The amino acid sequence of DNMT2 is very similar to the catalytic domains of bacterial and eukaryotic proteins. However, there is great variability in the region of recognition of the target sequence. While bacterial DNMT2 acts as a DNA methyltransferase, previous studies have indicated low DNA methylation activity in eukaryotic DNMT2, with preference by tRNA methylation. Drosophilids are known as DNMT2-only species and the DNA methylation phenomenon is a not elucidated case yet, as well as the ontogenetic and physiologic importance of DNMT2 for this species group. In addition, more recently study showed that methylation in the genome in Drosophila melanogaster is independent in relation to DNMT2. Despite these findings, Drosophilidae family has more than 4,200 species with great ecological diversity and historical evolution, thus we, therefore, aimed to examine the drosophilids DNMT2 in order to verify its conservation at the physicochemical and structural levels in a functional context. We examined the twenty-six DNMT2 models generated by molecular modelling and five crystallographic structures deposited in the Protein Data Bank (PDB) using different approaches. Our results showed that despite sequence and structural similarity between species close related, we found outstanding differences when they are analyzed in the context of surface distribution of electrostatic properties. The differences found in the electrostatic potentials may be linked with different affinities and processivity of DNMT2 for its different substrates (DNA, RNA or tRNA) and even for interactions with other proteins involved in the epigenetic mechanisms.

The DNA methyltransferase 2 (DNMT2) protein is the most conserved member of the DNA methyltransferase family. Nevertheless, its substrate specificity is still controversial and elusive. The genomic role and determinants of DNA methylation are poorly understood in invertebrates, and several mechanisms and associations are suggested. In Drosophila, the only known DNMT gene is Dnmt2. Here we present our findings from a wide search for Dnmt2 homologs in 68 species of Drosophilidae. We investigated its molecular evolution, and in our phylogenetic analyses the main clades of Drosophilidae species were recovered. We tested whether the Dnmt2 has evolved neutrally or under positive selection along the subgenera Drosophila and Sophophora and investigated positive selection in relation to several physicochemical properties. Despite of a major selective constraint on Dnmt2, we detected six sites under positive selection. Regarding the DNMT2 protein, 12 sites under positive-destabilizing selection were found, which suggests a selection that favors structural and functional shifts in the protein. The search for new potential protein partners with DNMT2 revealed 15 proteins with high evolutionary rate covariation (ERC), indicating a plurality of DNMT2 functions in different pathways. These events might represent signs of molecular adaptation, with molecular peculiarities arising from the diversity of evolutionary histories experienced by drosophilids.

Background: Organisms that have only the DNA methyltransferase 2 (Dnmt2) to mediate the DNA methylation are called "Dnmt2-only" and they have been investigated in recent surveys. Drosophila is one of the “Dnmt2-only” organisms and is also an ideal model for Dnmt2 research. However, the biological function of the Dnmt2 protein is still uncertain. Some studies have pointed to a putative role during the early stages of invertebrate development. In this work, we present our findings on the Dnmt2 expression in D. willistoni, a neotropical species of large ecological versatility and peculiar molecular features. Results: By RT-PCR and in situ hybridization we demonstrate here the presence of transcripts not only in the early stages of development, but also during the oogenesis. Using qPCR analysis, we verify that Dnmt2 transcription level is higher during early stages of development, though transcription levels are subtly higher in D. willistoni adults than in D. melanogaster levels found in previous studies. We also mapped the Dnmt2 on the IIL chromosome arm (Muller’s B element) of D. willistoni, near at the end of the singular telomeric region. Conclusions: Our findings give insights on the possible biological function of Dnmt2-related processes associated with the development and differentiation of oocytes since germinative tissue formation seems to require a higher expression of Dnmt2. The Dnmt2 localization in the subtelomeric region brings up a series of issues that involve the peculiar characteristics of D. willistoni Dnmt2 enzyme, like evolutionary patterns and the epigenetic phenomena of sex-specific methylation.