Chromatin as anti-restriction adaptation:

a hypothesis based on restriction enzymes of a novel structure

Abstract

Why and how the eukaryotic chromatin structure has evolved remains one of the intriguing questions in understanding life. It is absent from the eubacteria but is present in archaea in a variety of forms. A restriction enzyme (PabI) from archaeon Pyrococcus turned out to have a novel three-dimensional structure. Its homologue is found in eubacterium Helicobacter genomes, which carry extremely few PabI sites, likely through selection through past attacks by the PabI homologue. We hypothesize that Pyrococcus genomes are more resistant to this restriction enzyme family than Helicobacter. From this and several other lines of evidence, we further hypothesize that the chromatin structure may have evolved in the archaea to defend genome against attack by restriction enzymes. This hypothesis can explain the absence of restriction enzymes from the eukaryotes and is in harmony with the roles of DNA double-strand breakage in their programmed cell death and meiotic recombination.