Molecule of the Month: Histones Across the Tree of Life

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 as nucleosomes. 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.

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 archaeon Methanothermus 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.

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, in Bdellovibrio 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 and pdb_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 by Leptospira 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 and pdb_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.