The nucleoid (meaning 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.
- Visualization 1
- Composition 2
- DNA damage and repair 3
- See also 4
- References 5
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
- Thanbichler M, Wang S, Shapiro L (2005). "The bacterial nucleoid: a highly organized and dynamic structure". J Cell Biochem 96 (3): 506–21.
- Dame, R. T., Kalmykowa, O. J., & Grainger, D. C. (2011). Chromosomal macrodomains and associated proteins: implications for DNA organization and replication in gram negative bacteria. PLoS genetics, 7(6), e1002123. doi:10.1371/journal.pgen.1002123
- Wang, W., Li, G., Chen, C., Xie, X. S., & Zhuang, X. (2011). Chromosome organization by a nucleoid-associated protein in live bacteria. Science (New York, N.Y.), 333(6048), 1445–9. doi:10.1126/science.1204697
- Smith BT, Grossman AD, Walker GC. (2002). Localization of UvrA and effect of DNA damage on the chromosome of Bacillus subtilis. J Bacteriol 184(2):488-493. PMID 11751826
- Odsbu I, Morigen, Skarstad K. (2009). A reduction in ribonucleotide reductase activity slows down the chromosome replication fork but does not change its localization. PLoS One 4(10):e7617. doi: 10.1371/journal.pone.0007617. PMID 19898675
- Levin-Zaidman S, Frenkiel-Krispin D, Shimoni E, Sabanay I, Wolf SG, Minsky A. (2000). Ordered intracellular RecA-DNA assemblies: a potential site of in vivo RecA-mediated activities. Proc Natl Acad Sci U S A 97(12):6791-6796. PMID 10829063
- Delmas S, Duggin IG, Allers T. (2013). DNA damage induces nucleoid compaction via the Mre11-Rad50 complex in the archaeon Haloferax volcanii. Mol Microbiol. 87(1):168-179. doi: 10.1111/mmi.12091. PMID 23145964
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.
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.
DNA damage and repair
 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.