関: nuclear inclusion、nuclear inclusion body、pyrenoid

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出典(authority):フリー百科事典『ウィキペディア（Wikipedia）』「2015/09/16 00:13:59」(JST)

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Prokaryote cell (right) showing the nucleoid in comparison to a eukaryotic cell (left) showing the nucleus.

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.^[1] 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.

Visualization

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.

Composition

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.^[2] 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.^[3]

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.^[4]^[5] Formation of the compact structure in E. coli requires RecA activation through specific RecA-DNA interactions.^[6] 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.^[7] 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.^[7] 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.

References

^ Thanbichler M, Wang S, Shapiro L (2005). "The bacterial nucleoid: a highly organized and dynamic structure". J Cell Biochem 96 (3): 506–21. doi:10.1002/jcb.20519. PMID 15988757.
^ 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
^ ^a ^b 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

English Journal

Probing the relation between protein-protein interactions and DNA binding for a linker mutant of the bacterial nucleoid protein H-NS.

Giangrossi M1, Wintraecken K2, Spurio R1, de Vries R3.Author information 1University of Camerino, School of Biosciences and Biotechnologies, 62032 Camerino, MC, Italy.2Lab. Phys. Chem. Colloid Sci., Wageningen University, Dreijenplein 4, 6703 HB Wageningen, The Netherlands.3Lab. Phys. Chem. Colloid Sci., Wageningen University, Dreijenplein 4, 6703 HB Wageningen, The Netherlands. Electronic address: renko.devries@wur.nl.AbstractWe have investigated the relationship between oligomerization in solution and DNA binding for the bacterial nucleoid protein H-NS. This was done by comparing oligomerization and DNA binding of H-NS with that of a H-NS D68V-D71V linker mutant. The double linker mutation D68V-D71V, that makes the linker significantly more hydrophobic, leads to a dramatically enhanced and strongly temperature-dependent H-NS oligomerization in solution, as detected by dynamic light scattering. The DNA binding affinity of H-NS D68V-D71V for the hns promoter region is lower and has stronger temperature dependence than that of H-NS. DNase I footprinting experiments show that at high concentrations, regions protected by H-NS D68V-D71V are larger and less defined than for H-NS. In vitro transcription assays show that the enhanced protection also leads to enhanced transcriptional repression. Whereas the lower affinity of the H-NS D68V-D71V for DNA could be caused by competition between oligomerization in solution and oligomerization on DNA, the larger size of protected regions clearly confirms the notion that cooperative binding of H-NS to DNA is related to protein-protein interactions. These results emphasize the relative contributions of protein-protein interactions and substrate-dependent oligomerization in the control of gene repression operated by H-NS.
Biochimica et biophysica acta.Biochim Biophys Acta.2014 Feb;1844(2):339-45. doi: 10.1016/j.bbapap.2013.11.010. Epub 2013 Nov 23.
We have investigated the relationship between oligomerization in solution and DNA binding for the bacterial nucleoid protein H-NS. This was done by comparing oligomerization and DNA binding of H-NS with that of a H-NS D68V-D71V linker mutant. The double linker mutation D68V-D71V, that makes the link
PMID 24275506

Interaction of Apurinic/Apyrimidinic Endonucleases Nfo and ExoA with the DNA Integrity Scanning Protein DisA in the Processing of Oxidative DNA Damage during Bacillus subtilis Spore Outgrowth.

Campos SS, Ibarra-Rodriguez JR, Barajas-Ornelas RC, Ramírez-Guadiana FH, Obregón-Herrera A, Setlow P, Pedraza-Reyes M.Author information Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato, México.AbstractOxidative stress-induced damage, including 8-oxo-guanine and apurinic/apyrimidinic (AP) DNA lesions, were detected in dormant and outgrowing Bacillus subtilis spores lacking the AP endonucleases Nfo and ExoA. Spores of the Δnfo exoA strain exhibited slightly slowed germination and greatly slowed outgrowth that drastically slowed the spores' return to vegetative growth. A null mutation in the disA gene, encoding a DNA integrity scanning protein (DisA), suppressed this phenotype, as spores lacking Nfo, ExoA, and DisA exhibited germination and outgrowth kinetics very similar to those of wild-type spores. Overexpression of DisA also restored the slow germination and outgrowth phenotype to nfo exoA disA spores. A disA-lacZ fusion was expressed during sporulation but not in the forespore compartment. However, disA-lacZ was expressed during spore germination/outgrowth, as was a DisA-green fluorescent protein (GFP) fusion protein. Fluorescence microscopy revealed that, as previously shown in sporulating cells, DisA-GFP formed discrete globular foci that colocalized with the nucleoid of germinating and outgrowing spores and remained located primarily in a single cell during early vegetative growth. Finally, the slow-outgrowth phenotype of nfo exoA spores was accompanied by a delay in DNA synthesis to repair AP and 8-oxo-guanine lesions, and these effects were suppressed following disA disruption. We postulate that a DisA-dependent checkpoint arrests DNA replication during B. subtilis spore outgrowth until the germinating spore's genome is free of damage.
Journal of bacteriology.J Bacteriol.2014 Feb;196(3):568-78. doi: 10.1128/JB.01259-13. Epub 2013 Nov 15.
Oxidative stress-induced damage, including 8-oxo-guanine and apurinic/apyrimidinic (AP) DNA lesions, were detected in dormant and outgrowing Bacillus subtilis spores lacking the AP endonucleases Nfo and ExoA. Spores of the Δnfo exoA strain exhibited slightly slowed germination and greatly slowed ou
PMID 24244006

Tracking of Chromosome Dynamics in Live Streptococcus pneumoniae Reveals that Transcription Promotes Chromosome Segregation.

Kjos M, Veening JW.Author information Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.AbstractChromosome segregation is an essential part of the bacterial cell cycle but is poorly characterized in oval-shaped Streptococci. Using time-lapse fluorescence microscopy and total internal reflection fluorescence microscopy, we have tracked the dynamics of chromosome segregation in live cells of the human pathogen Streptococcus pneumoniae. Our observations show that the chromosome segregation process last for two-thirds of the total cell cycle; the origin region segregates rapidly in the early stages of the cell cycle while nucleoid segregation finishes just before cell division. Previously we have demonstrated that the DNA-binding protein ParB and the condensin SMC promote efficient chromosome segregation, likely by an active mechanism. We now show that in the absence of SMC, cell division can occur over the unsegregated chromosomes. However, neither smc nor parB are essential in S. pneumoniae, suggesting the importance of additional mechanisms. Here we have identified the process of transcription as one of these mechanisms important for chromosome segregation in S. pneumoniae. Transcription inhibitors rifampicin and streptolydigin as well as mutants affected in transcription elongation cause chromosome segregation defects. Together, our results highlight the importance of passive (or indirect) processes such as transcription for chromosome segregation in oval-shaped bacteria.
Molecular microbiology.Mol Microbiol.2014 Jan 14. doi: 10.1111/mmi.12517. [Epub ahead of print]
Chromosome segregation is an essential part of the bacterial cell cycle but is poorly characterized in oval-shaped Streptococci. Using time-lapse fluorescence microscopy and total internal reflection fluorescence microscopy, we have tracked the dynamics of chromosome segregation in live cells of the
PMID 24417389

Japanese Journal

Role of the Histone-Like Nucleoid Structuring Protein (H-NS) in the Regulation of Virulence Factor Expression and Stress Response in <i><i>Vibrio vulnificus</i></i>