CpG underrepresentation and the bacterial CpG-specific DNA methyltransferase M.MpeI

Abstract

Cytosine methylation promotes deamination. In eukaryotes, CpG methylation is thought to account for CpG underrepresentation. Whether scarcity of CpGs in prokaryotic genomes is diagnostic for methylation is not clear. Here, we report that Mycoplasms tend to be CpG depleted and to harbor a family of constitutively expressed or phase variable CpG-specific DNA methyltransferases. The very CpG poor Mycoplasma penetrans and its constitutively active CpGspecific methyltransferase M.MpeI were chosen for further characterization. Genome-wide sequencing of bisulfite-converted DNA indicated that M.MpeI methylated CpG target sites both in vivo and in vitro in a locus-nonselective manner. A crystal structure of M.MpeI with DNA at 2.15-Å resolution showed that the substrate base was flipped and that its place in the DNA stack was taken by a glutamine residue. A phenylalanine residue was intercalated into the "weak" CpG step of the nonsubstrate strand, indicating mechanistic similarities in the recognition of the short CpG target sequence by prokaryotic and eukaryotic DNA methyltransferases.bisulfite sequencing | cytosine deamination | genome evolution | microbiology | structural biology

Targeted DNA methylation in vivo using an engineered dCas9-MQ1 fusion protein

“…The best model structure was built using the template of Mycoplasma penetrans CpG-specific methyltransferase M. Mpel (Protein Data Bank entry: 4DKJ40) that shares over 90% sequence homology. The structure was visualized by using the programme PyMol (http://sourceforge.net/projects/pymol/).…”

Understanding the structural and dynamic consequences of DNA epigenetic modifications: Computational insights into cytosine methylation and hydroxymethylation

“…Direct comparison of these sequences with protein DNA complexes is not possible, since in all the crystals of protein-methylated DNA complexes the methylated nucleotide is flipped. [37][38][39] However, indirect readout or shape (topography) recognition is a well-known mechanism for DNA recognition. 40 This was further corroborated by Hansen et al, who showed that DNA shape is under evolutionary selection pressure.…”

Hypervirulent Clostridium difficile ribotypes are CpG depleted

“…codon usage bias); nonetheless we cannot rule out a role for mutational pressure. A recent report has documented CpG depletion in bacterial genomes [17]; this report also suggests a potential link between CpG-specific DNA methyltransferases encoded by bacteria and the loss of CpG dinucleotides. In addition, cytosine methylation in bacterial genomes has been associated with modulation of gene expression, motility, adhesion and virulence [18].…”

“…As with eukaryotic genomes, methylation of CpGs in bacterial genomes has been linked to the depletion of CpGs [17]. If the depletion of CpG dinucleotides from the hypervirulent ribotypes of C.difficile is due to mutational pressure, we would expect that the loss of CpGs from the whole genome is more pronounced than that from the coding.…”