prokaryotic nucleoid remodeling

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The nucleoid (meaning nucleus-like) is an irregularly-shaped region within the cell of prokaryotes which has nuclear material without a nuclear membrane and where the genetic material is localized. The genome of prokaryotic organisms generally is a circular, double-stranded 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.
A genophore is the DNA of a prokaryote. This is commonly referred to as a prokaryotic chromosome. The term chromosome is misleading for a genophore because the genophore lacks chromatin. The genophore is compacted through a mechanism known as supercoiling, whereas a chromosome is compacted via chromatin. The genophore is circular in most prokaryotes, and linear in very few. The circular nature of the genophore allows replication to occur without telomeres. Genophores are generally of a much smaller size than Eukaryotic chromosomes.
Proteins helping to maintain the supercoiled structure of the nucleic acid are known as nucleoid proteins or nucleoid-associated proteins 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 folded chromosome is organized into looped domains that are negatively supercoiled during the exponential phase of growth. In this phase, the abundant nucleoid-associated proteins histone-like nucleoid-structuring protein (H-NS) and factor for inversion stimulation (Fis) bind throughout the nucleoid and are associated with the seven ribosomal RNA operons. As shown here in two cases, these are organized into superstructures called transcription factories. b | In stationary phase the rRNA operons are quiescent and Fis is almost undetectable. The chromosome has fewer looped domains, and those that are visible consist of relaxed DNA.

Histone-like nucleoid-structuring protein (H-NS) binds to DNA and influences its structure. This binding can result in DNA coating (top right), in which the protein binds to two sites that are close together on the same strand, or DNA bridging (top left), in which it binds to two sites that are further apart and causes the DNA between them to form a loop. The integrity of the resulting bridge is compromised by the intervention of a DNA-wrapping protein (green; bottom left) or by a DNA-bending protein (turquoise; bottom right). The alternative interactions that result from DNA-binding of these proteins make the DNA–protein–DNA bridge untenable, and H-NS becomes displaced.

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ORTHOLOGY CLASS Homo sapiens L. (human) [HSA] Mus musculus L. (mouse) [MMU] Caenorhabditis elegans Maupas (nematode) [CEL] Drosophila melanogaster Meigen (fruit fly) [DME] Saccharomyces cerevisiae Meyen ex E.C. Hansen (budding yeast) [SCE] Schizo-saccharomyces pombe Lindner (fission yeast) [SPO] Escherichia coli Migula (bacterium) K-12 MG1655 [ECO] Arabidopsis thaliana (L.) Heynh. (mouse-ear cress) [ATH]
ko:K03169 (DNA topoisomerase III [EC:5.99.1.2]) TopB
ko:K03168 (DNA topoisomerase I [EC:5.99.1.2]) TopA
ko:K02622 (topoisomerase IV subunit B [EC:5.99.1.-]) ParE
ko:K02621 (topoisomerase IV subunit A [EC:5.99.1.-]) ParC
ko:K02469 (DNA gyrase subunit A [EC:5.99.1.3]) GyrA GYRA
ko:K02470 (DNA gyrase subunit B [EC:5.99.1.3]) GyrB GYRB1
GYRBM
ko:K05788 (integration host factor subunit beta) IhfB
ko:K04764 (integration host factor subunit alpha) IhfA
ko:K03530 (DNA-binding protein HU-beta) HU beta (histone-like)
ko:K05787 (DNA-binding protein HU-alpha) HU alfa (histone-like)
ko:K11685 (DNA-binding protein StpA) StpA
ko:K03746 (DNA-binding protein H-NS) Hns

Last modification date: Oct. 5, 2011