Mobility of DNA sequence recognition domains in DNA methyltransferases suggests epigenetics-driven adaptive evolution

Abstract

DNA methylation is one of the best studied epigenetic modifications observed in prokaryotes as well as eukaryotes. It affects nearby gene expression. Most DNA methylation reactions in prokaryotes are catalyzed by a DNA methyltransferase, the modification enzyme of a restriction-modification (RM) system. Its target recognition domain (TRD) recognizes a specific DNA sequence for methylation. In this commentary, we review recent evidence for movement of TRDs between non-orthologous genes and movement within a gene. These movements are likely mediated by DNA recombination machinery, and are expected to alter the methylation status of a genome. Such alterations potentially lead to changes in global gene expression pattern and various phenotypes. The targets of natural selection in adaptive evolution might be these diverse methylomes rather than diverse genome sequences, the target according to the current paradigm in biology. This “epigenetics-driven adaptive evolution” hypothesis can explain several observations in the evolution of prokaryotes and eukaryotes.

Keywords: :

• DNA methylation
• Helicobacter pylori
• domain movement
• epigenetics
• evolution
• genome evolution
• methylome
• protein evolution
• restriction-modification

This article refers to:

Disclosure of Potential Conflicts of Interest

No potential conflicts of interest were disclosed.

Acknowledgments

We are grateful to David Dryden for comments on the manuscript and Jacob Albritton for editing grammar, style and contents. This work was supported by the Grants-in-Aid for Scientific Research from the Japan Society for the Promotion of Science (21370001 to I.K., 24790412 to Y.F.) and from the Ministry of Education, Culture, Sports, Science and Technology (MEXT) (24113506 to I.K., 24119503 to Y.F.); the Global COE Project of Genome Information Big Bang from MEXT to I.K.; Grant in Promotion of Basic Research Activities for Innovative Biosciences from Bio-oriented Technology Research Advance Institution to I.K. and the Takeda Science Foundation to Y.F.