A directed evolution design of a GCG-specific DNA hemimethylase

Nucleic Acids Research

Volumn 37, Issue 21, 2009, Pages 7332-7341

  Gerasimaite, Ruta ^a   Vilkaitis, Giedrius ^a   Klimašauskas, Saulius ^a  

^a VILNIUS UNIVERSITY   (Lithuania)

Author keywords

[No Author keywords available]

Indexed keywords

ARGININE; CYTOSINE; DNA (CYTOSINE 5) METHYLTRANSFERASE; GUANINE; METHYL CPG BINDING PROTEIN; S ADENOSYLMETHIONINE; BACTERIAL PROTEIN; BSP6I METHYLTRANSFERASE, BACILLUS SP.; DNA; DNA MODIFICATION METHYLASE HHAI; DRUG DERIVATIVE;

ARTICLE; CATALYSIS; CONTROLLED STUDY; DIRECTED MOLECULAR EVOLUTION; DNA ISOLATION; DNA METHYLATION; DNA MODIFICATION; ENZYME KINETICS; ENZYME SPECIFICITY; GENE DELETION; GENE EXPRESSION REGULATION; MUTAGENESIS; NONHUMAN; NUCLEASE PROTECTION ASSAY; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SEQUENCE ANALYSIS; WILD TYPE; ALKYLATION; CHEMICAL STRUCTURE; CHEMISTRY; GENETICS; KINETICS; METABOLISM;

MAMMALIA;

ALKYLATION; BACTERIAL PROTEINS; BASE SEQUENCE; CATALYSIS; DIRECTED MOLECULAR EVOLUTION; DNA; DNA-CYTOSINE METHYLASES; KINETICS; MODELS, MOLECULAR; MUTAGENESIS; S-ADENOSYLMETHIONINE; SUBSTRATE SPECIFICITY;

EID: 75349101243     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp772     Document Type: Article

References (34)

1. Grosjean, H. (2009) DNA and RNA Modification Enzymes: Structure, Mechanism, Function and Evolution. Landes Bioscience, Austin.
2. Kilgore, J.A., Hoose, S.A., Gustafson, T.L., Porter, W. and Kladde, M.P. (2007) Single-molecule and population probing of chromatin structure using DNA methyltransferases. Methods, 41, 320-332.
3. Carvin, C.D., Parr, R.D. and Kladde, M.P. (2003) Site-selective in vivo targeting of cytosine-5 DNA methylation by zinc-finger proteins. Nucleic Acids Res, 31, 6493-6501.
4. Smith, A.E. and Ford, K.G. (2007) Specific targeting of cytosine methylation to DNA sequences in vivo. Nucleic Acids Res., 35, 740-754.
5. Singer, E.M. and Smith, S.S. (2006) Nucleoprotein assemblies for cellular biomarker detection. Nano Lett., 6, 1184-1189.
6. Klimasauskas, S. and Weinhold, E. (2007) A new tool for biotechnology: AdoMet-dependent methyltransferases. Trends Biotechnol., 25, 99-104.
7. Roberts, R.J., Vincze, T., Posfai, J. and Macelis, D. (2007) REBASE-enzymes and genes for DNA restriction and modification. Nucleic Acids Res., 35, D269-D270.
8. Lauster, R., Trautner, T.A. and Noyer-Weidner, M. (1989) Cytosinespecific type II DNA methyltransferases. A conserved enzyme core with variable target-recognizing domains. J. Mol. Biol., 206, 305-312.
9. Posfai, J., Bhagwat, A.S., Posfai, G. and Roberts, R.J. (1989) Predictive motifs derived from cytosine methyltransferases. Nucleic Acids Res., 17, 2421-2435.
10. Trautner, T.A., Balganesh, T.S. and Pawlek, B. (1988) Chimeric multispecific DNA methyltransferases with novel combinations of target recognition. Nucleic Acids Res., 16, 6649-6658.
11. Klimasauskas, S., Nelson, J.L. and Roberts, R.J. (1991) The sequence specificity domain of cytosine-C5 methylases. Nucleic Acids Res., 19, 6183-6190.
12. Klimasauskas, S., Kumar, S., Roberts, R.J. and Cheng, X. (1994) HhaI methyltransferase flips its target base out of the DNA helix. Cell, 76, 357-369.
13. Reinisch, K.M., Chen, L., Verdine, G.L. and Lipscomb, W.N. (1995) The crystal structure of HaeIII methyltransferase covalently complexed to DNA: an extrahelical cytosine and rearranged base pairing. Cell, 82, 143-153.
14. Lange, C., Wild, C. and Trautner, T.A. (1996) Identification of a subdomain within DNA-(cytosine-C5)-methyltransferases responsible for the recognition of the 5' part of their DNA target. EMBO J., 15, 1443-1450.
15. Vilkaitis, G. and Klimasauskas, S. (1998) Construction and analysis of monospecific DNA cytosine-C5 methyltransferases with chimeric target recognition domains. Biologija, 51-54.
16. Vilkaitis, G., Suetake, I., Klimasauskas, S. and Tajima, S. (2005) Processive methylation of hemimethylated CpG sites by mouse Dnmt1 DNA methyltransferase. J. Biol. Chem., 280, 64-72.
17. Dalhoff, C., Lukinavicius, G., Klimasauskas, S. and Weinhold, E. (2006) Direct transfer of extended groups from synthetic cofactors by DNA methyltransferases. Nat. Chem. Biol., 2, 31-32.
18. Lukinavicius, G., Lapiene, V., Stasevskij, Z., Dalhoff, C., Weinhold, E. and Klimasauskas, S. (2007) Targeted labeling of DNA by methyltransferase-directed transfer of activated groups (mTAG). J. Am. Chem. Soc., 129, 2758-2759.
19. Dalhoff, C., Lukinavicius, G., Klimasauskas, S. and Weinhold, E. (2006) Synthesis of S-adenosyl-L-methionine analogs and their use for sequence-specific transalkylation of DNA by methyltransferases. Nat. Protocols, 1, 1879-1886.
20. Dila, D., Sutherland, E., Moran, L., Slatko, B. and Raleigh, E.A. (1990) Genetic and sequence organization of the mcrBC locus of Escherichia coli K-12. J. Bacteriol., 172, 4888-4900.
21. Daujotyte, D., Vilkaitis, G., Manelyte, L., Skalicky, J., Szyperski, T. and Klimasauskas, S. (2003) Solubility engineering of the HhaI methyltransferase. Protein Eng., 16, 295-301.
22. Vilkaitis, G. and Klimasauskas, S. (1999) Bisulfite sequencing protocol displays both 5-methylcytosine and N4-methylcytosine. Anal. Biochem., 271, 116-119.
23. Bock, C., Reither, S., Mikeska, T., Paulsen, M., Walter, J. and Lengauer, T. (2005) BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing. Bioinformatics, 21, 4067-4068.
24. Vilkaitis, G., Merkiene, E., Serva, S., Weinhold, E. and Klimasauskas, S. (2001) The mechanism of DNA cytosine-5 methylation. Kinetic and mutational dissection of HhaI methyltransferase. J. Biol. Chem., 276, 20924-20934.
25. Merkiene, E. and Klimasauskas, S. (2005) Probing a rate-limiting step by mutational perturbation of AdoMet binding in the HhaI methyltransferase. Nucleic Acids Res., 33, 307-315.
26. Kuzmic, P. (1996) Program DYNAFIT for the analysis of enzyme kinetic data: application to HIV proteinase. Anal. Biochem., 237, 260-273.
27. Wu, J.C. and Santi, D.V. (1987) Kinetic and catalytic mechanism of HhaI methyltransferase. J. Biol. Chem., 262, 4778-4786.
28. 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.
29. Lee, Y.F., Tawfik, D.S. and Griffiths, A.D. (2002) Investigating the target recognition of DNA cytosine-5 methyltransferase HhaI by library selection using in vitro compartmentalisation. Nucleic Acids Res., 30, 4937-4944.
30. Timar, E., Groma, G., Kiss, A. and Venetianer, P. (2004) Changing the recognition specificity of a DNA-methyltransferase by in vitro evolution. Nucleic Acids Res., 32, 3898-3903.
31. Cohen, H.M., Tawfik, D.S. and Griffiths, A.D. (2004) Altering the sequence specificity of HaeIII methyltransferase by directed evolution using in vitro compartmentalization. Protein Eng. Des. Sel., 17, 3-11.
32. Youngblood, B., Buller, F. and Reich, N.O. (2006) Determinants of sequence-specific DNA methylation: target recognition and catalysis are coupled in M.HhaI. Biochemistry, 45, 15563-15572.
33. Subach, O.M., Maltseva, D.V., Shastry, A., Kolbanovskiy, A., Klimasauskas, S., Geacintov, N.E. and Gromova, E.S. (2007) The stereochemistry of benzo[a]pyrene-20-deoxyguanosine adducts affects DNA methylation by SssI and HhaI DNA methyltransferases. FEBS J., 274, 2121-2134.
34. Rathert, P., Raskó, T., Roth, M., Slaska-Kiss, K., Pingoud, A., Kiss, A. and Jeltsch, A. (2007) Reversible inactivation of the CG specific SssI DNA (cytosine-C5)-methyltransferase with a photocleavable protecting group. ChemBioChem, 8, 202-207.