The nucleoid (meaning nucleus-like) is an irregularly shaped region within the cell of a prokaryote that contains all or most of the genetic material, called genophore. In contrast to the nucleus of a eukaryotic cell, it is not surrounded by a nuclear membrane. The genome of prokaryotic organisms generally is a circular, double-stranded piece of DNA, of which multiple copies may exist at any time. The length of a genome widely varies, but generally is at least a few million base pairs. As in all cellular organisms, length of the DNA molecules of bacterial and archaeal chromosomes is very large compared to the dimensions of the cell, and the genomic DNA molecules must be compacted to fit.
The nucleoid can be clearly visualized on an electron micrograph at high magnification, where, although its appearance may differ, it is clearly visible against the cytosol. Sometimes even strands of what is thought to be DNA are visible. By staining with the Feulgen stain, which specifically stains DNA, the nucleoid can also be seen under a light microscope. The DNA-intercalating stains DAPI and ethidium bromide are widely used for fluorescence microscopy of nucleoids.
Experimental evidence suggests that the nucleoid is largely composed of DNA, about 60%, with a small amount of RNA and protein. The latter two constituents are likely to be mainly messenger RNA and the transcription factor proteins found regulating the bacterial genome. Proteins that carry out the dynamic spatial organization of the nucleic acid are known as nucleoid proteins or nucleoid-associated proteins (NAPs) and are distinct from histones of eukaryotic nuclei. In contrast to histones, the DNA-binding proteins of the nucleoid do not form nucleosomes, in which DNA is wrapped around a protein core. Instead, these proteins often use other mechanisms to promote compaction such as DNA looping. The most studied NAPs are HU, H-NS, Fis, CbpA, Dps that organize the genome by driving events such as DNA bending, bridging, and aggregation. These proteins can form clusters (like H-NS does) in order to locally compact specific genomic regions, or be scattered throughout the chromosome (HU, Fis) and they seem to be involved also in coordinating transcription events, spatially sequestering specific genes and participating in their regulation.
In E. coli small RNA transcribed from repeated extragenic palindromic element (REP325) called nucleoid-associated ncRNA 4 (naRNA4) collaborates with HU protein in condensing the DNA. The secondary structure but not the sequence of the RNA is important in nucleoid condensation.
DNA damage and repair
Changes in the structure of the nucleoid of bacteria and archaea are observed after exposure to DNA damaging conditions. The nucleoids of the bacteria Bacillus subtilis and Escherichia coli both become significantly more compact after UV irradiation. Formation of the compact structure in E. coli requires RecA activation through specific RecA-DNA interactions. The RecA protein plays a key role in homologous recombinational repair of DNA damage.
Similar to B. subtilis and E. coli above, exposure of the archaeon Haloferax volcanii to stresses that damage DNA cause compaction and reorganization of the nucleoid. Compaction depends on the Mre11-Rad50 protein complex that catalyzes an early step in homologous recombinational repair of double-strand breaks in DNA. Delmas et al. proposed that nucleoid compaction is part of a DNA damage response that accelerates cell recovery by helping DNA repair proteins to locate targets, and by facilitating the search for intact DNA sequences during homologous recombination.
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