Molecule of the Month: Histones Across the Tree of Life

Uncovering the evolutionary diversity of histones

Eukaryotic histones (shown in green on the left side, frompdb_00001aoi) form octamers from pairs of histone dimers. H2A-H2B and H3-H4 dimers are shown on the top, with full-length tails drawn in. On the right, HmfB (orange,pdb_00005t5k) is an archaeal histone that forms hypernucleosomes.

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All known cellular life on earth stores their genetic information as long strands of DNA that must be tightly packed in order to fit inside cells. The nearly 2 meters of genomic DNA in a human cell, for example, is condensed to fit into a nucleus that is about 6 micrometers in diameter. This impressive level of compaction is largely achieved through the action of proteins known as histones. In all eukaryotes, genomic DNA is wrapped around histones, forming structures known asnucleosomes. Nucleosomes interact with one another and additional proteins to form higher-order chromatin structures, allowing for dense packing of DNA within the nucleus.

The evolutionary tree of life consists of three major branches: eukaryotes (organisms with membrane-enclosed nuclei; a group that include all plants, animals, and fungi), archaea (single-celled prokaryotes that thrive often in harsh environments), and bacteria (ubiquitous single-celled prokaryotes). A large number of molecular innovations are shared amongst all of these branches. Histones, however, were long thought to be unique to the eukaryotic lineage. But recent studies have shown that histones exist in most archaeal and some bacterial cells, shedding light on DNA packaging mechanisms while also raising new questions about the evolution of histones.

Histones in eukaryotes and archaea

In eukaryotes, there are four core histones (H2A, H2B, H3, and H4) that form an octamer made up of two H2A-H2B and two H3-H4 heterodimers (shown in the image on the right in green,pdb_00001aoi). In the nucleosome, the positively-charged histones make numerous contacts with the negatively-charged backbone of DNA in a sequence non-specific manner. All eukaryotic histones show high structural conservation and share a common motif called the histone fold, consisting of three alpha helices connected by short linkers.

Structural studies have shown that some archaeal lineages encode histones with remarkable structural similarity to eukaryotic histones. Histones from the heat-loving archaeonMethanothermus fervidus, called HMfA and HMfB, possess the canonical histone fold, dimerize, and interact with DNA in a very similar manner to eukaryotic histones (shown in orange in the image above,pdb_00005t5k). However, significant differences are also seen. HMfA and HMfB share high sequence similarity with one another and readily form either homodimers or heterodimers that are structurally equivalent. As a result, instead of building discrete octameric nucleosomes, HMfA and HMfB dimers can oligomerize to form long superhelical assemblies called hypernucleosomes. HMfA and HMfB also lack the long, unstructured tails present in eukaryotic histones. Although only a limited number of structural studies of archaeal histones have been completed, genomic analyses suggest that a majority of archaeal genomes encode histone proteins, and that these sequences are far more diverse than those found in eukaryotes. This diversity suggests that future studies will reveal novel histone-DNA assemblies and provide further insight into the evolution of eukaryotic histones.

Bacterial histone assemblies fromBdellovibrio bacteriovorus (purple, end-on binding mode frompdb_00008fw7 andpdb_00009ezz shown in middle row, and center-binding mode frompdb_00009f0e shown in bottom row) andLeptospira perolatii (pink,pdb_00009qt1 andpdb_00009qt2).

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Histones in bacteria

Surprisingly, histones (broadly defined as proteins that contain a histone fold and bind to DNA) have also recently been characterized in bacteria. By searching for predicted histone-fold proteins in a large database of bacterial genomes, researchers identified a protein, called Bd0055 or HBb, inBdellovibrio bacteriovorus, a ubiquitous bacterium found in soil and aquatic environments. Structural studies have shown that Bd0055 forms dimers that can bind to DNA using one of two distinct interfaces (shown on the left in purple). DNA binding occurs in either an "end-on" position (pdb_00008fw7 andpdb_00009ezz) or a central position (pdb_00009f0e), with little DNA bending seen in either mode. It is currently unclear how Bd0055 interacts and impacts DNA organization in a cellular context. While biochemical and simulation studies suggest that Bd0055 dimers may be able to use both binding surfaces simultaneously to bend DNA, it has also been proposed that Bd0055 may form a protein-dense coat around DNA via its end-on binding mode.

Recent bioinformatics analyses have identified additional bacterial histones including HLp, a histone-fold containing protein expressed byLeptospira perolatii, a spiral-shaped gram-negative bacterium. Structural studies have shown that HLp forms tetramers that can bind to DNA in at least two distinct ways (shown in pink in the illustration on the left,pdb_00009qt1 andpdb_00009qt2). Additional in vitro and in silico experiments suggest that DNA can wrap around HLp tetramers in a manner similar to eukaryotic nucleosomes.

While the discovery of bacterial histones is intriguing, it appears that histones are rare in bacteria. It is estimated that only around two percent of sequenced bacterial genomes contain proteins with a histone fold. Bacteria largely rely on a variety of nucleoid-associated proteins (NAPs) to condense their genomic DNA into a small region of the cell, termed the nucleoid. Bacteria that have been found to express histones also express NAPs, and how bacterial histones and NAPs may work together to organize DNA is currently unknown.

Exploring the Structure

Compare eukaryotic, archaeal, and bacterial histones

Take a closer look at a nucleosome from the African clawed frogXenopus laevis (pdb_00001aoi), a segment of a hypernucleosome from the archaeonMethanothermus fervidus (pdb_00005t5k), and DNA-bound HLp from the bacteriumLeptospira perolatii (pdb_00009qt1).

Topics for Further Discussion

Learn more about theeukaryotic nucleosome and aboutDNA.
Cisplatin is a small molecule used for treatment of cancer that changes the conformation of DNA and causes cell death.

Related PDB-101 Resources

References

pdb_00001aoi: Luger K, Mäder AW, Richmond RK, Sargent DF, Richmond TJ. Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature. 1997 Sep 18;389(6648):251-60.
pdb_00005t5k: Mattiroli F, Bhattacharyya S, Dyer PN, White AE, Sandman K, Burkhart BW, Byrne KR, Lee T, Ahn NG, Santangelo TJ, Reeve JN, Luger K. Structure of histone-based chromatin in Archaea. Science. 2017 Aug 11;357(6351):609-612.
pdb_00009f0e,pdb_00009ezz: Hu Y, Schwab S, Deiss S, Escudeiro P, van Heesch T, Joiner JD, Vreede J, Hartmann MD, Lupas AN, Alvarez BH, Alva V, Dame RT. Bacterial histone HBb from Bdellovibrio bacteriovorus compacts DNA by bending. Nucleic Acids Res. 2024 Aug 12;52(14):8193-8204.
pdb_00009qt1,pdb_00009qt2: Hu Y, Schwab S, Qiu K, Zhang Y, Bär K, Reichle H, Panzera A, Lupas AN, Hartmann MD, Dame RT, Alva V, Hernandez Alvarez B. DNA Wrapping by a tetrameric bacterial histone. Nat Commun. 2025 Dec 11;16(1):11108.
pdb_00008fw7: Hocher A, Laursen SP, Radford P, Tyson J, Lambert C, Stevens KM, Montoya A, Shliaha PV, Picardeau M, Sockett RE, Luger K, Warnecke T. Histones with an unconventional DNA-binding mode in vitro are major chromatin constituents in the bacterium Bdellovibrio bacteriovorus. Nat Microbiol. 2023 Nov;8(11):2006-2019. Erratum in: Nat Microbiol. 2024 Nov;9(11):3075.
Villalta A, Weerawarana SR, Nosella ML, Hamel NL, Luger K. The Expanding Histone Universe: Histone-Based DNA Organization in Noneukaryotic Organisms. Annu Rev Biophys. 2025 Dec 2.

February 2026, Janet Iwasa

http://doi.org/10.2210/rcsb_pdb/mom_2026_2

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TheMolecule of the Month series presents short accounts on selected topics from the Protein Data Bank. Each installment includes an introduction to the structure and function of the molecule, a discussion of the relevance of the molecule to human health and welfare, and suggestions for how visitors might view these structures and access further details. The series is currently created by Janet Iwasa (University of Utah).

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