Comparative phylogenetic and biochemical

Abstract

DNA methylation is one of the major epigenetic marks essential for gene regulation in many eukaryotes. Arabidopsis DEMETER (DME) and its homologs play important roles in active DNA demethylation by directly removing 5-methylcytosine from DNA. DME family genes are exclusively found in the plant lineage but their counterparts have not been reported in animals. Therefore, it is of great interest not only to infer the origin and the function of an ancestral form of DME but also to understand how it has been changed during plant evolution. I performed comparative phylogenetic analysis on 135 DME homologs identified from 42 different species including green algae, mosses and seed plants. Three domains essential for catalytic function are highly conserved among distantly related nonvascular and vascular plants, but algal homologs display limited similarity. Biochemical analysis using recombinant proteins demonstrates that DME homologs derived from mosses have canonical DNA demethylase activity but algal DME lacks such a function. These findings suggest that the DNA demethylase function is essential even in lower plant species but algal DME may have distinct functions. This study provides evolutionary insight into the establishment of DNA demethylation system and its biological significance unique to the plant lineage.