Epigenetic views of life and evolution: Evidence from genomics, methylomics, and transcriptomics in bacteria
17 October 2017
Ichizo Kobayashi, PhD
Graduate School of Frontier Sciences, University of Tokyo, Japan
Institute of Medical Science, University of Tokyo, Japan
Faculty of Medicine, Kyorin University, Japan
Host: Elsa Anes e Filipa Vale
Faculdade de Farmácia, Universidade de Lisboa
The currently dominating model for adaptive evolution is selection from diverse genome sequences. Rather, diverse epigenomes may be regarded as the units of adaptive evolution. Indeed there are increasing lines of evidence for trans-generation epigenetic inheritance in multicellular eukaryotes. We explore this possibility in unicellular bacteria, in which germ-line cells can be equated with somatic cells, to the first approximation, such as Helicobacter pylori responsible for stomach cancer.
One form of bacterial immunity, restriction-modification (RM) systems, distinguishes between self and non-self, based DNA on epigenetic base methylation. We found RMs’ attack on host bacteria can increase their relative frequency (fitness) and proposed that they are selfish mobile elements just as viruses and transposons. Target sequence recognition domain (TRD) of several types of RMs move within a gene, between genes and beyond taxonomic barriers, changing sequence-specificity in DNA methylation systems.
Many of H. pylori’s RM systems (20-30 per 1.6 Mb genome) frequently change their TRDs and generate millions of diversity in DNA methylome. DNA methylation locally affects gene expression. The ever-changing methylome may change transcriptome and, therefore, adaptive phenotype sets. Our works involving genome decoding, methylome decoding (by single-molecule real-time sequencing in a PacBio machine), transcriptome analysis (RNA-seq) and phenotype analysis support this hypothesis of epigenome-based adaptive evolution. The emerging gene regulation network with many DNA methyltransferases continues changing through changes in their sequence specificity pursuing adaptation — a FIREWORK model for adaptive evolution.
Ichizo Kobayashi Google Scholar Citations