Histone diversity in the archaeal domain of life

Abstract

Abstract Two-thirds of all archaea encode histones, proteins that are ubiquitously used to structure chromatin in eukaryotes. Archaeal histone sequences are less conserved than their eukaryotic counterparts, and insight into how they structure DNA is limited to a few species that fail to represent the archaeal domain. Here, we use bioinformatics, structure prediction, and molecular dynamics simulations to survey the diversity of histone-like sequences in archaeal genomes and to understand how they might interact with DNA. We identify five distinct types of histones that combine in seven strategies, involving either single histones, multiple histones of the same type, or combinations of types in each genome. Some strategies correlate with environmental pressures and some are phylogenetically restricted. Despite highly divergent sequences, structure predictions and simulations suggest similar histone-DNA binding modes for most strategies. Our work provides a guide to surverying diverse strategies for histone-based DNA organization in archaea.