 2009. Cloning and analysis of a bifunctional methyltransferase/restriction endonuclease TspGWI, the prototype of a Thermus sp. enzyme family. BMC Mol Biol 10:52.
   Google Scholar