Nucleohyaloplasm: Difference between revisions

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'''Editor-In-Chief:''' Henry A. Hoff
'''Editor-In-Chief:''' Henry A. Hoff


=Introduction=
==Overview==


'''Nucleohyaloplasm''' is the [[cytosol]] within the [[nucleus]], without the [[microfilaments]] and the [[microtubules]], also known as nucleosol, vis à vis mitosol and cytosol<ref name=Solakidi>{{ cite journal |author=Solakidi S, Psarra AM, Sekeris CE |title=Differential distribution of glucocorticoid and estrogen receptor isoforms:localization of GRβ and ERα in nucleoli and GRα and ERβ in the mitochondria of human osteosarcoma SaOS-2 and hepatocarcinoma HepG2 cell lines |journal=J Musculoskelet Neuronal Interact. |volume=7 |issue=3 |pages=240-5 |month=Jul-Sep |year=2007 |url=http://www.ismni.org/jmni/pdf/29/07SOLAKIDI.pdf |pmid=17947807 }}</ref>. This liquid part contains [[enzyme]]s (which direct activities that take place in the nucleus), intermediate [[metabolite]]s, and many substances such as [[nucleotide]]s (necessary for purposes as the [[DNA replication|replication of DNA]] and production of [[Messenger RNA|mRNA]]). All are dissolved in the nucleohyaloplasm.
A hyaloplasm is the clear, structureless, apparently homogeneous fluid of the cytoplasm. Similar to the hyaloplasm of a cell, the nucleus contains nucleohyaloplasm. It is a highly viscous liquid. This liquid contains [[enzyme]]s (which direct activities that take place in the nucleus), intermediate [[metabolite]]s, and many substances such as [[nucleotide]]s (necessary for purposes as the [[DNA replication|replication of DNA]] and production of [[Messenger RNA|mRNA]]). All are dissolved in the nucleohyaloplasm. It is part of the [[nucleoplasm]] and is partly made up of [[nucleosol]].
 
==Introduction==
 
'''Nucleohyaloplasm''' is the [[cytosol]] within the [[nucleus]], without the [[microfilaments]] and the [[microtubules]], also known as [[nucleosol]], vis à vis mitosol and [[cytosol]]<ref name=Solakidi>{{ cite journal |author=Solakidi S, Psarra AM, Sekeris CE |title=Differential distribution of glucocorticoid and estrogen receptor isoforms:localization of GRβ and ERα in nucleoli and GRα and ERβ in the mitochondria of human osteosarcoma SaOS-2 and hepatocarcinoma HepG2 cell lines |journal=J Musculoskelet Neuronal Interact. |volume=7 |issue=3 |pages=240-5 |month=Jul-Sep |year=2007 |url=http://www.ismni.org/jmni/pdf/29/07SOLAKIDI.pdf |pmid=17947807 }}</ref>.


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.<ref name=Roos>{{cite journal |author=Roos A, Boron WF |title=Intracellular pH |journal=Physiol. Rev. |volume=61 |issue=2 |pages=296–434 |year=1981 |month=April |pmid=7012859 |url=http://physrev.physiology.org/cgi/pmidlookup?view=long&pmid=7012859}}</ref>
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.<ref name=Roos>{{cite journal |author=Roos A, Boron WF |title=Intracellular pH |journal=Physiol. Rev. |volume=61 |issue=2 |pages=296–434 |year=1981 |month=April |pmid=7012859 |url=http://physrev.physiology.org/cgi/pmidlookup?view=long&pmid=7012859}}</ref>


=Small particles=
As a '''plasm''' it contains formative material, portions of the [[nucleoskeleton]] as it is being shaped or reshaped, macromolecules with limited mobility, and portions of the nuclear envelope as it is recycled.
 
==Small particles==


Small particles (< 40 [[kDa]]<ref name=Naim>{{ cite journal |author=Naim B, Brumfeld V, Kapon R, Kiss V, Nevo R, Reich Z |title=Passive and Facilitated Transport in Nuclear Pore Complexes Is Largely Uncoupled |journal=J Biol Chem. |volume=282 |issue=6 |pages=3881-8 |month=Feb |year=2007 |doi=10.1074/jbc.M608329200 |pmid=17164246 |url=http://www.jbc.org/cgi/content/full/282/6/3881 }}</ref>, <50 kDa<ref name=wiley>{{ cite web |url=http://www3.interscience.wiley.com/journal/114215775/abstract |title=Research highlights |journal=Biopolymers. |volume=86 |issue=2 |year=2007 |month=Apr |page=fmiv |doi=10.1002/bip.20740 }}</ref>, <~70 kDa<ref name=Mahato>{{ cite journal |author=Mahato RI, Rolland A, Tomlinson E |title=Cationic Lipid-Based Gene Delivery Systems: Pharmaceutical Perspectives |journal=Pharm Res. |volume=14 |issue=7 |month=Jul |pages=853-9 |year=1997 |pmid=9244140 }}</ref>, ≤ 70 kDa<ref name=Chesnoy>{{ cite journal |author=Chesnoy S, Huang L |title=STRUCTURE AND FUNCTION OF LIPID-DNA COMPLEXES FOR GENE DELIVERY |journal=Annu Rev Biophys Biomol Struct. |volume=29 |issue= |month=Jun |year=2000 |pages=27-47 |doi=10.1146/annurev.biophys.29.1.27 |pmid=10940242 }}</ref>) are able to pass through the [[nuclear pore]] complex by [[passive transport]]. Larger proteins require a [[nuclear localization signal]] (NLS). The pores are 100 [[nm]] in total diameter, with an opening diameter of about 50 nm; however, the gap through which molecules freely diffuse is only about 9-10 nm wide,<ref name=Kramer>{{ cite journal |author=Kramer A, Ludwig Y, Shahin V, Oberleithner H |title=A Pathway Separate from the Central Channel through the Nuclear Pore Complex for Inorganic Ions and Small Macromolecules |journal=J Biol Chem. |volume=282 |issue=43 |pages=31437-43 |month=Oct |year=2007 |doi=10.1074/jbc.M703720200 |pmid=17726020 |url=http://www.jbc.org/cgi/content/full/282/43/31437 }}</ref> due to the presence of regulatory systems within the center of the pore. The 10 nm diameter corresponds to an upper mass limit of 70 kDa.<ref name=Melchior>{{ cite journal |author=Melchior F, Gerace L |title=Mechanisms of nuclear protein import |journal=Curr Opin Cell Biol. |volume=7 |issue=3 |month=Jun |year=1995 |pages=310-8 |pmid=7662359 }}</ref> The majority of the non-protein molecules have a [[molecular mass]] of less than 300&nbsp;[[Atomic mass unit|Da]].<ref name=Goodacre>{{cite journal |author=Goodacre R, Vaidyanathan S, Dunn WB, Harrigan GG, Kell DB |title=Metabolomics by numbers: acquiring and understanding global metabolite data |journal=Trends Biotechnol. |volume=22 |issue=5 |pages=245–52 |year=2004 |month=May |pmid=15109811 |doi=10.1016/j.tibtech.2004.03.007 |url=http://personalpages.manchester.ac.uk/staff/roy.goodacre/learning/metabprof/Goodacre-TibTech2004.pdf|format=PDF}}</ref>
Small particles (< 40 [[kDa]]<ref name=Naim>{{ cite journal |author=Naim B, Brumfeld V, Kapon R, Kiss V, Nevo R, Reich Z |title=Passive and Facilitated Transport in Nuclear Pore Complexes Is Largely Uncoupled |journal=J Biol Chem. |volume=282 |issue=6 |pages=3881-8 |month=Feb |year=2007 |doi=10.1074/jbc.M608329200 |pmid=17164246 |url=http://www.jbc.org/cgi/content/full/282/6/3881 }}</ref>, <50 kDa<ref name=wiley>{{ cite web |url=http://www3.interscience.wiley.com/journal/114215775/abstract |title=Research highlights |journal=Biopolymers. |volume=86 |issue=2 |year=2007 |month=Apr |page=fmiv |doi=10.1002/bip.20740 }}</ref>, <~70 kDa<ref name=Mahato>{{ cite journal |author=Mahato RI, Rolland A, Tomlinson E |title=Cationic Lipid-Based Gene Delivery Systems: Pharmaceutical Perspectives |journal=Pharm Res. |volume=14 |issue=7 |month=Jul |pages=853-9 |year=1997 |pmid=9244140 }}</ref>, ≤ 70 kDa<ref name=Chesnoy>{{ cite journal |author=Chesnoy S, Huang L |title=STRUCTURE AND FUNCTION OF LIPID-DNA COMPLEXES FOR GENE DELIVERY |journal=Annu Rev Biophys Biomol Struct. |volume=29 |issue= |month=Jun |year=2000 |pages=27-47 |doi=10.1146/annurev.biophys.29.1.27 |pmid=10940242 }}</ref>) are able to pass through the [[nuclear pore]] complex by [[passive transport]]. Larger proteins require a [[nuclear localization signal]] (NLS). The pores are 100 [[nm]] in total diameter, with an opening diameter of about 50 nm; however, the gap through which molecules freely diffuse is only about 9-10 nm wide,<ref name=Kramer>{{ cite journal |author=Kramer A, Ludwig Y, Shahin V, Oberleithner H |title=A Pathway Separate from the Central Channel through the Nuclear Pore Complex for Inorganic Ions and Small Macromolecules |journal=J Biol Chem. |volume=282 |issue=43 |pages=31437-43 |month=Oct |year=2007 |doi=10.1074/jbc.M703720200 |pmid=17726020 |url=http://www.jbc.org/cgi/content/full/282/43/31437 }}</ref> due to the presence of regulatory systems within the center of the pore. The 10 nm diameter corresponds to an upper mass limit of 70 kDa.<ref name=Melchior>{{ cite journal |author=Melchior F, Gerace L |title=Mechanisms of nuclear protein import |journal=Curr Opin Cell Biol. |volume=7 |issue=3 |month=Jun |year=1995 |pages=310-8 |pmid=7662359 }}</ref> The majority of the non-protein molecules have a [[molecular mass]] of less than 300&nbsp;[[Atomic mass unit|Da]].<ref name=Goodacre>{{cite journal |author=Goodacre R, Vaidyanathan S, Dunn WB, Harrigan GG, Kell DB |title=Metabolomics by numbers: acquiring and understanding global metabolite data |journal=Trends Biotechnol. |volume=22 |issue=5 |pages=245–52 |year=2004 |month=May |pmid=15109811 |doi=10.1016/j.tibtech.2004.03.007 |url=http://personalpages.manchester.ac.uk/staff/roy.goodacre/learning/metabprof/Goodacre-TibTech2004.pdf|format=PDF}}</ref>


This mixture of small molecules is extraordinarily complex, as the variety of molecules that are involved in metabolism (the [[metabolite]]s) 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.<ref name=Weckwerth>{{cite journal |author=Weckwerth W |title=Metabolomics in systems biology |journal=Annu Rev Plant Biol |volume=54 |issue= |pages=669–89 |year=2003 |pmid=14503007 |doi=10.1146/annurev.arplant.54.031902.135014}}</ref> Estimates of the number of metabolites in a single cell of ''[[Escherichia coli|E. coli]]'' or [[Saccharomyces cerevisiae|baker's yeast]] predict that under 1,000 are made.<ref name=Reed>{{cite journal |author=Reed JL, Vo TD, Schilling CH, Palsson BO |title=An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR) |journal=Genome Biol. |volume=4 |issue=9 |pages=R54 |year=2003 |pmid=12952533 |pmc=193654 |doi=10.1186/gb-2003-4-9-r54 |url=http://genomebiology.com/1465-6906/4/R54}}</ref><ref name=Förster>{{cite journal |author=Förster J, Famili I, Fu P, Palsson BØ, Nielsen J |title=Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network |journal=Genome Res. |volume=13 |issue=2 |pages=244–53 |year=2003 |month=February |pmid=12566402 |pmc=420374 |doi=10.1101/gr.234503 |url=http://www.genome.org/cgi/pmidlookup?view=long&pmid=12566402}}</ref>
This mixture of small molecules is extraordinarily complex, as the variety of molecules that are involved in metabolism (the [[metabolite]]s) 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.<ref name=Weckwerth>{{cite journal |author=Weckwerth W |title=Metabolomics in systems biology |journal=Annu Rev Plant Biol |volume=54 |issue= |pages=669–89 |year=2003 |pmid=14503007 |doi=10.1146/annurev.arplant.54.031902.135014}}</ref> Estimates of the number of metabolites in a single cell of ''[[Escherichia coli|E. coli]]'' or [[Saccharomyces cerevisiae|baker's yeast]] predict that under 1,000 are made.<ref name=Reed>{{cite journal |author=Reed JL, Vo TD, Schilling CH, Palsson BO |title=An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR) |journal=Genome Biol. |volume=4 |issue=9 |pages=R54 |year=2003 |pmid=12952533 |pmc=193654 |doi=10.1186/gb-2003-4-9-r54 |url=http://genomebiology.com/1465-6906/4/R54}}</ref><ref name=Förster>{{cite journal |author=Förster J, Famili I, Fu P, Palsson BØ, Nielsen J |title=Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network |journal=Genome Res. |volume=13 |issue=2 |pages=244–53 |year=2003 |month=February |pmid=12566402 |pmc=420374 |doi=10.1101/gr.234503 |url=http://www.genome.org/cgi/pmidlookup?view=long&pmid=12566402}}</ref>
==[[Miscibility|Miscible]] molecules==
Miscible molecules such as O<sub>2</sub>, CO<sub>2</sub>, N<sub>2</sub>, and NH<sub>3</sub> occur in any bodily fluid. These molecules are mixed into the liquid, but not turned into ions. Water contains only 1/20 parts O<sub>2</sub>. N<sub>2</sub> mixes into the bloodstream and body fats.
==[[Inorganic ions]]==
Relative to the outside of a cell, the concentration of Ca<sup>2+</sup> is low.<ref name=Berridge>{{cite journal |author=Berridge MJ |title=Elementary and global aspects of calcium signalling |journal=J. Physiol. (Lond.) |volume=499 ( Pt 2) |issue= |pages=291–306 |year=1997 |month=March |pmid=9080360 |pmc=1159305 |url=http://www.jphysiol.org/cgi/pmidlookup?view=long&pmid=9080360}}</ref> In addition to sodium and potassium ions the nucleohyaloplasm also contains Mg<sup>2+</sup><ref name=Langelier>{{ cite journal |author=Langelier MF, Baali D, Trinh V, Greenblatt J, Archambault J, Coulombe B |title=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 |journal=Nucleic Acids Res. |volume=33 |issue=8 |pages=2629-39 |year=2005 |month=May |pmid=15886393 }}</ref>. 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.<ref name=Langelier/> The remaining typical ions found in any cytosol include chloride and bicarbonate.<ref name=Lodish>{{cite book |author=Lodish, Harvey F. |title=Molecular cell biology |publisher=Scientific American Books |location=New York |year=1999 |pages= |isbn=0-7167-3136-3 |oclc=174431482}}</ref>
Intranuclear posttranscriptional modifications such as m[[RNA editing]] convert cytidine to uridine within some mRNA.<ref name=Ashkenas>{{ cite journal |author=Ashkenas J |title=Gene regulation by mRNA editing |journal=Am J Hum Genet. |volume=60 |issue=2 | pages=278-83 |month=Feb |year=1997 |pmid=9012400 }}</ref> This conversion by enzyme EC 3.5.4.5 though infrequent releases ammonia<ref name=3.5.4.5>{{cite web | title = NiceZyme View of ENZYME: EC 3.5.4.5| url = http://www.expasy.org/cgi-bin/nicezyme.pl?3.5.4.5| accessdate = }}</ref> or produces ammonium (NH<sub>4</sub><sup>+</sup>) in solution. This enzyme is Zn<sup>2+</sup> 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<sup>-</sup>) that performs a [[Nucleophile|nucleophilic]] attack on the [[Substrate (biochemistry)|substrate]].<ref name=c100269>{{cite web | title = NCBI Conserved Domains: cytidine_deaminase-like Super-family| url = http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=119679| accessdate = }}</ref>
Cells also maintain an intracellular iron ion (Fe<sup>2+</sup>) [[homeostasis]].<ref name=Mukhopadhyay>{{ cite journal |author=Mukhopadhyay CK, Attieh ZK, Fox PL |title=Role of ceruloplasmin in cellular iron uptake |journal=Science. |volume=279 |issue=5351 |pages=714-7 |month=Jan |year=1998 |pmid=9445478 }}</ref> Cu<sup>2+</sup> serves as a [[Cofactor (biochemistry)|cofactor]].<ref name=1.16.3.1>{{cite web | title = NiceZyme View of ENZYME: EC 1.16.3.1 | url = http://www.expasy.org/cgi-bin/nicezyme.pl? 1.16.3.1 | accessdate = }}</ref> Iron homeostasis involves interconversions of Fe<sup>2+</sup> with Fe<sup>3+</sup>.
When a [[nucleotide]] is incorporated into a growing [[DNA]] or [[RNA]] strand by a [[polymerase]], [[pyrophosphate]] (PP<sub>i</sub>) is released. The pyrophosphate anion has the structure P<sub>2</sub>O<sub>7</sub><sup>4&minus;</sup>, and is an [[acid]] [[anhydride]] of [[phosphate]]. It is unstable in [[aqueous solution]] and in the absence of enzymic catalysis [[hydrolysis|hydrolyze]]s extremely slowly into inorganic phosphate HPO<sub>4</sub><sup>2&minus;</sup> ([[Phosphoric acids and phosphates#Orthophosphate|orthophosphate]], P<sub>i</sub>) in all but highly acidic media.<ref name=Huebner>{{ cite journal |author=Huebner PWA, Milburn RM |title=Hydrolysis of pyrophosphate to orthophosphate promoted by cobalt(III). Evidence for the role of polynuclear species |journal=Inorg Chem. |year=1980 |volume=19 |issue=5 |pages=1267-72 |month=May |pmid= |doi=10.1021/ic50207a032 }}</ref>
Enzyme EC 3.6.1.1 catalyzes the hydrolysis of PP<sub>i</sub> to P<sub>i</sub>:
PP<sub>i</sub> + H<sub>2</sub>O <=> 2 P<sub>i</sub>.
The enzyme is Mg<sup>2+</sup> binding, occurs in the cytosol, has a 33 kDa form, and no NLS. The enzymes of EC 3.6.1.1, in general, exist as homooligomers.
==[[Carbohydrate]]s==
Of the carbohydrates, [[monosaccharide]]s and [[oligosaccharide]]s are water soluble. [[Polysaccharide]]s on the other hand tend to be insoluble in water. As to [[alcohol]]s, 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 ([[1-Pentanol|pentanol]] and higher) are effectively insoluble in water because of the hydrocarbon chain's dominance.
==[[Fatty acid]]s==
Short chain carboxylic acids such as [[formic acid]] and [[acetic acid]] are miscible with water and dissociate to form reasonably strong acids ([[acid dissociation constant|pK<sub>a</sub>]] 3.77 and 4.76, respectively). Longer-chain fatty acids do not show a great change in pK<sub>a</sub>.  [[Nonanoic acid]], for example, has a pK<sub>a</sub> 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 acid]]s==
The average mass range for amino acids: 75 - 222 Da. By comparison a water molecule is 18 Da. In addition to the proteinogenic [[List of standard amino acids|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 [[Carboxylic acid|carboxyl group]] it is not an aa, but since in its place it does contain a [[Sulfonic acid|sulfonate group]], it may be called an amino sulfonic acid.
==[[Nucleobase]]s==
[[Purine]] (Pur) 120 Da is not a protein. The [[purine]]s are the most widely distributed naturally occurring nitrogen-containing [[heterocycle]].<ref name="Rosemeyer">Rosemeyer, H. ''Chemistry & Biodiversity'' '''2004''', ''1'', 361.</ref> The purine nucleobases include [[adenine]] (A) 135 Da, [[hypoxanthine]] (Hx) 136 Da, [[guanine]] (G) 151 Da, and [[xanthine]] (Xan) 152 Da. The [[pyrimidine]]s include pyrimidine (Pyr) 80 Da, also a heterocycle and naturally occurring, [[cytosine]] (C) 111 Da, [[uracil]] (U) 112 Da, [[thymine]] (T) 126 Da, and [[queuine]] (Q) 275 Da.
==[[Nucleoside]]s==
Nucleosides are [[glycosylamine]]s, a nucleobase linked to a [[ribose]] or [[deoxyribose]] ring. Examples include purines: [[adenosine]] (Ado) 267 Da, [[guanosine]] (Guo) 283 Da, and [[inosine]] (Ino) 268 Da, and pyrimidines: [[cytidine]] (Cyd) 243 Da, [[thymidine]] (Thd) 242 Da, [[uridine]] (Urd) 244 Da, and queuosine (Quo) 409 Da. When the nucleobase is attached to deoxyribose, a 'd' is placed in front of the abbreviation, e.g., dCyd is [[deoxycytidine]] 227 Da and the molar mass decreases by one oxygen from Cyd.
==[[Nucleotide]]s==
Nucleotides such as [[orotidine 5'-monophosphate]] (OMP) range in size from 176 Da (OMP) to 523 Da (GTP). The purine nucleotides involved in RNA or DNA synthesis include: [[inosine monophosphate]] (IMP), [[adenosine triphosphate]] (ATP), and [[guanosine triphosphate]] (GTP). The pyrimidine nucleotides involved include OMP, [[cytidine triphosphate]] (CTP), [[uridine triphosphate]] (UTP), and [[thymidine triphosphate]] (TTP) for DNA in place of UTP. Although rare, higher phosphates do occur such as adenosine tetraphosphate (Ap4) 587 Da. The [[Nucleotide#Deoxynucleotides|deoxyribonucleotides]] have a 'd' in front, like dCTP, except for the thymidine deoxyribonucleotides.
==[[Cofactor (biochemistry)|Cofactor]]s==
Many cofactors are involved in the synthesis of amino acids and nucleotides. They range in size from [[ascorbic acid]] (ASA) 176 Da and [[biotin]] (BIO) 244 Da, which are vitamins, to [[nicotinamide adenine dinucleotide phosphate]] (NADP) 744 Da and flavin adenine dinucleotide ([[FAD]]) 785 Da.
One of the coenzymes essential for the synthesis of amino acids is [[nicotinamide adenine dinucleotide]] (NAD) 663 Da. Besides assembling NAD<sup>+</sup> ''de novo'' from simple amino acid precursors, cells also salvage preformed compounds containing nicotinamide. The three natural compounds containing the nicotinamide ring and used in these salvage metabolic pathways are [[Niacin|nicotinic acid]] (Na), [[nicotinamide]] (Nam) and nicotinamide riboside (NR).<ref name=Tempel>{{cite journal |author=Tempel W, Rabeh WM, Bogan KL, ''et al'' |title=Nicotinamide riboside kinase structures reveal new pathways to NAD+ |journal=PLoS Biol. |volume=5 |issue=10 |pages=e263 |year=2007 |pmid=17914902 |url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=17914902}}</ref> These compounds are also produced within cells, when the nicotinamide group is released from NAD<sup>+</sup> in ADP-ribose transfer reactions. Indeed, the enzymes involved in these salvage pathways appear to be concentrated in the [[cell nucleus]], which may compensate for the high level of reactions that consume NAD<sup>+</sup> in this [[organelle]].<ref name=Anderson>{{cite journal |author=Anderson RM, Bitterman KJ, Wood JG, ''et al'' |title=Manipulation of a nuclear NAD+ salvage pathway delays aging without altering steady-state NAD+ levels |journal=J. Biol. Chem. |volume=277 |issue=21 |pages=18881&ndash;90 |year=2002 |pmid=11884393 |url=http://www.jbc.org/cgi/pmidlookup?view=long&pmid=11884393}}</ref> Nicotinamide mononucleotide adenylyl transferase 1 ([[NMNAT1]]) ({{EC number|2.7.7.1}}) catalyzes a key step of NAD synthesis.<ref name=Schweiger>{{ cite journal |author=Schweiger M, Hennig K, Lerner F, Niere M, Hirsch-Kauffmann M, Specht T, Weise C, Oei SL, Ziegler M |title=Characterization of recombinant human nicotinamide mononucleotide adenylyl transferase (NMNAT), a nuclear enzyme essential for NAD synthesis |journal=FEBS Lett. |volume=492 |issue=1-2 |pages=95-100 |month=Mar |year=2001 |pmid=11248244 }}</ref> It has a [[nuclear localization signal]] (NLS).<ref name=Schweiger/> NMNAT1 may be a substrate for nuclear kinases.<ref name=Schweiger/>
==[[Peptide]]s==
Peptides are short [[polymer]]s formed from the linking, in a defined order, of α-amino acids. [[Protein]]s are polypeptide molecules (or consist of multiple polypeptide subunits). The distinction is that peptides are short and polypeptides/proteins are long. The digestion of dietary proteins produces dipeptides which are absorbed more rapidly than aa. A dipeptide is a molecule consisting of two amino acids joined by a single [[peptide bond]]. Examples of dipeptides include [[carnosine]] (Car) 244 Da, of the amino acids [[Beta-alanine|β-alanine]] (β-Ala) and [[histidine]] (His), homocarnosine (Hcn) 258 Da consisting of [[γ-aminobutyric acid]] (GABA) and His, and [[anserine]] (Ans) 240 Da.
===[[Oligopeptide]]s===
Some [[tripeptide]]s and [[tetrapeptide]]s are synthesized in humans. Oligopeptides can range up to 40 aa (9 kDa) generally.
==Small proteins ([[polypeptide]]s)==
Due to the size limitation of the nuclear pore, these polypeptides would range from 9 kDa to <70 kDa and not need or have a NLS. For example, [[emerin]] 18 kDa (no NLS) mediates inner nuclear membrane anchorage to the [[nuclear lamina]], regulates the flux of [[beta-catenin]] into the nucleus, and interacts with nuclear [[actin]].<ref name=emerin>{{ cite web |title=Entrez Gene: EMD emerin |url=http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=2010&ordinalpos=12&itool=EntrezSystem2.PEntrez.Gene.Gene_ResultsPanel.Gene_RVDocSum }}</ref><ref name=EMD>{{ cite web |title=GENATLAS: GENE Database EMD |url=http://genatlas.medecine.univ-paris5.fr/ }}</ref><ref name=EMERIN>{{ cite web |title=Apropos IpiRecord: IPI00032003 |url=http://apropos.mcw.edu/ipi_records/show/203523 }}</ref>
On the other hand, LEMD1 (20.3 kDa) is involved in the glutamine (Gln) metabolic process<ref name=LEMD1Human>{{ cite web |title=Apropos IpiRecord: IPI00438351 |url=http://apropos.mcw.edu/ipi_records/show/225643 }}</ref> and has a NLS.<ref name=LEMD1>{{ cite web |title=Nuclear Protein Database LEMD1 |url=https://npd.hgu.mrc.ac.uk/search.php?action=builddetails&geneid=1NP02100 }}</ref>
Many of the polypeptides are [[enzyme]]s including [[Protease|peptidase]]s and [[kinase]]s.
===[[Protease]]s===
Carnosinase occurs as EC 3.4.13.3 (Xaa-His [[dipeptidase]]) with Zn<sup>2+</sup> as cofactor, 3.4.13.18 (cytosol nonspecific dipeptidase) with Zn<sup>2+</sup> as cofactor and Mn<sup>2+</sup> activation, and 3.4.13.20 (beta-Ala-His dipeptidase), activated by Cd<sup>2+</sup> and [[citrate]], catalyzing the reaction
Car + H<sub>2</sub>O <=> His + β-Ala.
It is intracellular to the cytosol and can occur in 14 kDa, 35 kDa, and 44 kDa sizes, often forming a homodimer. As a nonspecific dipeptidase, it degrades a number of dipeptides including Car<ref name="Balion">{{cite journal |author=Balion CM, Benson C, Raina PS, Papaioannou A, Patterson C, Ismaila AS |title=Brain type carnosinase in dementia: a pilot study |journal=BMC Neurol. |volume=7 |issue=Nov 5 |pages=38 |year=2007 |pmid=17983474 |url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=17983474}}</ref>, Ans and Hcn<ref name="Balion"/> as EC 3.4.13.3 and EC 3.4.13.20 per the reaction:
Hcn + H<sub>2</sub>O <=> γ-aminobutyric acid (GABA) + His.
Oligopeptides can be degraded by [[aminopeptidase]]s such as EC 3.4.11.6 19-68 kDa forms (intracellular to the cytosol) with Zn<sup>2+</sup> as cofactor and activation by Cl<sup>-</sup> per the reactions:
oligopeptide (n) + H<sub>2</sub>O <=> Lys + oligopeptide (n-1)
oligopeptide (n) + H<sub>2</sub>O <=> Arg + oligopeptide (n-1).
===[[Synthase]]s===
Enzymes EC 2.3.1.37 (cofactor: [[pyridoxal phosphate]], PLP) [[D-Aminolevulinic acid|aminolevulinate]], delta-, synthase 1 (ALAS1) and aminolevulinate, delta-, synthase 2 (ALAS2) anabolically synthesize glycine (Gly) from the amino acid 5-amino-4-oxovaleric acid (ALA) in the two-step reaction:
5-aminolevulinate (C<sub>5</sub>H<sub>9</sub>NO<sub>3</sub>) (ALA) + CO<sub>2</sub> <=> 2-amino-3-oxoadipate (C<sub>6</sub>H<sub>9</sub>NO<sub>5</sub>)
+
2-amino-3-oxoadipate + CoA (C<sub>21</sub>H<sub>36</sub>N<sub>7</sub>O<sub>16</sub>P<sub>3</sub>S) <=> succinyl-CoA (C<sub>25</sub>H<sub>40</sub>N<sub>7</sub>O<sub>19</sub>P<sub>3</sub>S) + Gly
=
5-aminolevulinate + CoA + CO<sub>2</sub> <=> succinyl-CoA + Gly
The mRNA for ALAS1 is 82 kDa, the intracellular precursor is a homodimer of 71 kDa, and the mitochondrial mature protein is 65 kDa. But, ALAS1 also occurs in a 30 kDa form.<ref name=IPI00789294>{{ cite web |title=Apropos IpiRecord: IPI00789294 ALAS1, 30 KDA PROTEIN |url=http://apropos.mcw.edu/ipi_records/show/248710 }}</ref>
CTP synthase EC 6.3.4.2 is the final step in the de novo synthesis of CTP from UTP. As a monomer 67 kDa or dimer it is inactive because three monomers contribute to ligand binding at the active site.<ref name=Kursula>{{ cite journal |author=Kursula P, Flodin S, Ehn M, Hammarstrom M, Schüler H, Nordlund P, Stenmark P |title=Structure of the synthetase domain of human CTP synthetase, a target for anticancer therapy |journal= Acta Crystallogr Sect F Struct Biol Cryst Commun. |volume=62 |issue=Pt 7 |month=Jul |year=2006 |pages=613-7 |doi=10.1107/S1744309106018136 |pmid=16820675 }}</ref> The active form is a homotetramer (a dimer of dimers), with no NLS, intracellular to the cytosol,<ref name=Kursula/><ref name=CTPS1>{{ cite web |title=GENATLAS : GENE Database CTPS |url=http://genatlas.medecine.univ-paris5.fr/ }}</ref> for the following reactions.
UTP + Gln + ATP + H<sub>2</sub>O <=> CTP + Glu + ADP + P<sub>i</sub>
ATP + UTP + NH<sub>3</sub> <=> ADP + P<sub>i</sub> + CTP
The reactions
2 ATP + HCO<sub>3</sub><sup>-</sup> + NH<sub>3</sub> <=> 2 ADP + P<sub>i</sub> + [[carbamoyl phosphate]] (multistep)<ref name=R07641>{{ cite web |title=KEGG REACTION: R07641 |url=http://www.genome.jp/dbget-bin/www_bget?rn+R07641 }}</ref>
Gln + H<sub>2</sub>O <=> Glu + NH<sub>3</sub><ref name=R00256>{{ cite web |title=KEGG REACTION: R00256 |url=http://www.genome.jp/dbget-bin/www_bget?rn+R00256 }}</ref>
2 ADP + P<sub>i</sub> + Glu + carbamoyl phosphate <=> 2 ATP + Gln + HCO<sub>3</sub><sup>-</sup> + H<sub>2</sub>O<ref name=R00575>{{ cite web |title=KEGG REACTION: R00575 |url=http://www.genome.jp/dbget-bin/www_bget?rn+R00575 }}</ref>
are catalyzed by EC 6.3.5.5 [[Carbamoyl phosphate synthase II|carbamoyl-phosphate synthase II]] (CAD). It has no NLS, occurs as a homohexamer, uses Zn<sup>2+</sup> as a cofactor and is intracellular to the nucleus.<ref name=CAD-G>{{ cite web |title=GENATLAS : GENE Database CAD |url=http://genatlas.medecine.univ-paris5.fr/ }}</ref> It does occur in a 22 kDa form.<ref name=IPI00301263>{{ cite web |title=Apropos IpiRecord: IPI00301263 CAD |url=http://apropos.mcw.edu/ipi_records/show/215745 }}</ref>


===[[Polymerase]]s===
===[[Polymerase]]s===
Line 134: Line 24:
Many of the subunits of [[RNA polymerase II]] ({{EC number|2.7.7.6}}) are small polymerases. RNA polymerase IIC ([[POLR2C|PolR2C]]) has a mass of 33 kDa, no NLS, is intracellular to the nucleus and is part of the transcription complex. Of the others, PolR2D-L are 19 kDa or less without NLS, except RNA polymerase IIE ([[POLR2E|PolR2E]]) 23 kDa has a NLS and is the only one that localizes to the nucleolus.<ref name=POLR2E>{{ cite web |title=Nuclear Protein Database DNA-directed RNA polymerase II 23 kDa polypeptide |url=https://npd.hgu.mrc.ac.uk/search.php?action=builddetails&geneid=1NP01403 }}</ref> Although PolR2K and [[POLR2L|PolR2L]] are small enough in mass to be considered oligopeptides, their numbers of aa are over the usual limit: 58 aa and 67 aa, respectively, in humans.
Many of the subunits of [[RNA polymerase II]] ({{EC number|2.7.7.6}}) are small polymerases. RNA polymerase IIC ([[POLR2C|PolR2C]]) has a mass of 33 kDa, no NLS, is intracellular to the nucleus and is part of the transcription complex. Of the others, PolR2D-L are 19 kDa or less without NLS, except RNA polymerase IIE ([[POLR2E|PolR2E]]) 23 kDa has a NLS and is the only one that localizes to the nucleolus.<ref name=POLR2E>{{ cite web |title=Nuclear Protein Database DNA-directed RNA polymerase II 23 kDa polypeptide |url=https://npd.hgu.mrc.ac.uk/search.php?action=builddetails&geneid=1NP01403 }}</ref> Although PolR2K and [[POLR2L|PolR2L]] are small enough in mass to be considered oligopeptides, their numbers of aa are over the usual limit: 58 aa and 67 aa, respectively, in humans.


===[[Kinase]]s===
==Large particles==


EC 3.6.1.5 (cofactor: Ca<sup>2+</sup>) catalyzes the following reactions:
Larger particles are also able to pass through the large diameter of a nuclear pore but at almost negligible rates.<ref name=Campbell>{{cite book |last=Campbell |first=Neil A. |title=Biology |year=1987 |isbn=0-8053-1840-2 |pages=795}}</ref> However, the nucleohyaloplasm does contain large amounts of [[macromolecule]]s, which can alter how molecules behave, through [[macromolecular crowding]]. Since some of these macromolecules have less volume to move in, their [[activity (chemistry)|effective concentration]] is increased. This crowding effect can produce large changes in both the [[reaction rate|rates]] and [[chemical equilibrium]] for reactions in the nucleohyaloplasm.<ref name=Ellis>{{cite journal |author=Ellis RJ |title=Macromolecular crowding: obvious but underappreciated |journal=Trends Biochem. Sci. |volume=26 |issue=10 |pages=597–604 |year=2001 |month=October |pmid=11590012 |doi=10.1016/S0968-0004(01)01938-7}}</ref> It is particularly important in its ability to alter [[dissociation constant]]s by favoring the association of macromolecules, such as when multiple proteins come together to form [[protein complex]]es, or when [[DNA-binding protein]]s bind to their targets in the [[genome]].<ref name=Zhou>{{cite journal |author=Zhou HX, Rivas G, Minton AP |title=Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences |journal=Annu Rev Biophys |volume=37 |issue= |pages=375–97 |year=2008 |pmid=18573087 |doi=10.1146/annurev.biophys.37.032807.125817}}</ref>


AMP + P<sub>i</sub> <=> ADP + H<sub>2</sub>O
===Proteins===


AMP + 2 P<sub>i</sub> <=> ATP + 2 H<sub>2</sub>O
Proteins larger than those allowed through a nuclear pore by passive transport require a [[nuclear localization signal]] (NLS). This is an amino acid sequence that targets the cytosolic nuclear transport receptors of the [[Nuclear pore|nuclear pore complex]]. A nuclear import NLS will bind strongly to [[importin]], while an export NLS ([[nuclear export signal]], NES) binds to an [[exportin]]. For example, [[RNA polymerase II]]A (Rbp1) 220kDa has a NLS.<ref name=POLR2A>{{ cite web |title=Nuclear Protein Database: DNA-directed RNA polymerase II largest subunit |url=https://npd.hgu.mrc.ac.uk/search.php?action=builddetails&geneid=1NP01404 | accessdate = }}</ref>


ADP + P<sub>i</sub> <=> ATP + H<sub>2</sub>O
===Nuclear localization===


CMP + P<sub>i</sub> <=> CDP + H<sub>2</sub>O
The subcellular distribution of a substance to or within the nucleus is often referred to as '''nuclear localization'''.<ref name=Nieva>{{ cite journal |author=Nieva C, Gwoźdź T, Dutko-Gwoźdź J, Wiedenmann J, Spindler-Barth M, Wieczorek E, Dobrucki J, Duś D, Henrich V, Ożyhar A, Spindler KD |title=Ultraspiracle promotes the nuclear localization of ecdysteroid receptor in mammalian cells |year=2005 |journal=Biol Chem. |volume=386 |issue=5 |pages=463-70 |doi=10.1515/BC.2005.055 }}</ref> Many mechanisms have been found that produce nuclear localization in addition to a NLS.


CMP + 2 P<sub>i</sub> <=> CTP + 2 H<sub>2</sub>O
[[PLAGL1|Zac1]] is a seven-zinc-finger transcription factor that preferentially binds GC-rich DNA elements and has intrinsic transactivation activity.<ref name=Huang>{{ cite journal |author=Huang SM, Huang SP, Wang SL, Liu PY |title=Importin α1 is involved in the nuclear localization of Zac1 and the induction of p21WAF1/CIP1 by Zac1 |journal=Biochem J. |volume=402 |issue=Pt 2 |month=Mar |year=2007 |pages=359-66 |doi=10.1042/BJ20061295 |pmid=17109628 }}</ref> The zinc-finger motif is of a Cys<sub>2</sub>His<sub>2</sub>-type.<ref name=Huang/> This motif is involved in [[DNA-binding domain|DNA binding]], [[Dimer|dimerization]], [[transactivation]] activity, and nuclear localization of Zac1 through interacting with [[importin]] α<sub>1</sub>.<ref name=Huang/> Zac1 has no typical NLS.<ref name=Huang/> Any two or more zinc-finger motifs act in concert to facilitate nuclear localization.<ref name=Huang/> Apparently, as with importin α transport of [[Ca2+/calmodulin-dependent protein kinase|CaMKIV]] to the nucleus, importin α<sub>1</sub> may mediate transport of Zac1 to the nucleus without the involvement of [[Nuclear pore|importin β]].<ref name=Huang/> But, some other factors are involved, perhaps Ran-binding proteins such as [[RANBP9|RanBPM]] and Mog1<ref name=RANGRF>{{ cite web |title=Entrez Gene: RANGRF RAN guanine nucleotide release factor |url=http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=29098&ordinalpos=1&itool=EntrezSystem2.PEntrez.Gene.Gene_ResultsPanel.Gene_RVDocSum }}</ref>, which play roles in nucleocytoplasmic transport and [[transcription factor]] recruitment.<ref name=Huang/>


CDP + P<sub>i</sub> <=> CTP + H<sub>2</sub>O
===[[Transcription (genetics)#Transcription factories|Transcription factories]]===


GMP + P<sub>i</sub> <=> GDP + H<sub>2</sub>O
Active transcription units are clustered in the nucleus, in discrete sites called ‘transcription factories’. Such sites can be visualized after allowing engaged polymerases to extend their transcripts in tagged precursors (Br-UTP or Br-U), and immuno-labeling the tagged nascent RNA. Transcription factories can also be localized using fluorescence in situ hybridization, or marked by antibodies directed against polymerases. There are ~8,000 [[RNA polymerase II|polymerase II]] factories in the nucleoplasm of a [[HeLa cell]]. Each polymerase II factory contains ~8 polymerases. As most active transcription units are associated with only one polymerase, each factory can be associated with ~8 different transcription units. That's ~64,000 polymerase II active transcription units. These units might be associated through promoters and/or enhancers, with loops forming a ‘cloud’ around the factory.


GMP + 2 P<sub>i</sub> <=> GTP + 2 H<sub>2</sub>O
===[[RNA]]===


GDP + P<sub>i</sub> <=> GTP + H<sub>2</sub>O
Of the many different types of RNA that can occur within a cell, most also can occur dissolved in the nucleohyaloplasm. In addition to [[Messenger RNA|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<ref name= DISC2 >{{cite web | title = Entrez Gene: DISC2 disrupted in schizophrenia 2 (non-protein coding)| url = http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=27184| accessdate = }}</ref>, [[microRNA]], [[piwi-interacting RNA]] (piRNA), [[small interfering RNA]] (siRNA), [[7SL RNA|signal recognition particle RNA]] (SRP RNA), and [[guide RNA]] (gRNA).


UMP + P<sub>i</sub> <=> UDP + H<sub>2</sub>O
Each has to be [[Transcription (genetics)|transcribed]] from the applicable portion of [[DNA]] in the [[euchromatin]]. The unfolded structure of euchromatin allows gene regulatory proteins and [[RNA polymerase]] (RNAP) complexes to bind to the DNA sequence, which can then initiate the transcription process. Control of the process of gene transcription affects patterns of gene expression and thereby allows a cell to adapt to a changing environment, perform specialized roles within an organism, and maintain basic metabolic processes necessary for survival. RNAP can initiate [[transcription]] at specific DNA sequences known as [[promoter]]s. It then produces an RNA chain which is [[Complementarity (molecular biology)|complementary]] to the template DNA strand.


UMP + 2 P<sub>i</sub> <=> UTP + 2 H<sub>2</sub>O
{| class="wikitable sortable"
|+ RNAs involved in protein synthesis
|-
! Type !! Abbr. !! Function !! Distribution !! Ref.
|-
| [[Messenger RNA]] || mRNA || [[Genetic code|Codes]] for protein  || All cells
|-
| [[Ribosomal RNA]] || rRNA || [[Translation (genetics)|Translation]] || All cells
|-
| [[7SL RNA|Signal recognition particle RNA]] || 7SL RNA or SRP RNA|| Membrane integration / mRNA tagging for export|| All organisms ||<ref name= Gribaldo >{{cite journal | author=Gribaldo S, Brochier-Armanet C| title=The origin and evolution of Archaea: a state of the art| journal=Philos Trans R Soc Lond B Biol Sci.| year=2006| volume=361 | issue=1470| pages=1007–22| pmid=16754611| doi=10.1098/rstb.2006.1841}}</ref>
|-
| [[Transfer RNA]] || tRNA || Translation || All cells
|-
| [[tmRNA|Transfer-messenger RNA]] || tmRNA || Rescuing stalled ribosomes Terminating translation || Bacteria ||<ref name=Gillet>{{cite journal | author=Gillet R, Felden B| title=Emerging views on tmRNA-mediated protein tagging and ribosome rescue | journal = Molecular Microbiology| volume=42| issue=4 | pages=879–85| year=2001| doi=10.1046/j.1365-2958.2001.02701.x }}</ref>
|-
|}


UDP + P<sub>i</sub> <=> UTP + H<sub>2</sub>O
{| class="wikitable sortable"
|+ RNAs involved in post-transcriptional modification or DNA replication
|-
! Type !! Abbr. !! Function !! Distribution !! Ref.
|-
| [[Small nuclear RNA]] || snRNA || Splicing and other functions || [[Eukaryote]]s and [[archaea]] ||<ref name= Thore >{{cite journal | author=Thore S, Mayer C, Sauter C, Weeks S, Suck D| title=Crystal Structures of the ''Pyrococcus abyssi'' Sm Core and Its Complex with RNA | journal=J. Biol. Chem.| year=2003| volume=278| issue=2| pages=1239–47| doi=10.1074/jbc.M207685200 |url=http://www.jbc.org/cgi/content/full/278/2/1239 }}</ref>
|-
| [[Small nucleolar RNA]] || snoRNA || Nucleotide modification of RNAs [[RNA editing]] || Eukaryotes and archaea ||<ref name=Kiss>{{cite journal | author=Kiss T| title=Small nucleolar RNA-guided post-transcriptional modification of cellular RNAs| journal=The EMBO Journal| year=2001| volume=20| pages=3617–22| doi=10.1093/emboj/20.14.3617 |url=http://www.nature.com/emboj/journal/v20/n14/full/7593858a.html}}</ref>
|-
| [[SmY RNA]] || SmY || mRNA trans-splicing || Nematodes || <ref name=Jones>{{cite journal |author=Jones TA, Otto W, Marz M, Eddy SR, Stadler PF |title=A survey of nematode SmY RNAs |journal=RNA Biol |volume=6 |issue=1 |pages=5–8 |year=2009 |pmid=19106623 |doi= |url=http://www.landesbioscience.com/journals/rna/abstract.php?id=7634}}</ref>
|-
| [[Small Cajal body-specific RNA]] || scaRNA || Type of snoRNA; Nucleotide modification of RNAs || ||
|-
| [[Guide RNA]] || gRNA || mRNA nucleotide modification / [[RNA editing]] || [[Kinetoplastid]] [[mitochondria]] ||<ref name=Alfonzo>{{cite journal | author=Alfonzo JD, Thiemann O, Simpson L | title=The mechanism of U insertion/deletion RNA editing in kinetoplastid mitochondria| journal=Nucleic Acids Research| year=1997| volume=25| issue=19| pages=3751–59| pmid=9380494 | doi=10.1093/nar/25.19.3751 |url=http://nar.oxfordjournals.org/cgi/content/abstract/25/19/3751}}</ref>
|-
| [[RNase P|Ribonuclease P]] || RNase P || tRNA maturation || All organisms ||<ref>{{cite journal | author=Pannucci JA, Haas ES, Hall TA, Harris JK, Brown JW| title=RNase P RNAs from some Archaea are catalytically active | journal=Proc Natl Acad Sci USA| year=1999| volume=96 | issue=14| pages=7803–08| pmid=10393902| doi=10.1073/pnas.96.14.7803}}</ref>
|-
| [[RNase MRP|Ribonuclease MRP]] || RNase MRP || rRNA maturation, [[DNA replication]] || Eukaryotes ||<ref>{{cite journal | author=Woodhams MD, Stadler PF, Penny D, Collins LJ| title=RNase MRP and the RNA processing cascade in the eukaryotic ancestor| journal=BMC Evolutionary Biology| year=2007| volume=7| pages=S13| doi=10.1186/1471-2148-7-S1-S13}}</ref>
|-
| [[Y RNA]] || || RNA processing, DNA replication || Animals ||<ref>{{cite journal | author=Perreault J, Perreault J-P, Boire G| title=Ro-associated Y RNAs in metazoans: evolution and diversification| journal=Molecular Biology and Evolution | year=2007 | volume=24| issue=8| pages=1678–89 | doi=10.1093/molbev/msm084}}</ref>
|-
| [[Telomerase RNA]] || || [[Telomere]] synthesis || Most eukaryotes ||<ref>{{cite journal | author=Lustig AJ| title=Crisis intervention: The role of telomerase| journal=Proc Natl Acad Sci USA | year=1999| volume=96| issue=7| pages=3339–41| pmid=10097039| doi=10.1073/pnas.96.7.3339}}</ref>
|-
| [[Ribozyme]] || || [[Catalysis]] || All cells
|-
| [[Transposon]] || || Self-propagating || All cells
|-
|}


Ca<sup>2+</sup> or Mg<sup>2+</sup> can serve as activating ions. [[ENTPD1]] (CD39) is a 56 kDa protein.<ref name=CD39>{{ cite web |title=Apropos IpiRecord: IPI00382672 |url=http://apropos.mcw.edu/ipi_records/show/218991 }}</ref> CD39 associates with RanBPM ([[RANBP9]]).<ref name=Wu>{{ cite journal |author=Wu Y, Sun X, Kaczmarek E, Dwyer KM, Bianchi E, Usheva A, Robson SC |title=RanBPM associates with CD39 and modulates ecto-nucleotidase activity |journal=Biochem J. |volume=396 |issue=1 |month=May |year=2006 |pages=23-30 |pmid= 16478441 }}</ref> RANBP9 (90 kDa)<ref name=RANBPM>{{ cite web |title=GENATLAS: GENE Database RANBP9 |url=http://genatlas.medecine.univ-paris5.fr/ }}</ref> binds [[Ran (biology)|Ran]], a small GTP binding protein that is essential for the translocation of RNA and proteins through the nuclear pore complex.<ref name=RANBP9>{{ cite web |title=Entrex Gene: RANBP9 RAN binding protein 9 |url=http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=10048&ordinalpos=1&itool=EntrezSystem2.PEntrez.Gene.Gene_ResultsPanel.Gene_RVDocSum }}</ref> RanBPM localizes in the nucleus and cytoplasm,<ref name=Wu/> but RanBPM has no NLS. CANT1 (EC 3.6.1.6 and 3.6.1.5) 49 kDa<ref name=CANT1>{{ cite web |title=Apropos IpiRecord: IPI00413533 |url=http://apropos.mcw.edu/ipi_records/show/223868 }}</ref> catalyzes similar reactions:
{| class="wikitable sortable"
 
|+ Regulatory RNAs
a nucleotide + P<sub>i</sub> <=> a nucleoside diphosphate + H<sub>2</sub>O,
|-
 
! Type !! Abbr. !! Function !! Distribution !! Ref.
also acting on IDP, GDP, UDP and on D-ribose 5-diphosphate.<ref name=3.6.1.6>{{ cite web |title=NiceZyme View of ENZYME: EC 3.6.1.6 |url=http://www.expasy.org/cgi-bin/nicezyme.pl?3.6.1.6 }}</ref> ENTPD7 (EC 3.6.1.-) occurs in the mouse nucleus.<ref name=3.6.1.->{{ cite web |title=Apropos IpiRecord: IPI00828276 |url=http://apropos.mcw.edu/ipi_records/show/306338 }}</ref>
|-
 
| [[Antisense RNA]] || aRNA || Transcriptional attenuation / mRNA degradation / mRNA stabilisation / Translation block Gene regulation || All organisms ||<ref name=Brantl1>{{cite journal | author=Brantl S| title=Antisense-RNA regulation and RNA interference| journal=Biochimica et Biophysica Acta| year=2002| volume=1575| issue=1–3| pages=15–25| pmid=12020814}}</ref><ref name=Brantl2>{{cite journal |author=Brantl S |title=Regulatory mechanisms employed by cis-encoded antisense RNAs |journal=Curr Opin Microbiol. |volume=10 |issue=2 |pages=102–9 |year=2007 |pmid=17387036 |doi=10.1016/j.mib.2007.03.012}}</ref>
Enzymes 2.4.2.7 [[adenine phosphoribosyltransferase]] (APRT) 19.4 kDa (forms a dimer, 38.8 kDa) is intracellular (cytoplasm)<ref name=APRT>{{ cite web |title=GENATLAS : GENE Database APRT |url=http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol=APRT }}</ref> and 2.4.2.8 [[Hypoxanthine-guanine phosphoribosyltransferase|hypoxanthine phosphoribosyltransferase]] 1 (HPRT1) 24 kDa (forms a tetramer, 96 kDa) is intracellular (cytosolic)<ref name=HPRT1>{{ cite web |title=GENATLAS : GENE Database HPRT1 |url=http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol=HPRT1 }}</ref> catalyze the following reaction:
|-
 
| [[Cis-natural antisense transcript]] || || Gene regulation || ||
[[Adenine]] + [[Phosphoribosyl pyrophosphate|5-phospho-alpha-D-ribose 1-diphosphate]] (PRPP) <=> AMP + PP<sub>i</sub>
|-
 
| [[CRISPR]] RNA || crRNA || Resistance to parasites, probably by targeting their DNA || Bacteria and archaea ||<ref>{{cite journal |author=Brouns SJ, Jore MM, Lundgren M, ''et al'' |title=Small CRISPR RNAs guide antiviral defense in prokaryotes |journal=Science (New York, N.Y.) |volume=321 |issue=5891 |pages=960–4 |year=2008 |month=August |pmid=18703739 |doi=10.1126/science.1159689}}</ref>
Neither APRT nor HPRT1 has a NLS. APRT is a dimer in solution at pH 6.5, but a monomer at pH 8.0, and like HPRT1 needs Mg<sup>2+</sup>, or Mn<sup>2+</sup>.<ref name=Phillips>{{ cite journal |author=Phillips CL, Ullman B, Brennan RG, Hill CP |title=Crystal structures of adenine phosphoribosyltransferase from Leishmania donovani |journal=EMBO J. |volume=18 |issue=13 |pages=3533-45 |month= |year=1999 |doi=10.1093/emboj/18.13.3533 |pmid= 10393170 |url=http://www.nature.com/emboj/journal/v18/n13/full/7591771a.html }}</ref>
|-
 
| [[Long noncoding RNA]] || Long&nbsp;ncRNA || Various || Eukaryotes ||
Enzymes EC 3.6.1.5 ATP pyrophosphohydrolase, ADPase<ref name=Moodie>{{cite journal |author=Moodie FDL, Baum H, Peter J, Butterworth PJ, Timothy J, Peters TJ |title=Purification and characterisation of bovine spleen ADPase |journal=Eur. J. Biochem. |volume=202 |issue=3 |pages=1209-15 |year=1991 |pmid=1837267 |month=April}}</ref>/ADP synthase<ref name=Goodman>{{cite journal |author=Goodman JM |title=The gregarious lipid droplet |journal=J Biol Chem. |volume=283 |issue=42 |pages=28005-9 |year=2008 |pmid=18611863 |month=Oct | doi=10.1074/jbc.R80004220}}</ref> ectonucleoside triphosphate diphosphohydrolase 1 (ENTPD1) 56 kDa catalyzes the conversion of AMP into ADP (see below). Cofactor: Ca<sup>2+</sup>.<ref name=3.6.1.5>{{cite web | title = NiceZyme View of ENZYME: EC 3.6.1.5| url = http://www.expasy.org/cgi-bin/nicezyme.pl?3.6.1.5| accessdate = }}</ref> Ca<sup>2+</sup> or Mg<sup>2+</sup> can serve as activating ions. Also acts on ADP, and on other nucleoside triphosphates and diphosphates.<ref name=3.6.1.5/>
|-
 
| [[MicroRNA]] || miRNA || Gene regulation || Most eukaryotes ||<ref name=Lin>{{cite journal | author=Lin S-L, Miller JD, Ying S-Y| title=Intronic microRNA (miRNA)| journal=Journal of Biomedicine and Biotechnology| year=2006 |pages=1–13| pmid=17057362| doi=10.1155/JBB/2006/26818| volume=2006}}</ref>
AMP + P<sub>i</sub> <=> ADP + H<sub>2</sub>O
|-
 
| [[Piwi-interacting RNA]] || piRNA || Transposon defense Gene regulation|| Animal [[germline]] cells ||<ref name=Horwich>{{cite journal | author=Horwich MD, Li C Matranga C, Vagin V, Farley G, Wang P, Zamore PD| title=The ''Drosophila'' RNA methyltransferase, DmHen1, modifies germline piRNAs and single-stranded siRNAs in RISC| journal=Current Biology| year=2007| volume=17| pages=1265–72| doi=10.1016/j.cub.2007.06.030}}</ref><ref name=Ghildiyal>{{cite journal |author=Ghildiyal M, Zamore PD |title=Small silencing RNAs: an expanding universe |journal=Nat. Rev. Genet. |volume=10 |issue=2 |pages=94–108 |year=2009 |month=February |pmid=19148191 |doi=10.1038/nrg2504}}</ref>
Enzymes EC 2.7.4.6 [[nucleoside-diphosphate kinase]]s A, B, C, D (NDKA-D) catalyzes the following reaction inside the nucleohyaloplasm as it is intracellular (nucleus)<ref name=NME3>{{ cite web |title=GENATLAS : GENE Database NME3 |url=http://genatlas.medecine.univ-paris5.fr/fiche.php?symbol=NME3 }}</ref> and each gene is translated as a 7-11 kDa particle<ref name=NDKA>{{ cite web |title=Apropos IpiRecord: IPI00012048 |url=http://apropos.mcw.edu/ipi_records/show/198245 }}</ref>. However, these kinases exist either as tetramers (28-44 kDa) in bacteria or hexamers (42-66 kDa).<ref name=cd04413>{{ cite web |title=NCBI Conserved Domains cd04413: NDPK_I |url=http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=58528 }}</ref> Once the hexamer has formed the particle may be too big to pass through the nuclear pores. NDKA has been shown to mediate transcription, associate with a promoter region of a gene, and be a member of the SET or INHAT complex which can modulate gene expression.<ref name=Curtis>{{ cite journal |author=Curtis CD, Likhite VS, McLeod IX, Yates JR, Narulli AM |title=Interaction of the Tumor Metastasis Suppressor Nonmetastatic Protein 23 Homologue H1 and Estrogen Receptor {alpha} Alters Estrogen-Responsive Gene Expression |journal=Cancer Res. |volume=67 |issue=21 |pages=10600-7 |month=Nov |year=2007 |doi=1158/0008-5472.CAN-07-0055 |pmid=17975005 }}</ref> Nucleoside-diphosphate kinase does form nuclear and cytoplasmic hexamers.<ref name=Klouckova>{{ cite journal |author=Klouckova I, Hrncirova P, Mechref Y, Arnold RJ, Li TK, McBride WJ, Novotny MV |title=Changes in liver protein abundance in inbred alcohol-preferring rats due to chronic alcohol exposure, as measured through a proteomics approach |journal=Proteomics. |volume=6 |issue=10 |pages=3060-74 |month=May |year=2006 |doi=0.1002/pmic.200500725 |pmid= 16619309 }}</ref> NDKA-D do not have a NLS.
|-
 
| [[Small interfering RNA]] || siRNA || Gene regulation || Most [[eukaryote]]s ||<ref name=Ahmad>{{cite journal | author=Ahmad K, Henikoff S | title=Epigenetic consequences of nucleosome dynamics | journal=Cell| year=2002| volume=111 | issue=3| pages=281–84| doi=10.1016/S0092-8674(02)01081-4}}</ref>
ADP + GTP <=> ATP + GDP
|-
 
| [[Trans-acting siRNA]] || tasiRNA || Gene regulation || Land plants||<ref>{{cite journal | author=Vazquez F, Vaucheret H| title=Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs| journal=Mol. Cell| issue=16 | year=2004 |pages=1–13| pmid=17057362}}</ref>
===[[Transaminase]]s===
|-
 
| [[rasiRNA|Repeat associated siRNA]] || rasiRNA || Type of piRNA; transposon defense|| Drosophila || <ref>{{cite journal |author=Desset S, Buchon N, Meignin C, Coiffet M, Vaury C |title=In Drosophila melanogaster the COM locus directs the somatic silencing of two retrotransposons through both Piwi-dependent and -independent pathways |journal=PLoS ONE |volume=3 |issue=2 |pages=e1526 |year=2008 |pmid=18253480 |pmc=2211404 |doi=10.1371/journal.pone.0001526}}</ref>
In catabolic [[transamination]], with PLP as a cofactor, EC 2.6.1.2 transfers the amine from glutamic acid (glutamate) (Glu) to alanine (Ala) via a two step reaction:
|-
 
|}
PLP + Glu <=> pyridoxamine monophosphate (PMP) + [[Alpha-ketoglutaric acid|α-ketoglutarate]] (2-oxoglutarate)
 
+
 
PMP + pyruvate <=> PLP + Ala
 
=
 
[[Pyruvic acid|pyruvate]] + Glu <=> Ala + 2-oxoglutarate.
 
Although this enzyme has several different names, e.g., [[alanine transaminase]], glutamic-pyruvate transaminase (GPT), or alanine aminotransferase, it can occur as a monomer of 55 kDa or homodimer of 101 kDa, and as either a cytosolic (GPT1), or mitochondrial form (GPT2).
 
===[[Synthetase]]s===
 
The reactions
 
ATP + Glu + NH<sub>3</sub> (or NH<sub>4</sub><sup>+</sup>) <=> ADP + P<sub>i</sub> + Gln
 
ATP + Asp + NH<sub>4</sub><sup>+</sup> <=> ADP + P<sub>i</sub> + Asn
 
ATP + Asp + NH<sub>4</sub><sup>+</sup> <=> AMP + PP<sub>i</sub> + Asn
 
are catalyzed by the enzyme EC 6.3.1.2 glutamine synthetase (GS), glutamine-ammonia ligase (GLUL). GLUL 42 kDa is intracellular, occurs as a homooctamer,<ref name=GLNS>{{ cite web |title=GENATLAS : GENE Database GLUL |url=http://genatlas.medecine.univ-paris5.fr/ }}</ref>, also as 12 kDa and 22 kDa forms,<ref name=IPI00830929>{{ cite web |title=Apropos IpiRecord: IPI00830929 |url=http://apropos.mcw.edu/ipi_records/show/307659 }}</ref> and complexes with phosphate, ADP, and Mn<sup>2+</sup>.
 
=Large particles=
 
Larger particles are also able to pass through the large diameter of a nuclear pore but at almost negligible rates.<ref name=Campbell>{{cite book |last=Campbell |first=Neil A. |title=Biology |year=1987 |isbn=0-8053-1840-2 |pages=795}}</ref> However, the nucleohyaloplasm does contain large amounts of [[macromolecule]]s, which can alter how molecules behave, through [[macromolecular crowding]]. Since some of these macromolecules have less volume to move in, their [[activity (chemistry)|effective concentration]] is increased. This crowding effect can produce large changes in both the [[reaction rate|rates]] and [[chemical equilibrium]] for reactions in the nucleohyaloplasm.<ref name=Ellis>{{cite journal |author=Ellis RJ |title=Macromolecular crowding: obvious but underappreciated |journal=Trends Biochem. Sci. |volume=26 |issue=10 |pages=597–604 |year=2001 |month=October |pmid=11590012 |doi=10.1016/S0968-0004(01)01938-7}}</ref> It is particularly important in its ability to alter [[dissociation constant]]s by favoring the association of macromolecules, such as when multiple proteins come together to form [[protein complex]]es, or when [[DNA-binding protein]]s bind to their targets in the [[genome]].<ref name=Zhou>{{cite journal |author=Zhou HX, Rivas G, Minton AP |title=Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences |journal=Annu Rev Biophys |volume=37 |issue= |pages=375–97 |year=2008 |pmid=18573087 |doi=10.1146/annurev.biophys.37.032807.125817}}</ref>
 
==Proteins==
 
Proteins larger than those allowed through a nuclear pore by passive transport require a [[nuclear localization signal]] (NLS). This is an amino acid sequence that targets the cytosolic nuclear transport receptors of the nuclear pore complex. A nuclear import NLS will bind strongly to [[importin]], while an export NLS ([[nuclear export signal]], NES) binds to an [[exportin]]. For example, [[RNA polymerase II]]A (Rbp1) 220kDa has a NLS.<ref name=POLR2A>{{ cite web |title=Nuclear Protein Database: DNA-directed RNA polymerase II largest subunit |url=https://npd.hgu.mrc.ac.uk/search.php?action=builddetails&geneid=1NP01404 | accessdate = }}</ref>
 
==Nuclear localization==
 
[[PLAGL1|Zac1]] is a seven-zinc-finger transcription factor that preferentially binds GC-rich DNA elements and has intrinsic transactivation activity.<ref name=Huang>{{ cite journal |author=Huang SM, Huang SP, Wang SL, Liu PY |title=Importin α1 is involved in the nuclear localization of Zac1 and the induction of p21WAF1/CIP1 by Zac1 |journal=Biochem J. |volume=402 |issue=Pt 2 |month=Mar |year=2007 |pages=359-66 |doi=10.1042/BJ20061295 |pmid=17109628 }}</ref> The zinc-finger motif is of a Cys<sub>2</sub>His<sub>2</sub>-type.<ref name=Huang/> This motif is involved in [[DNA-binding domain|DNA binding]], [[Dimer|dimerization]], [[transactivation]] activity, and nuclear localization of Zac1 through interacting with [[importin]] α<sub>1</sub>.<ref name=Huang/> Zac1 has no typical NLS.<ref name=Huang/> Any two or more zinc-finger motifs act in concert to facilitate nuclear localization.<ref name=Huang/> Apparently, as with importin α transport of [[Ca2+/calmodulin-dependent protein kinase|CaMKIV]] to the nucleus, importin α<sub>1</sub> may mediate transport of Zac1 to the nucleus without the involvement of [[Nuclear pore|importin β]].<ref name=Huang/> But, some other factors are involved, perhaps Ran-binding proteins such as [[RANBP9|RanBPM]] and Mog1<ref name=RANGRF>{{ cite web |title=Entrez Gene: RANGRF RAN guanine nucleotide release factor |url=http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=29098&ordinalpos=1&itool=EntrezSystem2.PEntrez.Gene.Gene_ResultsPanel.Gene_RVDocSum }}</ref>, which play roles in nucleocytoplasmic transport and [[transcription factor]] recruitment.<ref name=Huang/>
 
==[[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 [[Messenger RNA|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<ref name= DISC2 >{{cite web | title = Entrez Gene: DISC2 disrupted in schizophrenia 2 (non-protein coding)| url = http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=27184| accessdate = }}</ref>, [[microRNA]], [[piwi-interacting RNA]] (piRNA), [[small interfering RNA]] (siRNA), [[7SL RNA|signal recognition particle RNA]] (SRP RNA), and [[guide RNA]] (gRNA).


[[Ribozyme]]s 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 Mg<sup>2+</sup> as cofactors. Ribozyme RNase P 30kDa has a NLS.<ref name=RNaseP>{{ cite web |title=Nuclear Protein Database: Rnase P 30kD |url=https://npd.hgu.mrc.ac.uk/search.php?action=builddetails&geneid=1NP00372 |accessdate= }}</ref> But, RNase P subunit p25 (25 kDa), which is also localized to the nucleolus does not.<ref name=RPP25>{{ cite web |title=Nuclear Protein Database: RPP25 |url=https://npd.hgu.mrc.ac.uk/search.php?action=builddetails&geneid=1NP02179 |accessdate= }}</ref>
[[Ribozyme]]s 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 Mg<sup>2+</sup> as cofactors. Ribozyme RNase P 30kDa has a NLS.<ref name=RNaseP>{{ cite web |title=Nuclear Protein Database: Rnase P 30kD |url=https://npd.hgu.mrc.ac.uk/search.php?action=builddetails&geneid=1NP00372 |accessdate= }}</ref> But, RNase P subunit p25 (25 kDa), which is also localized to the nucleolus does not.<ref name=RPP25>{{ cite web |title=Nuclear Protein Database: RPP25 |url=https://npd.hgu.mrc.ac.uk/search.php?action=builddetails&geneid=1NP02179 |accessdate= }}</ref>


Probably the largest mRNA transcripted into the nucleohyaloplasm is from the gene for [[dystrophin]] (427 kDA protein). The primary transcript measures 2.4 megabases (thus the gene comprises 0.008% of the human genome), and takes 16 hours to transcribe. The 79 exons code for a protein of 3685 amino acid residues. Its mRNA is 14 kb or ~550kDa.
Probably the largest mRNA transcripted into the nucleohyaloplasm is from the gene for [[dystrophin]] (427 kDA protein). The primary transcript measures 2.4 megabases (thus the gene comprises 0.008% of the human genome), and takes 16 hours to transcribe. The 79 exons code for a protein of 3685 amino acid residues. Its mRNA is 14 kb or ~550 kDa.


==[[Chromatin]]==
===[[Chromatin]]===


[[Euchromatin]] is the less compact DNA form, and contains genes that are frequently [[gene expression|expressed]] by the cell.<ref name=Ehrenhofer-Murray>{{cite  journal  | author = Ehrenhofer-Murray A | title = Chromatin dynamics at DNA replication, transcription and repair | journal = Eur J Biochem | volume = 271 | issue = 12 | pages = 2335–2349 | year = 2004 | pmid = 15182349 | doi = 10.1111/j.1432-1033.2004.04162.x  }}</ref> Active genes, which are generally found in the euchromatic region of the chromosome, tend to be located towards the chromosome's territory boundary.<ref name=Kurz>{{cite journal  |author= Kurz A , Lampel S,  Nickolenko JE, Bradl J, Benner A, Zirbel RM, Cremer T, Lichter P |title = Active and inactive genes localize preferentially in the periphery of chromosome territories  |doi = 10.1083/jcb.135.5.1195 | journal = J of Cell Biol.  |volume=135  |issue =  | pages =1195–1205  | publisher = The Rockefeller University Press | year = 1996 | url = http://intl.jcb.org/cgi/content/abstract/135/5/1195 | pmid =8947544 }}</ref>
[[Euchromatin]] is the less compact DNA form, and contains genes that are frequently [[gene expression|expressed]] by the cell.<ref name=Ehrenhofer-Murray>{{cite  journal  | author = Ehrenhofer-Murray A | title = Chromatin dynamics at DNA replication, transcription and repair | journal = Eur J Biochem | volume = 271 | issue = 12 | pages = 2335–2349 | year = 2004 | pmid = 15182349 | doi = 10.1111/j.1432-1033.2004.04162.x  }}</ref> Active genes, which are generally found in the euchromatic region of the chromosome, tend to be located towards the chromosome's territory boundary.<ref name=Kurz>{{cite journal  |author= Kurz A , Lampel S,  Nickolenko JE, Bradl J, Benner A, Zirbel RM, Cremer T, Lichter P |title = Active and inactive genes localize preferentially in the periphery of chromosome territories  |doi = 10.1083/jcb.135.5.1195 | journal = J of Cell Biol.  |volume=135  |issue =  | pages =1195–1205  | publisher = The Rockefeller University Press | year = 1996 | url = http://intl.jcb.org/cgi/content/abstract/135/5/1195 | pmid =8947544 }}</ref>
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[[Heterochromatin]] is usually localized to the periphery of the nucleus along the nuclear envelope. It mainly consists of genetically inactive [[satellite DNA|satellite sequences]],<ref name=Lohe>{{cite journal| author = Lohe, A.R., ''et al.''| title = Mapping simple repeated DNA sequences in heterochromatin of ''Drosophila melanogaster''| year = 1993| journal = [[Genetics (journal)|Genetics]]| volume = 134| issue = 4| pages = 1149–1174| issn = 0016-6731| url = http://www.genetics.org/cgi/content/full/134/4/1149| pmid = 8375654}}</ref> and many genes are repressed to various extents, although some cannot be expressed in euchromatin at all.<ref name=Lu>{{cite journal| author = Lu, B.Y., ''et al.''| year = 2000| title = Heterochromatin protein 1 is required for the normal expression of two heterochromatin genes in Drosophila| journal = [[Genetics (journal)|Genetics]]| volume = 155| issue = 2| pages = 699–708| url = http://www.genetics.org/cgi/content/full/155/2/699| issn = 0016-6731| pmid = 10835392}}</ref>
[[Heterochromatin]] is usually localized to the periphery of the nucleus along the nuclear envelope. It mainly consists of genetically inactive [[satellite DNA|satellite sequences]],<ref name=Lohe>{{cite journal| author = Lohe, A.R., ''et al.''| title = Mapping simple repeated DNA sequences in heterochromatin of ''Drosophila melanogaster''| year = 1993| journal = [[Genetics (journal)|Genetics]]| volume = 134| issue = 4| pages = 1149–1174| issn = 0016-6731| url = http://www.genetics.org/cgi/content/full/134/4/1149| pmid = 8375654}}</ref> and many genes are repressed to various extents, although some cannot be expressed in euchromatin at all.<ref name=Lu>{{cite journal| author = Lu, B.Y., ''et al.''| year = 2000| title = Heterochromatin protein 1 is required for the normal expression of two heterochromatin genes in Drosophila| journal = [[Genetics (journal)|Genetics]]| volume = 155| issue = 2| pages = 699–708| url = http://www.genetics.org/cgi/content/full/155/2/699| issn = 0016-6731| pmid = 10835392}}</ref>


===Mobile chromatin===
====Mobile chromatin====


During interphase euchromatin is known to be attached to the nucleolus or nucleoli and heterochromatin is attached to the nuclear envelope.<ref name=Abney>{{ cite journal |author=Abney JR, Cutler B, Fillbach ML, Axelrod D, Scalettar BA |title=Chromatin Dynamics in Interphase Nuclei and Its Implications for Nuclear Structure |journal=J Cell Biol. |volume=137 |issue=7 |pages=1459-68 |month=Jun |year=1997 |pmid=2137814 }}</ref> Further, in some cell types interphase euchromatin and heterochromatin are translationally immobile over distances ≥400 nm.<ref name=Abney/>
During [[interphase]] euchromatin is known to be attached to the nucleolus or nucleoli and heterochromatin is attached to the nuclear envelope.<ref name=Abney>{{ cite journal |author=Abney JR, Cutler B, Fillbach ML, Axelrod D, Scalettar BA |title=Chromatin Dynamics in Interphase Nuclei and Its Implications for Nuclear Structure |journal=J Cell Biol. |volume=137 |issue=7 |pages=1459-68 |month=Jun |year=1997 |pmid=2137814 }}</ref> Further, in some cell types interphase euchromatin and heterochromatin are translationally immobile over distances ≥400 nm.<ref name=Abney/> Mobile chromatin can move with velocities averaging 50-70 nm/sec.<ref name=Eskiw>{{ cite journal |author=Eskiw CH, Dellaire G, Mymryk JS, Bazett-Jones DP |title=Size, position and dynamic behavior of PML nuclear bodies following cell stress as a paradigm for supramolecular trafficking and assembly |journal=J Cell Sci. |volume=116 |issue=Pt 21 |month=Nov |pages=4455-66 |year=2003 |doi=10.1242/jcs.00758 |pmid= 13130097 }}</ref>


==Nucleolus==
===[[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.
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 [[ribosome]]s. 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.<ref name=Schwarzacher>{{ cite journal |author=Schwarzacher HG, Wachtler F |title=The nucleolus |journal=Anat Embryol (Berl). |volume=188 |issue=6 |year=1993 |month=Dec |pages=515-36 |pmid=8129175 }}</ref>
 
Direct contact between the nucleolus and the [[nuclear envelope]] is frequently observed but is not dependent on nucleolar activity.<ref name=Schwarzacher>{{ cite journal |author=Schwarzacher HG, Wachtler F |title=The nucleolus |journal=Anat Embryol (Berl). |volume=188 |issue=6 |year=1993 |month=Dec |pages=515-36 |pmid=8129175 }}</ref>


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.<ref name=Coggeshall>{{ cite journal |author=Coggeshall RE, Chung K, Bee DE |title=The relation of nucleolus diameter to cell body diameter in mammalian dorsal root ganglion cells |journal=Anat Rec. |volume=211 |issue=2 |year=1985 |pages=213-7 |month=Feb |pmid= 3977089 }}</ref> Based on this correlation, for an average mammalian cell of 6000 nm, the nucleolus would be ~300 nm in diameter. Interferometric analysis of nucleolus mass for mesothelial cells in culture places its mass average at 40 x 10<sup>-12</sup> gm (40 pgm)<ref name=Blumenstein>{{ cite journal |author=Blumenstein R, Amenta PS |title=An interferometric analysis of nucleoli in cultured mesothelial cells
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.<ref name=Coggeshall>{{ cite journal |author=Coggeshall RE, Chung K, Bee DE |title=The relation of nucleolus diameter to cell body diameter in mammalian dorsal root ganglion cells |journal=Anat Rec. |volume=211 |issue=2 |year=1985 |pages=213-7 |month=Feb |pmid= 3977089 }}</ref> Based on this correlation, for an average mammalian cell of 6000 nm, the nucleolus would be ~300 nm in diameter. Interferometric analysis of nucleolus mass for mesothelial cells in culture places its mass average at 40 x 10<sup>-12</sup> gm (40 pgm)<ref name=Blumenstein>{{ cite journal |author=Blumenstein R, Amenta PS |title=An interferometric analysis of nucleoli in cultured mesothelial cells
|journal=Anat Rec. |volume=201 |issue=1 |pages=13-21 |year=1981 |month=Sep |pmid=7030143 |doi=10.1002/ar.1092010103 }}</ref> or approximately 24 TDa (teradaltons).  In addition, each cell may have approximately the same total nucleolar mass regardless of the number of nucleoli.<ref name=Blumenstein/>
|journal=Anat Rec. |volume=201 |issue=1 |pages=13-21 |year=1981 |month=Sep |pmid=7030143 |doi=10.1002/ar.1092010103 }}</ref> or approximately 24 TDa (teradaltons).  In addition, each cell may have approximately the same total nucleolar mass regardless of the number of nucleoli.<ref name=Blumenstein/>


=Structures=
==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]]<ref name=Nickerson>{{cite journal |author=Nickerson J |title=Experimental observations of a nuclear matrix |journal=J. Cell. Sci. |volume=114 |issue=Pt 3 |pages=463–74 |year=2001 |month=February |pmid=11171316 |url=http://jcs.biologists.org/cgi/content/abstract/114/3/463}}</ref><ref name=Tetko>{{cite journal |author=Tetko IV, Haberer G, Rudd S, Meyers B, Mewes HW, Mayer KF |title=Spatiotemporal expression control correlates with intragenic scaffold matrix attachment regions (S/MARs) in Arabidopsis thaliana |journal=PLoS Comput. Biol. |volume=2 |issue=3 |pages=e21 |year=2006 |month=March |pmid=16604187 |pmc=1420657 |doi=10.1371/journal.pcbi.0020021 }}</ref> and [[nuclear lamina]] are found throughout the inside of the nucleus, some as part of the [[nucleoskeleton]].
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]]<ref name=Nickerson>{{cite journal |author=Nickerson J |title=Experimental observations of a nuclear matrix |journal=J. Cell. Sci. |volume=114 |issue=Pt 3 |pages=463–74 |year=2001 |month=February |pmid=11171316 |url=http://jcs.biologists.org/cgi/content/abstract/114/3/463}}</ref><ref name=Tetko>{{cite journal |author=Tetko IV, Haberer G, Rudd S, Meyers B, Mewes HW, Mayer KF |title=Spatiotemporal expression control correlates with intragenic scaffold matrix attachment regions (S/MARs) in Arabidopsis thaliana |journal=PLoS Comput. Biol. |volume=2 |issue=3 |pages=e21 |year=2006 |month=March |pmid=16604187 |pmc=1420657 |doi=10.1371/journal.pcbi.0020021 }}</ref> and [[nuclear lamina]] are found throughout the inside of the nucleus, some as part of the [[nucleoskeleton]].
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Besides the nucleolus, the [[Cell nucleus|nucleus]] contains a number of other non-membrane delineated bodies. These include [[Cajal body|Cajal bodies]], Gemini of coiled bodies, polymorphic interphase karyosomal association (PIKA), promyelocytic leukaemia (PML) bodies, [[paraspeckle]]s 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.<ref name=Dundr>{{cite  journal |author= Dundr M, Misteli T |title = Functional architecture in the cell nucleus | journal = Biochem J. | issue = 356 | pages = 297–310 | year = 2001 | pmid = 11368755 | doi = 10.1146/annurev.cellbio.20.010403.103738}}</ref>
Besides the nucleolus, the [[Cell nucleus|nucleus]] contains a number of other non-membrane delineated bodies. These include [[Cajal body|Cajal bodies]], Gemini of coiled bodies, polymorphic interphase karyosomal association (PIKA), promyelocytic leukaemia (PML) bodies, [[paraspeckle]]s 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.<ref name=Dundr>{{cite  journal |author= Dundr M, Misteli T |title = Functional architecture in the cell nucleus | journal = Biochem J. | issue = 356 | pages = 297–310 | year = 2001 | pmid = 11368755 | doi = 10.1146/annurev.cellbio.20.010403.103738}}</ref>


=Intra-nuclear transport=
==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 [[mammal]]ian cells, the average diameter of the nucleus is approximately 6 μm.<ref name=Alberts>{{cite book | year = 2002 | title = Molecular Biology of the Cell, Chapter 4, pages 191-234 | editor = Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, Peter Walter | publisher = Garland Science | edition = 4th}}</ref> 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.<ref name=Misteli>{{ cite journal |author=Misteli T |title=Protein dynamics: implications for nuclear architecture and gene expression |journal=Science. |volume=291 |issue=5505 |month=Feb |pages=843-7 |year=2001 |pmid=11225636 }}</ref>
The [[Nucleosol#Average speed for water molecules|lateral speed of a water molecule]] is ~35 µm/sec. The lateral speed of larger biological molecules in [[Passive transport|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 [[mammal]]ian cells, the average diameter of the nucleus is approximately 6 μm.<ref name=Alberts>{{cite book | year = 2002 | title = Molecular Biology of the Cell, Chapter 4, pages 191-234 | editor = Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, Peter Walter | publisher = Garland Science | edition = 4th}}</ref> 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.<ref name=Misteli>{{ cite journal |author=Misteli T |title=Protein dynamics: implications for nuclear architecture and gene expression |journal=Science. |volume=291 |issue=5505 |month=Feb |pages=843-7 |year=2001 |pmid=11225636 }}</ref>


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.<ref name=Lodish>{{ cite book | author=Lodish H, Berk A, Zipursky SL, Matsudaira P, Baltimore D, Darnell JE |title=Molecular Cell Biology |publisher=WH Freeman and Company |location=New York | isbn=0-7167-3136-3 |year 2000 |edition=4th |url=http://www.ncbi.nlm.nih.gov/books/bv.fcgi?highlight=transport,Intracellular&rid=mcb.section.5452 }}</ref> One motor protein that localizes intracellularly to the nucleus is myosin 1F (125 kDa).<ref name=MYO1F>{{ cite web |title=GENATLAS : GENE Database MYO1F |url=http://genatlas.medecine.univ-paris5.fr/ }}</ref> It does not have a NLS. Its N terminal motor domain uses ATP and has actin binding sites.<ref name=MYO1F/>
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. [[Microtubule]]s function as tracks and the movement is propelled by [[motor protein]]s. Movement can occur in both directions and at velocities between ~5 and 3000 nm/sec.<ref name=Lodish>{{ cite book | author=Lodish H, Berk A, Zipursky SL, Matsudaira P, Baltimore D, Darnell JE |title=Molecular Cell Biology |publisher=WH Freeman and Company |location=New York | isbn=0-7167-3136-3 |year 2000 |edition=4th |url=http://www.ncbi.nlm.nih.gov/books/bv.fcgi?highlight=transport,Intracellular&rid=mcb.section.5452 }}</ref> One motor protein that localizes intracellularly to the nucleus is myosin 1F ({{Gene|MYO1F}}) 125 kDa.<ref name=MYO1F>{{ cite web |title=GENATLAS : GENE Database MYO1F |url=http://genatlas.medecine.univ-paris5.fr/ }}</ref> It does not have a NLS. Its N terminal motor domain uses ATP and has actin binding sites.<ref name=MYO1F/>


All Cajal bodies move through the nucleohyaloplasm.<ref name=Platani>{{ cite journal |author=Platani M, Goldberg I, Swedlow JR, Lamond AI |title=In Vivo Analysis of Cajal Body Movement, Separation, and Joining in Live Human Cells |journal=J Cell Biol. |volume=151 |issue=7 |pages=1561-74 |year=2000 |month=Dec |doi=10.1083/jcb.151.7.1561 |pmid= 11134083 }}</ref> These movements include translocations and moving to or from the nucleolus at velocities of ~10-15 nm/sec.<ref name=Platani/>
All Cajal bodies move through the nucleohyaloplasm.<ref name=Platani>{{ cite journal |author=Platani M, Goldberg I, Swedlow JR, Lamond AI |title=In Vivo Analysis of Cajal Body Movement, Separation, and Joining in Live Human Cells |journal=J Cell Biol. |volume=151 |issue=7 |pages=1561-74 |year=2000 |month=Dec |doi=10.1083/jcb.151.7.1561 |pmid= 11134083 }}</ref> These movements include translocations and moving to or from the nucleolus at velocities of ~10-15 nm/sec.<ref name=Platani/>


Constrained microstructures (~40-100 nm in size, on the order of 0.5-5 [[Atomic mass unit|MDa]]) 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.<ref name=Eskiw>{{ cite journal |author=Eskiw CH, Dellaire G, Mymryk JS, Bazett-Jones DP |title=Size, position and dynamic behavior of PML nuclear bodies following cell stress as a paradigm for supramolecular trafficking and assembly |journal=J Cell Sci. |volume=116 |issue=Pt 21 |month=Nov |pages=4455-66 |year=2003 |doi=10.1242/jcs.00758 |pmid= 13130097 }}</ref> The movement of PML-containing microstructures is energy-independent.<ref name=Eskiw/> Such mobility is characteristic of constrained diffusion.<ref name=Eskiw/>
Constrained microstructures (~40-100 nm in size, on the order of 0.5-5 [[Atomic mass unit|MDa]]) 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.<ref name=Eskiw/> The movement of PML-containing microstructures is energy-independent.<ref name=Eskiw/> Such mobility is characteristic of constrained diffusion.<ref name=Eskiw/>


The movement of elongated chromosomes throughout the chromatin filled nucleus may be associated with intranuclear motor protein action.<ref name=Scherthan>{{ cite book |author=Scherthan H, Orr-Weaver T, Arana P, Gill B |page=225 |title=Meiotic mobility and recombination |pages=215-248 |editor=Henriques-Gil N, Parker JS, Puertas MJ |proceedings title=Chromosomes Today |volume=12 |year=1997 |publisher=Springer |isbn=0412752409, 9780412752407 }}</ref>
The movement of elongated chromosomes throughout the chromatin filled nucleus may be associated with intranuclear motor protein action.<ref name=Scherthan>{{ cite book |author=Scherthan H, Orr-Weaver T, Arana P, Gill B |page=225 |title=Meiotic mobility and recombination |pages=215-248 |editor=Henriques-Gil N, Parker JS, Puertas MJ |proceedings title=Chromosomes Today |volume=12 |year=1997 |publisher=Springer |isbn=0412752409, 9780412752407 }}</ref>


=Human nucleohyaloplasm=
==[[Human]] nucleohyaloplasm==
 
The [[human genome]] contains many of the genes discussed in the sections above regarding the structure, composition, and physiology of the nucleohyaloplasm. These genes and comparable ones in similar species help to understand [[human evolutionary genetics]].
 
Mature [[monocyte]]s circulating in human [[Venous blood|peripheral blood]] contain multiple nucleoli of various sizes in one and the same nucleus.<ref name=Smetana>{{ cite journal |author=Smetana K, Jirásková I, Otevrelová P, Kalousek I |title=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 |journal=Folia Biol (Praha). |volume=54 |issue=4 |pages=130-3 |year=2008 |pmid=18808739 }}</ref> The nucleolar RNA content is apparently related to the nucleolar size.<ref name=Smetana/>


Mature monocytes circulating in human peripheral blood contain multiple nucleoli of various sizes in one and the same nucleus.<ref name=Smetana>{{ cite journal |author=Smetana K, Jirásková I, Otevrelová P, Kalousek I |title=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 |journal=Folia Biol (Praha). |volume=54 |issue=4 |pages=130-3 |year=2008 |pmid=18808739 }}</ref> The nucleolar RNA content is apparently related to the nucleolar size.<ref name=Smetana/>
Increases in the number of nucleoli, their size, and their activity reflect the proliferating activity of exponentially growing cells.<ref name=Horky>{{ cite journal |author=Horký M, Kotala V, Anton M, Wesierska-Gadek J |title=Nucleolus and apoptosis |journal=Ann N Y Acad Sci. |volume=973 |month=Nov |pages=258-64 |year=2002 |pmid=12485873 }}</ref>
Increases in the number of nucleoli, their size, and their activity reflect the proliferating activity of exponentially growing cells.<ref name=Horky>{{ cite journal |author=Horký M, Kotala V, Anton M, Wesierska-Gadek J |title=Nucleolus and apoptosis |journal=Ann N Y Acad Sci. |volume=973 |month=Nov |pages=258-64 |year=2002 |pmid=12485873 }}</ref>


=References=
==Acknowledgements==
 
The content on this page was first contributed by: Henry A. Hoff.
 
Initial content for this page in some instances came from [http://www.wikipedia.org Wikipedia].
 
==References==


{{reflist}}
{{reflist|2}}
 
==See also==


{{AminoAcids}}
{{AminoAcids}}
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{{Protein primary structure}}
{{Protein primary structure}}
{{Protein topics}}
{{Protein topics}}
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[[Category:Cell anatomy]]
[[Category:Cell anatomy]]

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Editor-In-Chief: Henry A. Hoff

Overview

A hyaloplasm is the clear, structureless, apparently homogeneous fluid of the cytoplasm. Similar to the hyaloplasm of a cell, the nucleus contains nucleohyaloplasm. It is a highly viscous liquid. This liquid contains enzymes (which direct activities that take place in the nucleus), intermediate metabolites, and many substances such as nucleotides (necessary for purposes as the replication of DNA and production of mRNA). All are dissolved in the nucleohyaloplasm. It is part of the nucleoplasm and is partly made up of nucleosol.

Introduction

Nucleohyaloplasm is the cytosol within the nucleus, without the microfilaments and the microtubules, also known as nucleosol, vis à vis mitosol and cytosol[1].

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.[2]

As a plasm it contains formative material, portions of the nucleoskeleton as it is being shaped or reshaped, macromolecules with limited mobility, and portions of the nuclear envelope as it is recycled.

Small particles

Small particles (< 40 kDa[3], <50 kDa[4], <~70 kDa[5], ≤ 70 kDa[6]) are able to pass through the nuclear pore complex by passive transport. Larger proteins require a nuclear localization signal (NLS). The pores are 100 nm in total diameter, with an opening diameter of about 50 nm; however, the gap through which molecules freely diffuse is only about 9-10 nm wide,[7] due to the presence of regulatory systems within the center of the pore. The 10 nm diameter corresponds to an upper mass limit of 70 kDa.[8] The majority of the non-protein molecules have a molecular mass of less than 300 Da.[9]

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.[10] Estimates of the number of metabolites in a single cell of E. coli or baker's yeast predict that under 1,000 are made.[11][12]

Polymerases

Many of the subunits of RNA polymerase II (EC 2.7.7.6) are small polymerases. RNA polymerase IIC (PolR2C) has a mass of 33 kDa, no NLS, is intracellular to the nucleus and is part of the transcription complex. Of the others, PolR2D-L are 19 kDa or less without NLS, except RNA polymerase IIE (PolR2E) 23 kDa has a NLS and is the only one that localizes to the nucleolus.[13] Although PolR2K and PolR2L are small enough in mass to be considered oligopeptides, their numbers of aa are over the usual limit: 58 aa and 67 aa, respectively, in humans.

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]

Proteins

Proteins larger than those allowed through a nuclear pore by passive transport require a nuclear localization signal (NLS). This is an amino acid sequence that targets the cytosolic nuclear transport receptors of the nuclear pore complex. A nuclear import NLS will bind strongly to importin, while an export NLS (nuclear export signal, NES) binds to an exportin. For example, RNA polymerase IIA (Rbp1) 220kDa has a NLS.[17]

Nuclear localization

The subcellular distribution of a substance to or within the nucleus is often referred to as nuclear localization.[18] Many mechanisms have been found that produce nuclear localization in addition to a NLS.

Zac1 is a seven-zinc-finger transcription factor that preferentially binds GC-rich DNA elements and has intrinsic transactivation activity.[19] The zinc-finger motif is of a Cys2His2-type.[19] This motif is involved in DNA binding, dimerization, transactivation activity, and nuclear localization of Zac1 through interacting with importin α1.[19] Zac1 has no typical NLS.[19] Any two or more zinc-finger motifs act in concert to facilitate nuclear localization.[19] Apparently, as with importin α transport of CaMKIV to the nucleus, importin α1 may mediate transport of Zac1 to the nucleus without the involvement of importin β.[19] But, some other factors are involved, perhaps Ran-binding proteins such as RanBPM and Mog1[20], which play roles in nucleocytoplasmic transport and transcription factor recruitment.[19]

Transcription factories

Active transcription units are clustered in the nucleus, in discrete sites called ‘transcription factories’. Such sites can be visualized after allowing engaged polymerases to extend their transcripts in tagged precursors (Br-UTP or Br-U), and immuno-labeling the tagged nascent RNA. Transcription factories can also be localized using fluorescence in situ hybridization, or marked by antibodies directed against polymerases. There are ~8,000 polymerase II factories in the nucleoplasm of a HeLa cell. Each polymerase II factory contains ~8 polymerases. As most active transcription units are associated with only one polymerase, each factory can be associated with ~8 different transcription units. That's ~64,000 polymerase II active transcription units. These units might be associated through promoters and/or enhancers, with loops forming a ‘cloud’ around the factory.

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[21], microRNA, piwi-interacting RNA (piRNA), small interfering RNA (siRNA), signal recognition particle RNA (SRP RNA), and guide RNA (gRNA).

Each has to be transcribed from the applicable portion of DNA in the euchromatin. The unfolded structure of euchromatin allows gene regulatory proteins and RNA polymerase (RNAP) complexes to bind to the DNA sequence, which can then initiate the transcription process. Control of the process of gene transcription affects patterns of gene expression and thereby allows a cell to adapt to a changing environment, perform specialized roles within an organism, and maintain basic metabolic processes necessary for survival. RNAP can initiate transcription at specific DNA sequences known as promoters. It then produces an RNA chain which is complementary to the template DNA strand.

RNAs involved in protein synthesis
Type Abbr. Function Distribution Ref.
Messenger RNA mRNA Codes for protein All cells
Ribosomal RNA rRNA Translation All cells
Signal recognition particle RNA 7SL RNA or SRP RNA Membrane integration / mRNA tagging for export All organisms [22]
Transfer RNA tRNA Translation All cells
Transfer-messenger RNA tmRNA Rescuing stalled ribosomes Terminating translation Bacteria [23]
RNAs involved in post-transcriptional modification or DNA replication
Type Abbr. Function Distribution Ref.
Small nuclear RNA snRNA Splicing and other functions Eukaryotes and archaea [24]
Small nucleolar RNA snoRNA Nucleotide modification of RNAs RNA editing Eukaryotes and archaea [25]
SmY RNA SmY mRNA trans-splicing Nematodes [26]
Small Cajal body-specific RNA scaRNA Type of snoRNA; Nucleotide modification of RNAs
Guide RNA gRNA mRNA nucleotide modification / RNA editing Kinetoplastid mitochondria [27]
Ribonuclease P RNase P tRNA maturation All organisms [28]
Ribonuclease MRP RNase MRP rRNA maturation, DNA replication Eukaryotes [29]
Y RNA RNA processing, DNA replication Animals [30]
Telomerase RNA Telomere synthesis Most eukaryotes [31]
Ribozyme Catalysis All cells
Transposon Self-propagating All cells
Regulatory RNAs
Type Abbr. Function Distribution Ref.
Antisense RNA aRNA Transcriptional attenuation / mRNA degradation / mRNA stabilisation / Translation block Gene regulation All organisms [32][33]
Cis-natural antisense transcript Gene regulation
CRISPR RNA crRNA Resistance to parasites, probably by targeting their DNA Bacteria and archaea [34]
Long noncoding RNA Long ncRNA Various Eukaryotes
MicroRNA miRNA Gene regulation Most eukaryotes [35]
Piwi-interacting RNA piRNA Transposon defense Gene regulation Animal germline cells [36][37]
Small interfering RNA siRNA Gene regulation Most eukaryotes [38]
Trans-acting siRNA tasiRNA Gene regulation Land plants [39]
Repeat associated siRNA rasiRNA Type of piRNA; transposon defense Drosophila [40]

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. Ribozyme RNase P 30kDa has a NLS.[41] But, RNase P subunit p25 (25 kDa), which is also localized to the nucleolus does not.[42]

Probably the largest mRNA transcripted into the nucleohyaloplasm is from the gene for dystrophin (427 kDA protein). The primary transcript measures 2.4 megabases (thus the gene comprises 0.008% of the human genome), and takes 16 hours to transcribe. The 79 exons code for a protein of 3685 amino acid residues. Its mRNA is 14 kb or ~550 kDa.

Chromatin

Euchromatin is the less compact DNA form, and contains genes that are frequently expressed by the cell.[43] Active genes, which are generally found in the euchromatic region of the chromosome, tend to be located towards the chromosome's territory boundary.[44]

Heterochromatin is usually localized to the periphery of the nucleus along the nuclear envelope. It mainly consists of genetically inactive satellite sequences,[45] and many genes are repressed to various extents, although some cannot be expressed in euchromatin at all.[46]

Mobile chromatin

During interphase euchromatin is known to be attached to the nucleolus or nucleoli and heterochromatin is attached to the nuclear envelope.[47] Further, in some cell types interphase euchromatin and heterochromatin are translationally immobile over distances ≥400 nm.[47] Mobile chromatin can move with velocities averaging 50-70 nm/sec.[48]

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.[49]

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.[50] Based on this correlation, for an average mammalian cell of 6000 nm, the nucleolus would be ~300 nm in diameter. Interferometric analysis of nucleolus mass for mesothelial cells in culture places its mass average at 40 x 10-12 gm (40 pgm)[51] or approximately 24 TDa (teradaltons). In addition, each cell may have approximately the same total nucleolar mass regardless of the number of nucleoli.[51]

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[52][53] and nuclear lamina are found throughout the inside of the nucleus, some as part of the nucleoskeleton.

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.[54]

Intra-nuclear transport

The lateral speed of a water molecule is ~35 µm/sec. The lateral speed of larger 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.[55] 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.[56]

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.[57] One motor protein that localizes intracellularly to the nucleus is myosin 1F (MYO1F) 125 kDa.[58] It does not have a NLS. Its N terminal motor domain uses ATP and has actin binding sites.[58]

All Cajal bodies move through the nucleohyaloplasm.[59] These movements include translocations and moving to or from the nucleolus at velocities of ~10-15 nm/sec.[59]

Constrained microstructures (~40-100 nm in size, on the order of 0.5-5 MDa) 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.[48] The movement of PML-containing microstructures is energy-independent.[48] Such mobility is characteristic of constrained diffusion.[48]

The movement of elongated chromosomes throughout the chromatin filled nucleus may be associated with intranuclear motor protein action.[60]

Human nucleohyaloplasm

The human genome contains many of the genes discussed in the sections above regarding the structure, composition, and physiology of the nucleohyaloplasm. These genes and comparable ones in similar species help to understand human evolutionary genetics.

Mature monocytes circulating in human peripheral blood contain multiple nucleoli of various sizes in one and the same nucleus.[61] The nucleolar RNA content is apparently related to the nucleolar size.[61]

Increases in the number of nucleoli, their size, and their activity reflect the proliferating activity of exponentially growing cells.[62]

Acknowledgements

The content on this page was first contributed by: Henry A. Hoff.

Initial content for this page in some instances came from Wikipedia.

References

  1. ↑ Solakidi S, Psarra AM, Sekeris CE (2007). "Differential distribution of glucocorticoid and estrogen receptor isoforms:localization of GRβ and ERα in nucleoli and GRα and ERβ in the mitochondria of human osteosarcoma SaOS-2 and hepatocarcinoma HepG2 cell lines" (PDF). J Musculoskelet Neuronal Interact. 7 (3): 240–5. PMID 17947807. Unknown parameter |month= ignored (help)
  2. ↑ Roos A, Boron WF (1981). "Intracellular pH". Physiol. Rev. 61 (2): 296–434. PMID 7012859. Unknown parameter |month= ignored (help)
  3. ↑ Naim B, Brumfeld V, Kapon R, Kiss V, Nevo R, Reich Z (2007). "Passive and Facilitated Transport in Nuclear Pore Complexes Is Largely Uncoupled". J Biol Chem. 282 (6): 3881–8. doi:10.1074/jbc.M608329200. PMID 17164246. Unknown parameter |month= ignored (help)
  4. ↑ "Research highlights". Biopolymers. 2007. p. fmiv. doi:10.1002/bip.20740. Unknown parameter |month= ignored (help)
  5. ↑ Mahato RI, Rolland A, Tomlinson E (1997). "Cationic Lipid-Based Gene Delivery Systems: Pharmaceutical Perspectives". Pharm Res. 14 (7): 853–9. PMID 9244140. Unknown parameter |month= ignored (help)
  6. ↑ Chesnoy S, Huang L (2000). "STRUCTURE AND FUNCTION OF LIPID-DNA COMPLEXES FOR GENE DELIVERY". Annu Rev Biophys Biomol Struct. 29: 27–47. doi:10.1146/annurev.biophys.29.1.27. PMID 10940242. Unknown parameter |month= ignored (help)
  7. ↑ Kramer A, Ludwig Y, Shahin V, Oberleithner H (2007). "A Pathway Separate from the Central Channel through the Nuclear Pore Complex for Inorganic Ions and Small Macromolecules". J Biol Chem. 282 (43): 31437–43. doi:10.1074/jbc.M703720200. PMID 17726020. Unknown parameter |month= ignored (help)
  8. ↑ Melchior F, Gerace L (1995). "Mechanisms of nuclear protein import". Curr Opin Cell Biol. 7 (3): 310–8. PMID 7662359. Unknown parameter |month= ignored (help)
  9. ↑ 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)
  10. ↑ Weckwerth W (2003). "Metabolomics in systems biology". Annu Rev Plant Biol. 54: 669–89. doi:10.1146/annurev.arplant.54.031902.135014. PMID 14503007.
  11. ↑ 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.
  12. ↑ 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)
  13. ↑ "Nuclear Protein Database DNA-directed RNA polymerase II 23 kDa polypeptide".
  14. ↑ Campbell, Neil A. (1987). Biology. p. 795. ISBN 0-8053-1840-2.
  15. ↑ 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)
  16. ↑ 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.
  17. ↑ "Nuclear Protein Database: DNA-directed RNA polymerase II largest subunit".
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  58. ↑ 58.0 58.1 "GENATLAS : GENE Database MYO1F".
  59. ↑ 59.0 59.1 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)
  60. ↑ Scherthan H, Orr-Weaver T, Arana P, Gill B (1997). Henriques-Gil N, Parker JS, Puertas MJ, ed. Meiotic mobility and recombination. 12. Springer. p. 225. ISBN 0412752409, 9780412752407 Check |isbn= value: invalid character (help). Unknown parameter |proceedings title= ignored (help); More than one of |pages= and |page= specified (help)
  61. ↑ 61.0 61.1 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.
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See also


Template:Biochemical families
Alanine (dp) | Arginine (dp) | Asparagine (dp) | Aspartic acid (dp) | Cysteine (dp) | Glutamic acid (dp) | Glutamine (dp) | Glycine (dp) | Histidine (dp) | Isoleucine (dp) | Leucine (dp) | Lysine (dp) | Methionine (dp) | Phenylalanine (dp) | Proline (dp) | Serine (dp) | Threonine (dp) | Tryptophan (dp) | Tyrosine (dp) | Valine (dp)


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