Comparative analysis of genome-wide protein-DNA interactions across domains of life reveals unique binding patterns for hypersaline archaeal histones

Abstract

DNA-binding proteins with roles in chromatin architecture and transcriptional regulation are present in all three domains of life. Histones package DNA and regulate gene expression in eukaryotes, and find their evolutionary origin in the domain of life Archaea. Previously characterised archaeal histones have a somewhat conserved functional role in nucleosome formation and DNA packaging. However, previous research has indicated that the histone-like proteins of high salt-adapted archaea, or halophiles, appear to function differently. The sole histone protein encoded by the model halophilic species Halobacterium salinarum is non-essential, is involved in direct and indirect transcriptional regulation, and does not appear to package DNA. Here we use protein-DNA binding assays, computational analysis, and quantitative phenotyping to compare DNA binding patterns across halophilic histone proteins, bacterial and archaeal TFs, NAPs, and eukaryotic histones. Like TFs, halophilic histones bind the genome too sparsely to compact the genome. However, unlike TFs, binding occurs in both coding and intergenic regions. Unlike histones, halophilic histone occupancy is not depleted at the start sites of genes, and halophilic genomes lack the dinucleotide periodicity known to facilitate histone binding. We detect unique sequence preferences for histone binding in halophiles. Together these data suggest that the non-essentiality and genome-wide binding features of halophilic histone-like proteins are conserved across halophiles; they bind DNA in ways resembling both TFs and chromatin proteins, but do not appear to play a role in forming chromatin. IMPORTANCEMost cells in eukaryotic species - from yeast to humans- possess histone proteins that pack and unpack DNA in response to environmental cues. These essential proteins regulate the genes necessary for important cellular processes, including development and stress protection. The domain of life Archaea represent the evolutionary progenitors of eukaryotes. The universal conservation of the primary sequences of histone proteins across archaeal lineages suggests that eukaryotic histones originated in the Archaea. However, archaeal histones lack N-terminal tails and, in some species, package DNA in a continuous helix with no linker DNA between nucleosomes. We recently discovered that histones in hypersaline adapted archaeal species do not package DNA, and can act like transcription factors (TFs) to regulate stress response gene expression. Here we compare hypersaline histone function to a variety of DNA binding proteins across the tree of life, revealing a mosaic of functions for hypersaline-adapted histones.