Conserved eukaryotic histone-fold residues substituted into an archaeal histone increase DNA affinity but reduce complex flexibility

Histone variants in archaea and the evolution of combinatorial chromatin complexity

Nucleosomes in eukaryotes act as platforms for the dynamic integration of epigenetic information. Posttranslational 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 modeling with phylogenetic analysis to shed light on archaeal histone paralogs, their evolutionary history, and capacity to generate 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. Using molecular dynamics simulations, we go on to identify unique paralogs in M. stadtmanae and Methanobrevibacter smithii that are characterized by unstable interfaces between dimers. 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.

Old cogs, new tricks: the evolution of gene expression in a chromatin context

Sophisticated gene-regulatory mechanisms probably evolved in prokaryotes billions of years before the emergence of modern eukaryotes, which inherited the same basic enzymatic machineries. However, the epigenomic landscapes of eukaryotes are dominated by nucleosomes, which have acquired roles in genome packaging, mitotic condensation and silencing parasitic genomic elements. Although the molecular mechanisms by which nucleosomes are displaced and modified have been described, just how transcription factors, histone variants and modifications and chromatin regulators act on nucleosomes to regulate transcription is the subject of considerable ongoing study. We explore the extent to which these transcriptional regulatory components function in the context of the evolutionarily ancient role of chromatin as a barrier to processes acting on DNA and how chromatin proteins have diversified to carry out evolutionarily recent functions that accompanied the emergence of differentiation and development in multicellular eukaryotes.

Structure and function of archaeal histones

The genomes of all organisms throughout the tree of life are compacted and organized in chromatin by association of chromatin proteins. Eukaryotic genomes encode histones, which are assembled on the genome into octamers, yielding nucleosomes. Post-translational modifications of the histones, which occur mostly on their N-terminal tails, define the functional state of chromatin. Like eukaryotes, most archaeal genomes encode histones, which are believed to be involved in the compaction and organization of their genomes. Instead of discrete multimers, in vivo data suggest assembly of “nucleosomes” of variable size, consisting of multiples of dimers, which are able to induce repression of transcription. Based on these data and a model derived from X-ray crystallography, it was recently proposed that archaeal histones assemble on DNA into “endless” hypernucleosomes. In this review, we discuss the amino acid determinants of hypernucleosome formation and highlight differences with the canonical eukaryotic octamer. We identify archaeal histones differing from the consensus, which are expected to be unable to assemble into hypernucleosomes. Finally, we identify atypical archaeal histones with short N- or C-terminal extensions and C-terminal tails similar to the tails of eukaryotic histones, which are subject to post-translational modification. Based on the expected characteristics of these archaeal histones, we discuss possibilities of involvement of histones in archaeal transcription regulation.

Both Archaea and eukaryotes express histones, but whereas the tertiary structure of histones is conserved, the quaternary structure of histone–DNA complexes is very different. In a recent study, the crystal structure of the archaeal hypernucleosome was revealed to be an “endless” core of interacting histones that wraps the DNA around it in a left-handed manner. The ability to form a hypernucleosome is likely determined by dimer–dimer interactions as well as stacking interactions between individual layers of the hypernucleosome. We analyzed a wide variety of archaeal histones and found that most but not all histones possess residues able to facilitate hypernucleosome formation. Among these are histones with truncated termini or extended histone tails. Based on our analysis, we propose several possibilities of archaeal histone involvement in transcription regulation.

Structure of histone-based chromatin in Archaea

Small basic proteins present in most Archaea share a common ancestor with the eukaryotic core histones. We report the crystal structure of an archaeal histone-DNA complex. DNA wraps around an extended polymer, formed by archaeal histone homodimers, in a quasi-continuous superhelix with the same geometry as DNA in the eukaryotic nucleosome. Substitutions of a conserved glycine at the interface of adjacent protein layers destabilize archaeal chromatin, reduce growth rate, and impair transcription regulation, confirming the biological importance of the polymeric structure. Our data establish that the histone-based mechanism of DNA compaction predates the nucleosome, illuminating the origin of the nucleosome.

A mutational mimic analysis of histone H3 post-translational modifications: specific sites influence the conformational state of H3/H4, causing either positive or negative supercoiling of DNA

Histone H3 has specific sites of post-translational modifications that serve as epigenetic signals to cellular machinery to direct various processes. Mutational mimics of these modifications (glutamine for acetylation, methionine and leucine for methylation, and glutamic acid for phosphorylation) were constructed at the relevant sites of the major histone variant, H3.2, and their effects on the conformational equilibrium of the H3/H4 tetramer at physiological ionic strength were determined when bound to or free of DNA. The deposition vehicle used for this analysis was NAP1, nucleosome assembly protein 1. Acetylation mimics in the N-terminus preferentially stabilized the left-handed conformer (DNA negatively supercoiled), and mutations within the globular region preferred the right-handed conformer (DNA positively supercoiled). The methylation mimics in the N-terminus tended to maintain characteristics similar to those of wild-type H3/H4; i.e., the conformational equilibrium maintains similar levels of both left- and right-handed conformers. Phosphorylation mimics facilitated a mixed effect, i.e., when at serines, the left-handed conformer, and at threonines, a mixture of both conformers. When double mutations were present, the conformational equilibrium was shifted dramatically, either leftward or rightward depending on the specific sites. In contrast, these mutations tended not to affect the direction and extent of supercoiling for variants H3.1 and H3.3. Variant H3.3 promoted only the left-handed conformer, and H3.1 tended to maintain both conformers. Additional experiments indicate the importance of a propagation mechanism for ensuring the formation of a particular superhelical state over an extended region of the DNA. The potential relevance of these results to the maintenance of epigenetic information on a gene is discussed.

Archaeal histones and the origin of the histone fold

Histone sequences have been identified in many archaeal genomes and in environmental samples, and they constitute a family of proteins that are structural homologs of the eukaryotic core histones. Most archaeal histones conform to the single histone-fold structural models that have been described, but a few histone variants exhibit short insertions, additional domains or fusions. Interpretation of these structural variations offers clues to the steps that might have occurred during the evolution and specialization of eukaryotic core histones.

Archaeal chromatin proteins: different structures but common function?

Chromatin proteins promote chromosome flexibility in vivo, maintaining a compact yet decondensed template that permits polymerase accessibility. All Archaea have at least two types of chromatin proteins, and diversity in the chromatin protein population appears to prevent polymerization of a single type of protein. Of the numerous chromatin proteins that have been described in Archaea, only two--histones and Alba homologs--are present in all archaeal phyla. Although their structures and complexes with DNA have no similarities, their functions probably overlap as mutants that lack single chromatin proteins are viable.

The hydrophobicity of the H3 histone fold differs from the hydrophobicity of the other three folds

The eukaryotic histone dimers, H3-H4 and H2A-H2B, are formed in the cytosol prior to being transported into the nucleus and assembled into the nucleosome. Residue side-chain distances from the interior of the histone dimers are obtained with an ellipsoidal spatial metric and structural information provided by X-ray analyses at atomic resolution of the nucleosome core particles. While the spatial hydrophobic moment profiles of the dimers are comparable with profiles obtained previously that characterize the hydrophobic core of single-chain, single-domain globular soluble proteins, correlation coefficients between the side-chain hydrophobicities and distances from the interior of the H3-H4 dimer and H2A-H2B dimer differ significantly. This difference is traced to the H3 histone fold, which segregates fewer hydrophobic residues within the protein interior than the three other folds. Examination of the correlation coefficient between residue hydrophobicity and side-chain distance from the dimer interior over local regions of the fold sequence shows that the region of reduced correlation is associated mainly with the residues at the carboxyl end of the H3 histone fold, the helical region of the fold involved in the H3-H3' binding of the (H3-H4)(2) tetramer of the nucleosome. Hydrophobic interactions apparently contribute to the binding of this fourfold helical bundle and this evolutionary requirement may trade off against the requirement for H3-H4 dimer stability. The present results provide a different view than previously proposed, albeit of similar origin, to account for the reduced stability of the H3-H4 dimer compared with the H2A-H2B dimer.