Multiple DNA methyltransferase genes in Arabidopsis thaliana.

Methylation of plant DNA occurs at cytosines in any sequence context, and as the Arabidopsis methyltransferase, METI, preferentially methylates cytosines in CG dinucleotides, it is likely that Arabidopsis has other methyltransferases with different target specificities. We have identified five additional genes encoding putative DNA methyltransferases. Three of these genes are very similar to METI throughout the coding region; these genes probably arose by a series of gene duplication events, the most recent giving rise to METIIa and METIIb. METIIa and b are expressed at low levels in vegetative and floral organs and the level of transcripts is not affected by the introduction of a METI antisense transgene, nor do the METII enzymes substitute for the reduced activity of METI in methylating CG dinucleotides. METIII is not essential as it encodes a truncated protein. Two other genes encode a second class of DNA methyltransferase with the conserved motifs characteristic of cytosine methyltransferases, but with little homology to the METI-like methyltransferases through the remainder of the protein. These two methyltransferases are characterized by the presence of a chromodomain inserted within the methyltransferase domain, suggesting that they may be associated with heterochromatin. Both these genes are transcribed at low levels in vegetative and reproductive tissues.

Molecular evolution of DNA-(cytosine-N4) methyltransferases: evidence for their polyphyletic origin.

DNA N4-cytosine methyltransferases (N4mC MTases) are a family of S-adenosyl-L-methionine (AdoMet)-dependent MTases. Members of this family were previously found to share nine conserved sequence motifs, but the evolutionary basis of these similarities has never been studied in detail. We performed phylogenetic analysis of 37 known and potential new family members from the multiple sequence alignment using distance matrix, parsimony and maximum likelihood approaches to infer the evolutionary relationship among the N4mC MTases and classify them into groups of orthologs. All the treeing algorithms employed as well as results of exhaustive sequence database searching support a scenario, in which the majority of N4mC MTases, except for M. Bal I and M. Bam HI, arose by divergence from a common ancestor. Interestingly, MTases M. Bal I and M. Bam HI apparently originated from N6-adenine MTases and represent the most recent addendum to the N4mC MTase family. In addition to the previously reported nine sequence motifs, two more conserved sequence patches were detected. Phylogenetic analysis also provided the evidence for massive horizontal transfer of MTase genes, presumably with the whole restriction-modification systems, between Bacteria and Archaea.

Chemistry and biology of DNA methyltransferases.

Recognition of a specific DNA sequence by a protein is probably the best example of macromolecular interactions leading to various events. It is a prerequisite to understanding the basis of protein-DNA interactions to obtain a better insight into fundamental processes such as transcription, replication, repair, and recombination. DNA methyltransferases with varying sequence specificities provide an excellent model system for understanding the molecular mechanism of specific DNA recognition. Sequence comparison of cloned genes, along with mutational analyses and recent crystallographic studies, have clearly defined the functions of various conserved motifs. These enzymes access their target base in an elegant manner by flipping it out of the DNA double helix. The drastic protein-induced DNA distortion, first reported for HhaI DNA methyltransferase, appears to be a common mechanism employed by various proteins that need to act on bases. A remarkable feature of the catalytic mechanism of DNA (cytosine-5) methyltransferases is the ability of these enzymes to induce deamination of the target cytosine in the absence of S-adenosyl-L-methionine or its analogs. The enzyme-catalyzed deamination reaction is postulated to be the major cause of mutational hotspots at CpG islands responsible for various human genetic disorders. Methylation of adenine residues in Escherichia coli is known to regulate various processes such as transcription, replication, repair, recombination, transposition, and phage packaging.

[Multiple forms of DNA methylases in hepatic cell nuclei of animals in the normal state and in pathology]. / Mnozhestvennye formy DNK-metilaziz iader pechenizhivotnykh v norme i pri patologii.

Using hydrophobic chromatography multiple nature of DNA-methylating enzymes have been revealed. It was established that the most active enzymatic fraction of rats' liver and that of chicken are completely identical.

Sequence motifs specific for cytosine methyltransferases.

Using a new alignment method, the sequences of 13 m5C methyltransferases (MTases) have been examined. Five extremely well-conserved blocks of sequence have been detected and have been used as fixed points for the alignment of the 13 sequences. Following this initial alignment, five further blocks of similarity have been identified to give a total of ten recognizable blocks of sequence homology that are all arranged in a common order. The structures of these MTases consist of a variable-length N-terminal arm followed by eight well-conserved blocks each separated by small variable-length regions. A large variable-length segment of 90 to 270 amino acids (aa) then follows. After this are two blocks, and a variable-length C-terminal segment completes the sequence. Within the final alignment, 20 aa in the protein sequences, and 86 nucleotides in the nucleotide sequences are invariant. The strongest conservation is found in proximity to a suspected functional site that contains the dipeptide proline-cysteine. Consensus patterns can be defined for the five best conserved blocks and, when used as search motifs, are able to clearly distinguish between the m5C MTases and all other identified proteins in the PIR database. This suggests they may be of use in identifying putative MTases among protein sequences of unknown function.