Histone variants in archaea and the evolution of combinatorial chromatin complexity

Abstract

Nucleosomes in eukaryotes act as platforms for the dynamic integration of epigenetic information. Post-translational modifications are reversibly added or removed and core histones exchanged for paralogous variants, in concert with changing demands on transcription and genome accessibility. Histones are also common in archaea. Their role in genome regulation, however, and the capacity of individual paralogs to assemble into histone-DNA complexes with distinct properties remain poorly understood. Here, we combine structural modelling with phylogenetic analysis to shed light on archaeal histone paralogs, their evolutionary history and capacity to generate complex combinatorial chromatin states through hetero-oligomeric assembly. Focusing on the human commensal Methanosphaera stadtmanae as a model archaeal system, we show that the heteromeric complexes that can be assembled from its seven histone paralogs vary substantially in DNA binding affinity and tetramer stability, occupying a large but densely populated chromatin state space. Using molecular dynamics simulations, we go on to identify unique paralogs in M. stadtmanae and Methanobrevibacter smithii that are characterized by unstable dimer:dimer interfaces. We propose that these paralogs act as capstones that prevent stable tetramer formation and extension into longer oligomers characteristic of model archaeal histones. Importantly, we provide evidence from phylogeny and genome architecture that these capstones, as well as other paralogs in the Methanobacteriales, have been maintained for hundreds of millions of years following ancient duplication events. Taken together, our findings indicate that at least some archaeal histone paralogs have evolved to play distinct and conserved functional roles, reminiscent of eukaryotic histone variants. We conclude that combinatorially complex histone-based chromatin is not restricted to eukaryotes and likely predates their emergence.

Slaying the last unicorn: discovery of histones in the microalga Nanochlorum eucaryotum

“…To place candidate histone hits in phylogenetic context, we added putative N. eucaryotum (SAG 55.87) histones to a large prior alignment of eukaryotic and archaeal histones [ 22 ] and subsequently built a phylogenetic tree (see Methods) from N. eucaryotum (SAG 55.87) candidate histones and the histones of C. variabilis NC64 , for which a high-quality genome assembly is available. We find candidate N. eucaryotum (SAG 55.87) histones that have high similarity to and cluster with C. variabilis H2A, H2B, H3 and H4 ( figure 1 ; electronic supplementary material, figure S1).…”

Archaeal chromatin ‘slinkies’ are inherently dynamic complexes with deflected DNA wrapping pathways

“…While in vivo studies have identified disparate roles of variant histones in archaea (27), very little is known about the structural modifications that they invoke. In a recent study by Stevens et al (28), molecular dynamics trajectories showed that substituting major type histones in Methanosphaera stadtmanae with a "capstone" paralog, a histone variant with sequence modifications at the four-helix bundle, disrupts the tetramer interface and separates histone dimers on a continuous DNA fragment, thereby limiting archaeasome size. In the context of the capstone model, our EM-derived structures suggest that destabilizing the fourhelix bundle interface may yield a subtle increase in DNA accessibility through increased exposure of the major groove, and without the need to fully displace the archaeasome subunit.…”

Slaying the last unicorn - discovery of histones in the microalgaNanochlorum eucaryotum

“…To place candidate hits in phylogenetic context, we added putative N. eucaryotum (SAG 55.87) histones to a large prior alignment of eukaryotic and archaeal histones (Stevens et al 2020) and subsequently built a phylogenetic tree (see Methods) from N. eucaryotum (SAG 55.87) candidate histones and the histones of C. variabilis NC64, for which a high quality genome assembly is available. We find candidate N. eucaryotum (SAG 55.87) histones that have high similarity to and cluster with C. variabilis H2A, H2B, H3, and H4 ( Figure 1).…”

“…The remaining set of candidate histone-fold proteins were added to a pre-existing alignment of eukaryotic and archaeal histone-fold proteins (Stevens et al 2020) using Mafft v7.310 (add -reorder) along with annotated histones from C. variabilis NC64A obtained from Uniprot. A sub-alignment of candidate N. eucaryotum (SAG 55.87) and C. variabilis NC64A histones was extracted and used to build a maximum likelihood phylogenetic tree using .…”

“…Histones from C. variabilis and histone candidates from Nanochlorum eucaryotum (SAG 55.87) associate with each of the eukaryotic clusters, suggesting that orthologs for all four core histones are present in these species. The alignment underlying this analysis is provided in Stevens et al (2020). (B) Maximum likelihood phylogenetic tree of C. variabilis and Nanochlorum eucaryotum (SAG 55.87) histones.…”