Specificity of DNA binding and methylation by the M.FokI DNA methyltransferase

Friedrich, Tatjana; Fatemi, Mehrnaz; Gowhar, Humaira; Leismann, Oliver; Jeltsch, Albert

doi:10.1016/s0167-4838(00)00065-0

Cited by 17 publications

(10 citation statements)

References 64 publications

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“…Interestingly, the M.FokI enzyme has been well-studied in this regard, since it is composed of two domains that have distinct recognition sequences (GGATG/CATCC). Friedrich et al (47) characterized the star activity (the ability of the enzyme to modify sites that differ from the known target sequence by one base) of the two M.FokI domains independently and found that, while the N-terminal domain (recognizing GGATG) is rather specific, the C-terminal domain will also readily modify sites that differ by one base from its CATCC recognition sequence, with a rate reduction in the methylation reaction of only 1- to 3-fold. We see some indications from the maps we produced that M.FokI may retain less specificity than M.TaqI, for example, in Figure 4B there are several clusters of sites in the experimental map that do not correspond to expected sites for FokI labelling in the reference map.…”

Section: Discussionmentioning

confidence: 99%

Super-resolution optical DNA Mapping via DNA methyltransferase-directed click chemistry

Vranken

Deen

Dirix

et al. 2014

Nucleic Acids Research

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We demonstrate an approach to optical DNA mapping, which enables near single-molecule characterization of whole bacteriophage genomes. Our approach uses a DNA methyltransferase enzyme to target labelling to specific sites and copper-catalysed azide-alkyne cycloaddition to couple a fluorophore to the DNA. We achieve a labelling efficiency of ∼70% with an average labelling density approaching one site every 500 bp. Such labelling density bridges the gap between the output of a typical DNA sequencing experiment and the long-range information derived from traditional optical DNA mapping. We lay the foundations for a wider-scale adoption of DNA mapping by screening 11 methyltransferases for their ability to direct sequence-specific DNA transalkylation; the first step of the DNA labelling process and by optimizing reaction conditions for fluorophore coupling via a click reaction. Three of 11 enzymes transalkylate DNA with the cofactor we tested (a readily prepared s-adenosyl-l-methionine analogue).

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Section: Discussionmentioning

confidence: 99%

Super-resolution optical DNA Mapping via DNA methyltransferase-directed click chemistry

Vranken

Deen

Dirix

et al. 2014

Nucleic Acids Research

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“…However, it was shown that M.AvaIX, which shares high homology with its C-terminal part of the TRD with M.NmeDI, methylates only within the sequence 59-RCCGGY-39 (Matveyev et al, 2001). Although DNA MTases are viewed as highly sequence specific (Dryden, 1999), recent observations suggest that methylation of non-canonical sites may be a common feature of these enzymes (Bandaru et al, 1996;Beck et al, 2001;Cohen et al, 2002;Friedrich et al, 2000). What could be the biological role of the ability to recognize the non-canonical form of the recognition sequence?…”

Section: Discussionmentioning

confidence: 99%

DNA methyltransferases from Neisseria meningitidis and Neisseria gonorrhoeae FA1090 associated with mismatch nicking endonucleases

et al. 2004

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The genes encoding the DNA methyltransferases M.NmeDI and M.NmeAI from Neisseria meningitidis associated with the genes encoding putative Vsr endonucleases were overexpressed in Escherichia coli. The enzymes were purified to apparent homogeneity on Ni-NTA agarose columns, yielding proteins of 49+/-1 kDa and 39.6+/-1 kDa, respectively, under denaturing conditions. M.NmeDI recognizes the degenerate sequence 5'-RCCGGB-3'. It methylates the first 5' cytosine residue on both strands within the core sequence CCGG. The enzyme shows higher affinity with the hemimethylated degenerate sequence than with the unmethylated degenerate sequence. Comparison of the amino acid sequence of the target-recognizing domain of M.NmeDI with the closest neighbours recognizing the sequence 5'-RCCGGY-3' showed the presence of the homologous domain and an additional domain that may be responsible for recognizing the degenerate sequence. M.NmeAI recognizes the sequence 5'-CCGG-3' and methylates the second 5' cytosine residue on both DNA strands. In Neisseria gonorrhoeae strain FA1090 the homologues of these ORFs are truncated due to a variety of mutations.

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“…In contrast, a specific MTase could evolve to possess broad specificity without altering the modification of the cognate recognition site. Indeed, it was observed that many MTase clones exhibit promiscuous activity, viz., M.HaeIII, M.EcoRI, M.EcoRV, and M.FokI (160,(215)(216)(217).…”

Section: Future Perspectivesmentioning

confidence: 99%

Diverse Functions of Restriction-Modification Systems in Addition to Cellular Defense

Vasu

Nagaraja

2013

Microbiol Mol Biol Rev

523

462

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SUMMARY Restriction-modification (R-M) systems are ubiquitous and are often considered primitive immune systems in bacteria. Their diversity and prevalence across the prokaryotic kingdom are an indication of their success as a defense mechanism against invading genomes. However, their cellular defense function does not adequately explain the basis for their immaculate specificity in sequence recognition and nonuniform distribution, ranging from none to too many, in diverse species. The present review deals with new developments which provide insights into the roles of these enzymes in other aspects of cellular function. In this review, emphasis is placed on novel hypotheses and various findings that have not yet been dealt with in a critical review. Emerging studies indicate their role in various cellular processes other than host defense, virulence, and even controlling the rate of evolution of the organism. We also discuss how R-M systems could have successfully evolved and be involved in additional cellular portfolios, thereby increasing the relative fitness of their hosts in the population.

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Specificity of DNA binding and methylation by the M.FokI DNA methyltransferase

Cited by 17 publications

References 64 publications

Super-resolution optical DNA Mapping via DNA methyltransferase-directed click chemistry

Super-resolution optical DNA Mapping via DNA methyltransferase-directed click chemistry

DNA methyltransferases from Neisseria meningitidis and Neisseria gonorrhoeae FA1090 associated with mismatch nicking endonucleases

Diverse Functions of Restriction-Modification Systems in Addition to Cellular Defense

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