Figure 1.
Multiple sequence alignment of the conserved amino acid sequence motifs from representative sequences of prokaryotic and eukaryotic DNA- and RNA-(cytosine-C5)-methyltransferases.
The motif numbers are indicated on top of the sequence alignment. Note that the CFT motif is present only in Dnmt2.
Figure 2.
Consensus phylogenetic tree of the eukaryotic DNA-(cytosine C5)-MTases and Dnmt2 proteins constructed from 100 generated bootstrap trees.
The bootstrap values of the branch points are indicated. Branch points with less than 30% incidence among the generated trees were collapsed representing that the phylogeny at this point cannot be reliably inferred.
Figure 3.
Consensus phylogenetic tree of prokaryotic and eukaryotic DNA-(cytosine C5)-MTases and Dnmt2 proteins constructed from 100 generated bootstrap trees.
The bootstrap values of the branch points are indicated. Branch points with less than 30% incidence among the generated trees were collapsed representing that the phylogeny at this point cannot be reliably inferred.
Figure 4.
Compilation of different topologies 100 alternative the phylogenetic trees of prokaryotic and eukaryotic DNA-(cytosine C5)-MTases and Dnmt2 proteins generated during the bootstrapping analysis of the tree shown in Fig. 3.
Figure 5.
3D clustering of methyltransferase sequences based on pairwise BLAST similarity scores prepared using CLANS [26].
A) Clustering of 2935 sequences of prokaryotic and eukaryotic DNA-(cytosine C5)-MTases and Dnmt2 proteins. B) Clustering of the sequences of prokaryotic and eukaryotic DNA-(cytosine C5)-MTases and Dnmt2 proteins including sequences of RNA-(cytosine C5)-MTases.
Figure 6.
Distribution of the methyltransferases in different eukaryotic species.
The tree was prepared using NCBI taxonomy and Interactive Tree Of Life. Dnmts were categorized into the Dnmt1 (1, colored red), Dnmt3 (3, colored blue), Chromomethylase (C, colored orange) and Dim2 families (D, colored green). The Dnmt1 enzymes were subdivided into animal, plant and fungi subgroups, Dnmt3 enzymes into the canonical Dnmt3 enzymes and the plant DRM enzymes. Lineages that underwent loss of Dnmt2 are indicated by green crosses. Dnmt1 orthologues are found in all the branches of eukaryotes. Chromomethylases are related to Dnmt1 enzyme appearing in the plant lineage only (indicated by the orange arrow). Dnmt3 enzymes apparently have been lost in the fungal lineage (indicated by a blue cross).
Figure 7.
Consensus model of the phylogeny of DNA methyltransferases and Dnmt2 indicating that Dnmt1 and Dnmt2/3 enzymes have an independent origin in the prokaryotic DNA methyltransferases.