Nucleohyaloplasm
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Editor In-Chief: Henry A. Hoff
Introduction
Nucleohyaloplasm is the cytosol within the nucleus, without the microfilaments and the microtubules. This liquid part contains enzymes and intermediate metabolites. Many substances such as nucleotides (necessary for purposes such as the replication of DNA and production of mRNA) and enzymes (which direct activities that take place in the nucleus) are dissolved in the nucleohyaloplasm.
As a cytosol, it consists mostly of water, dissolved ions, small molecules, and large water-soluble molecules (such as protein). It contains about 20% to 30% protein. It has a high concentration of K⁺ ions and a low concentration of Na⁺ ions. Normal human cytosolic pH ranges between 7.3 - 7.5, depending on the cell type involved.[1]
Small particles
Small particles (< 30 kDa) are able to pass through the nuclear pore complex by passive transport. The pores are 100 nm in total diameter; however, the gap through which molecules freely diffuse is only about 9 nm wide, due to the presence of regulatory systems within the center of the pore. The majority of the non-protein molecules have a molecular mass of less than 300 Da.[2]
This mixture of small molecules is extraordinarily complex, as the variety of molecules that are involved in metabolism (the metabolites) is immense. For example up to 200,000 different small molecules might be made in plants, although not all these will be present in the same species, or in a single cell.[3] Estimates of the number of metabolites in a single cell of E. coli or baker's yeast predict that under 1,000 are made.[4][5]
Miscible molecules
Miscible molecules such as O2, CO2, N2, and NH3 occur in any bodily fluid. These molecules are mixed into the liquid, but not turned into ions. Water contains only 1/20 parts O2. N2 mixes into the bloodstream and body fats.
Inorganic ions
Relative to the outside of a cell, the concentration of Ca2+ is low.[6] In addition to sodium and potassium ions the nucleohyaloplasm also contains Mg2+[7]. Some of these magnesium ions are associated with incoming ribonucleoside triphosphate (NTP) as they enter the catalytic center for transcription by RNA polymerase (RNAP) II.[7] The remaining typical ions found in any cytosol include chloride and bicarbonate.[8]
Intranuclear posttranscriptional modifications such as mRNA editing convert cytidine to uridine within some mRNA.[9] This conversion by enzyme EC 3.5.4.5 though infrequent releases ammonia[10] or produces ammonium in solution. This enzyme is Zn2+ dependent. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion (OH-) that performs a nucleophilic attack on the substrate.[11]
Cells also maintain an intracellular iron ion (Fe2+) homeostasis.[12] Cu2+ serves as a cofactor.[13]
When a nucleotide is incorporated into a growing DNA or RNA strand by a polymerase, pyrophosphate (PPi) is released. The pyrophosphate anion has the structure P2O74−, and is an acid anhydride of phosphate. It is unstable in aqueous solution and rapidly hydrolyzes into inorganic phosphate HPO42− (orthophosphate, Pi).
Carbohydrates
Of the carbohydrates, monosaccharides and oligosaccharides are water soluble. Polysaccharides on the other hand tend to be insouble in water. As to alcohols, there are two opposing solubility trends: the tendency of the polar OH to promote solubility in water, and of the carbon chain to resist it. Thus, methanol, ethanol, and propanol are miscible in water because the hydroxyl group wins out over the short carbon chain. Butanol, with a four-carbon chain, is moderately soluble because of a balance between the two trends. Alcohols of five or more carbons (Pentanol and higher) are effectively insoluble in water because of the hydrocarbon chain's dominance.
Fatty acids
Short chain carboxylic acids such as formic acid and acetic acid are miscible with water and dissociate to form reasonably strong acids (pKa 3.77 and 4.76, respectively). Longer-chain fatty acids do not show a great change in pKa. Nonanoic acid, for example, has a pKa of 4.96. However, as the chain length increases the solubility of the fatty acids in water decreases very rapidly, so that the longer-chain fatty acids have very little effect on the pH of a solution.
When the body uses stored fat as a source of energy, glycerol and fatty acids are released into the bloodstream. The glycerol component can be converted to glucose by the liver and provides energy for cellular metabolism.
Amino acids
The average mass range for amino acids: 75 - 222 Da. By comparison a water molecule is 18 Da. In addition to the proteinogenic standard amino acids, there are a number of other amino acids (aa) involved in the synthesis of the proteinogenic aa: citrulline (Cit), cystathionine (Cth), homocysteine (Hcy), ornithine (Orn), sarcosine (Sar) and taurine (Tau), for example. As Tau does not contain a carboxyl group it is not an aa, but since in its place it does contain a sulfonate group, it may be called an amino sulfonic acid.
Nucleotides
Nucleotides such as orotidine 5'-monophosphate (OMP) range in size from 176 Da (OMP) to 523 Da (GTP).
Cofactors
Many cofactors are involved in the synthesis of amino acids and nucleotides. They range in size from 176 Da (ascorbic acid) and 244 Da (biotin), which are vitamins, to 744 Da (nicotinamide adenine dinucleotide phosphate, NADP) and 785 Da (flavin adenine dinucleotide, FAD).
Large particles
Larger particles are also able to pass through the large diameter of a nuclear pore but at almost negligible rates.[14] However, the nucleohyaloplasm does contain large amounts of macromolecules, which can alter how molecules behave, through macromolecular crowding. Since some of these macromolecules have less volume to move in, their effective concentration is increased. This crowding effect can produce large changes in both the rates and chemical equilibrium for reactions in the nucleohyaloplasm.[15] It is particularly important in its ability to alter dissociation constants by favoring the association of macromolecules, such as when multiple proteins come together to form protein complexes, or when DNA-binding proteins bind to their targets in the genome.[16]
The lamins of mammalian nuclei are polypeptides of 60-80 kDa: A (70 kDa), B (68 kDa), and C (60 kDa).[17] A- and B-type lamins, which form separate, but interacting, stable meshworks in the lamina, have different mobilities.[18]
RNA
Of the many different types of RNA that can occur within a cell, most also can occur dissolved in the nucleohyaloplasm. In addition to mRNA, which is constructed during gene transcription to produce protein, there are a variety of RNAs that are transcripted from genes for their own sake into the nucleohyaloplasm: ribosomal RNA (rRNA), transfer RNA (tRNA), small nuclear RNA (snRNA), small nucleolar RNA (snRNA), non-coding RNA (ncRNA), miscRNA, microRNA, piwi-interacting RNA (piRNA), small interfering RNA (siRNA), signal recognition particle RNA (SRP RNA), and guide RNA (gRNA).
Ribozymes are transcripted into the nucleohyaloplasm. The functional part of the ribosome, the molecular machine that translates RNA into proteins, is fundamentally a ribozyme. Ribozymes often have divalent metal ions such as Mg2+ as cofactors.
Chromatin
Euchromatin is the less compact DNA form, and contains genes that are frequently expressed by the cell.[19] Active genes, which are generally found in the euchromatic region of the chromosome, tend to be located towards the chromosome's territory boundary.[20]
Heterochromatin is usually localized to the periphery of the nucleus along the nuclear envelope. It mainly consists of genetically inactive satellite sequences,[21] and many genes are repressed to various extents, although some cannot be expressed in euchromatin at all.[22]
Nucleolus
The nucleolus is roughly spherical, and is surrounded by the euchromatin. No membrane separates the nucleolus from the nucleohyaloplasm. Nucleoli carry out the production and maturation of ribosomes. Large numbers of ribosomes are found inside. Direct contact between the nucleolus and the nuclear envelope is frequently observed but is not dependent on nucleolar activity.[23]
Although the size of the nucleolus is highly variable in any particular cell nucleus, there is in some cells a correlation with cell diameter: increasing cell size to increasing rounded diameter of the nucleolus.[24] Based on this correlation, for an average mammalian cell of 6000 nm, the nucleolus would be ~300 nm in diameter.
Structures
Of the structures local to the nucleohyaloplasm, some serve to confine it such as the inner membrane of the nuclear envelope. While others are completely suspended within it, for example, the nucleolus. Still others such as the nuclear matrix[25][26] and nuclear lamina are found throughout the inside of the nucleus.
Lamins within the nucleohyaloplasm form another regular structure the nucleoplasmic veil[27]. The veil is excluded from the nucleolus and is present during interphase.[28] The lamin structures that make up the veil bind chromatin and disrupting their structure inhibits transcription of protein-coding genes.[29] Changes also occur in the lamina mesh size.[18]
In addition to forming a fibrous nucleoskeleton of intermediate-sized filaments that underlies the inner nuclear membrane, with the nuclear pore complexes embedded in it, the lamins can form intranuclear structures.[30]
Besides the nucleolus, the nucleus contains a number of other non-membrane delineated bodies. These include Cajal bodies, Gemini of coiled bodies, polymorphic interphase karyosomal association (PIKA), promyelocytic leukaemia (PML) bodies, paraspeckles and splicing speckles. Although little is known about a number of these domains, they are significant in that they show that the nucleohyaloplasm is not a uniform mixture, but rather contains organized functional subdomains.[31]
Intra-nuclear transport
The lateral speed of biological molecules in passive diffusion in water is on the order of 500 - 50 nm/sec. But in cytosol such as the nucleohyaloplasm: ~120 - 10 nm/sec due to crowding and collisions with large molecules. In mammalian cells, the average diameter of the nucleus is approximately 6 μm.[32] The large amount of DNA and RNA should hinder the migration of nuclear proteins, but a protein could traverse the entire diameter of a nucleus in a matter of minutes.[33]
Proteins are frequently transported across the cytosol, along well-defined routes, and delivered to particular addresses. Passive diffusion cannot account for the rate, directionality, or destination of such transport. Microtubules function as tracks and the movement is propelled by motor proteins. Movement can occur in both directions and at velocities between ~5 and 3000 nm/sec.[8]
All Cajal bodies move through the nucleohyaloplasm.[34] These movements include translocations and moving to or from the nucleolus at velocities of ~10-15 nm/sec.[34]
Constrained microstructures (~40-100 nm in size, on the order of 0.5-5MDa) move with velocities averaging 50-70 nm/sec (comparable to that of mobile chromatin), but free-moving microstructures (in chromatin-free channels) can move at speeds of up to 500 nm/sec.[35] The movement of PML-containing microstructures is energy-independent.[35] Such mobility is characteristic of constrained diffusion.[35]
Human nucleohyaloplasm
Mature monocytes circulating in human peripheral blood contain multiple nucleoli of various sizes in one and the same nucleus.[36] The nucleolar RNA content is apparently related to the nucleolar size.[36] Increases in the number of nucleoli, their size, and their activity reflect the proliferating activity of exponentially growing cells.[37]
References
- ↑ Roos A, Boron WF (1981). "Intracellular pH". Physiol. Rev. 61 (2): 296–434. PMID 7012859. Unknown parameter
|month=ignored (help) - ↑ Goodacre R, Vaidyanathan S, Dunn WB, Harrigan GG, Kell DB (2004). "Metabolomics by numbers: acquiring and understanding global metabolite data" (PDF). Trends Biotechnol. 22 (5): 245–52. doi:10.1016/j.tibtech.2004.03.007. PMID 15109811. Unknown parameter
|month=ignored (help) - ↑ Weckwerth W (2003). "Metabolomics in systems biology". Annu Rev Plant Biol. 54: 669–89. doi:10.1146/annurev.arplant.54.031902.135014. PMID 14503007.
- ↑ Reed JL, Vo TD, Schilling CH, Palsson BO (2003). "An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)". Genome Biol. 4 (9): R54. doi:10.1186/gb-2003-4-9-r54. PMC 193654. PMID 12952533.
- ↑ Förster J, Famili I, Fu P, Palsson BØ, Nielsen J (2003). "Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network". Genome Res. 13 (2): 244–53. doi:10.1101/gr.234503. PMC 420374. PMID 12566402. Unknown parameter
|month=ignored (help) - ↑ Berridge MJ (1997). "Elementary and global aspects of calcium signalling". J. Physiol. (Lond.). 499 ( Pt 2): 291–306. PMC 1159305. PMID 9080360. Unknown parameter
|month=ignored (help) - ↑ 7.0 7.1 Langelier MF, Baali D, Trinh V, Greenblatt J, Archambault J, Coulombe B (2005). "The highly conserved glutamic acid 791 of Rpb2 is involved in the binding of NTP and Mg(B) in the active center of human RNA polymerase II". Nucleic Acids Res. 33 (8): 2629–39. PMID 15886393. Unknown parameter
|month=ignored (help) - ↑ 8.0 8.1 Lodish, Harvey F. (1999). Molecular cell biology. New York: Scientific American Books. ISBN 0-7167-3136-3. OCLC 174431482.
- ↑ Ashkenas J (1997). "Gene regulation by mRNA editing". Am J Hum Genet. 60 (2): 278–83. PMID 9012400. Unknown parameter
|month=ignored (help) - ↑ "NiceZyme View of ENZYME: EC 3.5.4.5".
- ↑ "NCBI Conserved Domains: cytidine_deaminase-like Super-family".
- ↑ Mukhopadhyay CK, Attieh ZK, Fox PL (1998). "Role of ceruloplasmin in cellular iron uptake". Science. 279 (5351): 714–7. PMID 9445478. Unknown parameter
|month=ignored (help) - ↑ 1.16.3.1 "NiceZyme View of ENZYME: EC 1.16.3.1" Check
|url=value (help). - ↑ Campbell, Neil A. (1987). Biology. p. 795. ISBN 0-8053-1840-2.
- ↑ Ellis RJ (2001). "Macromolecular crowding: obvious but underappreciated". Trends Biochem. Sci. 26 (10): 597–604. doi:10.1016/S0968-0004(01)01938-7. PMID 11590012. Unknown parameter
|month=ignored (help) - ↑ Zhou HX, Rivas G, Minton AP (2008). "Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences". Annu Rev Biophys. 37: 375–97. doi:10.1146/annurev.biophys.37.032807.125817. PMID 18573087.
- ↑ Klaus Urich (1994). Comparative Animal Biochemistry. Springer. p. 359. ISBN 3540574204, 9783540574200 Check
|isbn=value: invalid character (help). - ↑ 18.0 18.1 Shimi T, Pfleghaar K, Kojima S, Pack CG, Solovei I, Goldman AE, Adam SA, Shumaker DK, Kinjo M, Cremer T, Goldman RD (2008). "The A- and B-type nuclear lamin networks: microdomains involved in chromatin organization and transcription". Genes Dev. 22 (24): 3409–21. PMID 19141474. Unknown parameter
|month=ignored (help) - ↑ Ehrenhofer-Murray A (2004). "Chromatin dynamics at DNA replication, transcription and repair". Eur J Biochem. 271 (12): 2335–2349. doi:10.1111/j.1432-1033.2004.04162.x. PMID 15182349.
- ↑ Kurz A , Lampel S, Nickolenko JE, Bradl J, Benner A, Zirbel RM, Cremer T, Lichter P (1996). "Active and inactive genes localize preferentially in the periphery of chromosome territories". J of Cell Biol. The Rockefeller University Press. 135: 1195–1205. doi:10.1083/jcb.135.5.1195. PMID 8947544.
- ↑ Lohe, A.R.; et al. (1993). "Mapping simple repeated DNA sequences in heterochromatin of Drosophila melanogaster". Genetics. 134 (4): 1149–1174. ISSN 0016-6731. PMID 8375654.
- ↑ Lu, B.Y.; et al. (2000). "Heterochromatin protein 1 is required for the normal expression of two heterochromatin genes in Drosophila". Genetics. 155 (2): 699–708. ISSN 0016-6731. PMID 10835392.
- ↑ Schwarzacher HG, Wachtler F (1993). "The nucleolus". Anat Embryol (Berl). 188 (6): 515–36. PMID 8129175. Unknown parameter
|month=ignored (help) - ↑ Coggeshall RE, Chung K, Bee DE (1985). "The relation of nucleolus diameter to cell body diameter in mammalian dorsal root ganglion cells". Anat Rec. 211 (2): 213–7. PMID 3977089. Unknown parameter
|month=ignored (help) - ↑ Nickerson J (2001). "Experimental observations of a nuclear matrix". J. Cell. Sci. 114 (Pt 3): 463–74. PMID 11171316. Unknown parameter
|month=ignored (help) - ↑ Tetko IV, Haberer G, Rudd S, Meyers B, Mewes HW, Mayer KF (2006). "Spatiotemporal expression control correlates with intragenic scaffold matrix attachment regions (S/MARs) in Arabidopsis thaliana". PLoS Comput. Biol. 2 (3): e21. doi:10.1371/journal.pcbi.0020021. PMC 1420657. PMID 16604187. Unknown parameter
|month=ignored (help) - ↑ Goldman R, Gruenbaum Y, Moir R, Shumaker D, Spann T (2002). "Nuclear lamins: building blocks of nuclear architecture". Genes Dev. 16 (5): 533–547. doi:10.1101/gad.960502. PMID 11877373.
- ↑ Moir RD, Yoona M, Khuona S, Goldman RD. (2000). "Nuclear Lamins A and B1: Different Pathways of Assembly during Nuclear Envelope Formation in Living Cells". Journal of Cell Biology. 151 (6): 1155–1168. doi:10.1083/jcb.151.6.1155. PMID 11121432.
- ↑ Spann TP, Goldman AE, Wang C, Huang S, Goldman RD (2002). "Alteration of nuclear lamin organization inhibits RNA polymerase II–dependent transcription". J of Cell Biol. 156 (4): 603–608. doi:10.1083/jcb.200112047. PMID 11854306.
- ↑ Broers JL, Hutchison CJ, Ramaekers FC (2004). "Laminopathies". J Pathol. 204 (4): 478–88. PMID 15495262. Unknown parameter
|month=ignored (help) - ↑ Dundr M, Misteli T (2001). "Functional architecture in the cell nucleus". Biochem J. (356): 297–310. doi:10.1146/annurev.cellbio.20.010403.103738. PMID 11368755.
- ↑ Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, Peter Walter, ed. (2002). Molecular Biology of the Cell, Chapter 4, pages 191-234 (4th ed.). Garland Science.
- ↑ Misteli T (2001). "Protein dynamics: implications for nuclear architecture and gene expression". Science. 291 (5505): 843–7. PMID 11225636. Unknown parameter
|month=ignored (help) - ↑ 34.0 34.1 Platani M, Goldberg I, Swedlow JR, Lamond AI (2000). "In Vivo Analysis of Cajal Body Movement, Separation, and Joining in Live Human Cells". J Cell Biol. 151 (7): 1561–74. doi:10.1083/jcb.151.7.1561. PMID 11134083. Unknown parameter
|month=ignored (help) - ↑ 35.0 35.1 35.2 Eskiw CH, Dellaire G, Mymryk JS, Bazett-Jones DP (2003). "Size, position and dynamic behavior of PML nuclear bodies following cell stress as a paradigm for supramolecular trafficking and assembly". J Cell Sci. 116 (Pt 21): 4455–66. doi:10.1242/jcs.00758. PMID 13130097. Unknown parameter
|month=ignored (help) - ↑ 36.0 36.1 Smetana K, Jirásková I, Otevrelová P, Kalousek I (2008). "The RNA content of nucleolar bodies is related to their size - a cytochemical study on human monocytes and lymphocytes in blood smears and blood cytospins". Folia Biol (Praha). 54 (4): 130–3. PMID 18808739.
- ↑ Horký M, Kotala V, Anton M, Wesierska-Gadek J (2002). "Nucleolus and apoptosis". Ann N Y Acad Sci. 973: 258–64. PMID 12485873. Unknown parameter
|month=ignored (help)