Nucleoid

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 . 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.

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