CLASSIFICATION OF PROKARYOTIC DNA METHYLTRANSFERASES BY TOPOLOGY AND SEQUENCE SIMILARITY

Abstract

ABSTRACTProkaryotic DNA methyltrasferases (MTases) are obligatory enzymes within restriction-modification (R-M) systems, preventing self DNA cleavage by restriction enzymes. Also MTases regulate gene expression, there are well studied examples of the prokaryotic MTases participation in cell cycle regulation, mismatch repair, phase variation. In the Restriction Enzyme Database (REBASE), which is a fundamental resource about R-M systems, MTases from R-M systems are classified according to the type of R-M system to which they belong, the remaining MTases are considered orphan MTases. Also MTases were classified by the order of conserved motifs, catalytic and SAM-binding, and variable DNA recognition subdomains. It was created basically in two key publications of T.Malone et al (1995) and J. Bujnicki (2002). Over twenty years, the number of available MTase sequences has increased drastically. We propose a new two-step homology classification of prokaryotic MTases. The first level of the classification is based on topologies of catalytic domains and conserved motifs. Second level is based on sequence similarity of MTases based on domain architectures. Such a classification is necessary for constructing an evolutionary model of MTases, it is useful for identifying and correcting errors in MTase annotations and for annotating MTases in recently sequenced genomes and metagenomes.GRAPHICAL ABSTRACT