DNA Methylation in Dictyostelium

Methylation of cytosines is a predominant epigenetic regulatory mechanism, i.e. it carries information on top of the primary DNA sequence. DNA Methylation is involved in imprinting mechanisms in mammals, heterochromatin formation and transgene silencing in plants. Posttranscriptional gene silencing (PTGS) mediated by RNAi and transcriptional gene silencing (TGS) by DNA methylation are related in that siRNAs appear to be involved in both at least in some organisms.

In eukaryotes, different methyltransferases have been identified, the Dnmt1 type maintains the methylation pattern while the Dnmt3 type can generate de novo methylation. Dnmt2, is a further evolutionary highly conserved methyltransferase but its biochemical and biological function has for long been elusive.
Dictyostelium discoideum, Entamoeba histolytica, Schizosaccharomyces pombe and Drosophila melanogaster belong to a group of organisms that only have a Dnmt2 type methyltransferase and lack the others. At least for Dictyostelium, Entamoeba, and Drosophila it has been shown that they contain low but significant amounts of methylated cytosine. Disruption of the Dnmt2 (DnmA) gene in the Dictyostelium genome, results in a loss of methylation and a mobilization of the retroelement Skipper [1]. Similar observations have now been made on the Drosophila retroelement invader (G. Reuter group, submitted).

More recently, T. Bestor’s group (Goll et al., 2006) found that mammalian Dnmt2 could efficiently methylate tRNAAsp in various organisms. We have therefore proposed that the enzyme may have an unusual dual activity [2]. We have shown that Dictyostelium tRNA can also be methylated by mammalian Dnmt2 [3] and have seen similar activity with the recombinant Dictyostelium enzyme. By gel shift assays, we observed different but specific affinities of Dnmt2 to different DNA and RNA substrates that we will now correlate with methylation activity in vitro. Collaboration with groups working on Dnmt2 in other organisms will allow comparative analysis of biochemical and biological functions of the enzyme. In a joint effort we will also search for additional target molecules.

This project is carried out in close collaboration with the following groups:
Frank Lyko and Matthias Schaefer, DKFZ Heidelberg
Gunter Reuter, Univ. Halle 
Mark Helm, Univ. Heidelberg
Ann Ehrenhofer-Murray, Univ. Duisburg-Essen
Serge Ankri, Technion, Haifa, Israel
Albert Jeltsch, Jakobs Univ. Bremen

In Kassel, the work is carried out by Vladimir Maximov and Sara Müller.

Publications:

1. Kuhlmann, M., et al., Silencing of retrotransposons in Dictyostelium by DNA methylation and RNAi. Nucleic Acids Res, 2005. 33(19): p. 6405-17.
2. Jeltsch, A., W. Nellen, and F. Lyko, Two substrates are better than one: dual specificities for Dnmt2 methyltransferases. Trends Biochem Sci, 2006. 31(6): p. 306-8.
3. Jurkowski, T.P., et al., Human DNMT2 methylates tRNA(Asp) molecules using a DNA methyltransferase-like catalytic mechanism. Rna, 2008. 14(8): p. 1663-70.