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MBE Advance Access published online on February 2, 2005
Molecular Biology and Evolution, doi:10.1093/molbev/msi098
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Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2005; all rights reserved.
Accepted January 25, 2005

Research Article

Evolutionary Diversification of DNA Methyltransferases in Eukaryotic Genomes

Loïc Ponger * and Wen-Hsiung Li

* To whom correspondence should be addressed.
Loïc Ponger, E-mail: ponger{at}uchicago.edu


  Abstract

In eukaryotes, C5-cytosine methylation is a common mechanism associated with a variety of functions such as gene regulation or control of genomic stability. Different subfamilies of eukaryotic methyltransferases (MTases) have been identified, mainly in metazoa, plants, and fungi. In this paper, we used hidden Markov models to detect MTases in completed or almost completed eukaryotic genomes, including different species of Protozoa. A phylogenetic analysis of MTases enabled us to define 6 subfamilies of MTases, including two new subfamilies. The dnmt1 subfamily that includes all the known MTases with a maintenance activity seems to be absent in the protozoa. The dnmt2 subfamily seems to be the most widespread, being present even in the non-methylated Dictyostelium discoideum. We also found two dnmt2 members in the bacterial genus Geobacter, suggesting that horizontal transfers of MTases occurred in eukaryotes as well as in prokaryotes. Even if the direction of transfer cannot be determined, this relationship might be useful for understanding the function of this enigmatic subfamily of MTase. Globally, our analysis reveals a great diversity of MTases in eukaryotes, suggesting the existence of different methylation systems. Our results also suggest acquisitions and losses of different MTases in every eukaryotic lineage studied and that some eukaryotes appear to be devoid of methylation.

Keywords: DNA methylation; DNA methyltransferases; Eukaryotes; Repeat-Induced Point mutation.
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