The long term goal of this project is to understand how m5-cytosine methylases (m5C-methylases) achieve their exquisite specificity in recognizing DNA sequences. To achieve this goal we are studying a set of enzymes that are related both structurally and functionally. Comparison of the sequences of a large number of methylases that form 5methylcytosine in DNA shows there is a great,deal of similarity. We propose to study three of these m5C-methylases in great detail These are the MspI methylase (forms meCCGG), the HpaII methylase (forms CmeCGG) and the HhaI methylase (forms GmeCGC). We have prepared an overexpressing clone of the MspI methylase and have purified this methylase to homogeneity. We are now attempting the crystallization of this protein either alone, complexed with DNA or complexed with known inhibitors of the enzyme such as S-adenosylhomocysteine or sinefungin. These structural studies will be complemented by biochemical and genetic approaches. We have also completed the sequence of the HpaII methylase gene and find that it shows striking similarities both to the Mspl methylase gene and the HhaI methylase gene. A key goal for the immediate future is to define in detail the DNA recognition domains for at least one of these methylase genes. This will be accomplished through a series of domain swap experiments between pairs of methylases. These domain swaps will involve both exact exchanges at selected sites, using a PCR-based strategy, as well as more random exchanges followed by genetic screening to detect recombinant methylases. We will also try to swap in other DNA-recognizing domains, such as homeo-box domains, so as to change methylase specificity. Truncated versions of the methylases will be prepared and tested to see if functional domains can be isolated that are able to bind DNA. We will use genetic techniques to analyse these methylases and their hybrids and derivatives, and will search for specific mutants that would extend the usefulness of the methylases for genome tagging and mapping studies.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM046127-02
Application #
3305549
Study Section
Biochemistry Study Section (BIO)
Project Start
1991-04-01
Project End
1995-03-31
Budget Start
1992-04-01
Budget End
1993-03-31
Support Year
2
Fiscal Year
1992
Total Cost
Indirect Cost
Name
Cold Spring Harbor Laboratory
Department
Type
DUNS #
065968786
City
Cold Spring Harbor
State
NY
Country
United States
Zip Code
11724
Dong, Aiping; Zhou, Lan; Zhang, Xing et al. (2004) Structure of the Q237W mutant of HhaI DNA methyltransferase: an insight into protein-protein interactions. Biol Chem 385:373-9
Pradhan, Sriharsa; Kim, Gun-Do (2002) The retinoblastoma gene product interacts with maintenance human DNA (cytosine-5) methyltransferase and modulates its activity. EMBO J 21:779-88
Bacolla, A; Pradhan, S; Larson, J E et al. (2001) Recombinant human DNA (cytosine-5) methyltransferase. III. Allosteric control, reaction order, and influence of plasmid topology and triplet repeat length on methylation of the fragile X CGG.CCG sequence. J Biol Chem 276:18605-13
Cheng, X; Roberts, R J (2001) AdoMet-dependent methylation, DNA methyltransferases and base flipping. Nucleic Acids Res 29:3784-95
Margot, J B; Aguirre-Arteta, A M; Di Giacco, B V et al. (2000) Structure and function of the mouse DNA methyltransferase gene: Dnmt1 shows a tripartite structure. J Mol Biol 297:293-300
Pradhan, S; Roberts, R J (2000) Hybrid mouse-prokaryotic DNA (cytosine-5) methyltransferases retain the specificity of the parental C-terminal domain. EMBO J 19:2103-14
Bacolla, A; Pradhan, S; Roberts, R J et al. (1999) Recombinant human DNA (cytosine-5) methyltransferase. II. Steady-state kinetics reveal allosteric activation by methylated dna. J Biol Chem 274:33011-9
O'Gara, M; Zhang, X; Roberts, R J et al. (1999) Structure of a binary complex of HhaI methyltransferase with S-adenosyl-L-methionine formed in the presence of a short non-specific DNA oligonucleotide. J Mol Biol 287:201-9
Pradhan, S; Bacolla, A; Wells, R D et al. (1999) Recombinant human DNA (cytosine-5) methyltransferase. I. Expression, purification, and comparison of de novo and maintenance methylation. J Biol Chem 274:33002-10
Roberts, R J; Cheng, X (1998) Base flipping. Annu Rev Biochem 67:181-98

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