Deoxyribonucleic acid, or DNA, serves as the fundamental genetic blueprint for all known life forms. For this incredibly long molecule to fit within the confines of a microscopic cell, it must undergo intricate packaging. This process compacts DNA, making it manageable and accessible to cellular machinery. A central question in understanding cellular organization involves the proteins responsible for this packaging: do bacteria, like more complex organisms, possess histones for DNA organization?
The Eukaryotic Blueprint: DNA and Histones
In eukaryotic cells, which include organisms such as plants, animals, and fungi, DNA packaging relies heavily on a specialized set of proteins called histones. These highly conserved proteins act as spools around which the long DNA strands are wound. This initial level of compaction forms structures known as nucleosomes, which resemble “beads on a string” when viewed under a microscope.
Each nucleosome consists of approximately 146 to 147 base pairs of DNA wrapped around a core of eight histone proteins, specifically two copies each of histones H2A, H2B, H3, and H4. Another histone, H1, binds to the linker DNA between nucleosomes, helping to stabilize the structure. These nucleosomes then coil further, forming a more compact 30-nanometer chromatin fiber, and subsequently higher-order structures that ultimately condense into chromosomes. This sophisticated packaging allows meters of DNA to fit into a nucleus that is merely micrometers in diameter.
Beyond spatial efficiency, this organized DNA arrangement regulates gene expression, DNA replication, and cell division. The degree of DNA compaction around histones can control access for enzymes and other proteins involved in these processes. For example, loosely packed regions, known as euchromatin, are generally accessible for gene transcription, while tightly packed heterochromatin is typically transcriptionally inactive.
Bacterial DNA Organization: A Different Approach
Bacteria, which are prokaryotic organisms, were traditionally thought to lack the histones found in eukaryotes. Their genetic material, typically a single circular chromosome, resides in a region of the cytoplasm called the nucleoid, rather than within a membrane-bound nucleus. To compact their DNA, bacteria primarily employ a combination of supercoiling and various nucleoid-associated proteins (NAPs).
DNA supercoiling involves the twisting of the DNA helix upon itself, either under-winding or over-winding, to achieve significant compaction. NAPs are small, abundant proteins that bind to the DNA, helping to organize it into a compact structure within the nucleoid. These proteins, such as HU, H-NS, IHF, and Fis, achieve compaction by bending the DNA, bridging different DNA segments, or wrapping DNA in ways distinct from eukaryotic histones.
Recent research, however, challenges the long-held belief that bacteria entirely lack histones. Studies published in 2023 have identified hundreds of proteins in bacteria that possess a signature 3D histone fold, suggesting the presence of histones in some bacterial species. For instance, a histone found in the bacterium Bdellovibrio bacteriovorus interacts with DNA by encasing it, a mechanism different from the spool-like wrapping seen in eukaryotes. This discovery indicates that while not universally present or acting identically to eukaryotic histones, these proteins can be integral to bacterial chromatin structure and cellular processes.
Why Packaging Differences Matter
The distinct strategies for DNA packaging in bacteria and eukaryotes have important functional and evolutionary implications. The presence of histones in eukaryotes allows for a highly organized and dynamic chromatin structure, which is instrumental for complex gene regulation, multicellularity, and cellular differentiation. The ability to switch between accessible and inaccessible states of DNA through histone modifications provides fine-tuned control over which genes are active at any given time.
In bacteria, the nucleoid-associated proteins and DNA supercoiling contribute to gene regulation and adaptability. While NAPs also influence gene accessibility, their mechanisms often differ from histone-mediated control. These differences in packaging reflect the distinct cellular complexities and lifestyles of prokaryotes and eukaryotes. Eukaryotic genomes are significantly larger and require more extensive compaction, while the more compact bacterial genomes benefit from rapid access to genetic information, allowing for faster responses to environmental changes and rapid RNA and protein synthesis due to lack of compartmentalization.
The recent identification of histone-like proteins in some bacteria also provides new insights into the evolutionary history of DNA packaging. It suggests that simpler forms of these DNA-organizing proteins might have emerged earlier in evolution than previously understood, representing an ancient mechanism that diversified across prokaryotes and eukaryotes.