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==Pseudouridine==
==Pseudouridine==
In addition to the [[Standard Residues|standard ribonucleotides]], many [[RNA]] molecules contain '''modified nucleotides''' formed post-transcriptionally. [[Pseudouridine]] is formed in the context of a polyribonucleotide chain by the isomerization of uridine monophospate into [[Pseudouridine|pseudouridine]] and is the most abundant of these [[Non-Standard Residue|non-standard ribonucleotides]]. For that reason, it is sometimes referred to as the 'fifth ribonucleotide' of [[RNA]], along with adenine (A), uridine (U), guanine(G), and cytosine(C) monophosphates.  
In addition to the [[Standard Residues|standard ribonucleotides]], many [[RNA]] molecules contain '''modified nucleotides''' formed post-transcriptionally. [[Pseudouridine]] is formed in the context of a polyribonucleotide chain by the isomerization of uridine into [[Pseudouridine|pseudouridine]] and is the most abundant of these [[Non-Standard Residue|non-standard ribonucleotides]]. For that reason, it is sometimes referred to as the 'fifth ribonucleotide' of [[RNA]], along with adenosine (A), guanosine(G), uridine (U) and cytidine(C) monophosphates.  


: ''Note:'' pseudouridine, as well as uridine, adenosine, cytidine and guanosine are nucleo'''s'''ides. The respective nucleo'''t'''ides are their monophosphates. It is nucleotides that constitute the monomer units in a nucleic acid (a polynucleotide). Their one-letter abbreviation is frequently used when referring either to the base or the nucleoside, as well as to the nucleotide when it is part of a nucleic acid (i.e. describing the sequence of the nucleic acid).
<!----[[Image:Pseudouridine.png|center|350px]] DELETED THIS IMAGE FOR NOW BECAUSE, AS POINTED OUT BY ANGEL, THEY SHOW IT AS A NUCLEOSIDE WHICH IS NOT BIOLOGICALLY RELEVANT FOR PSEUDOURIDINE FORMATION, since the reaction occurs on RNA chains where nucleotides would be present. ---->
<!----[[Image:Pseudouridine.png|center|350px]] DELETED THIS IMAGE FOR NOW BECAUSE, AS POINTED OUT BY ANGEL, THEY SHOW IT AS A NUCLEOSIDE WHICH IS NOT BIOLOGICALLY RELEVANT FOR PSEUDOURIDINE FORMATION, since the reaction occurs on RNA chains where nucleotides would be present. ---->


In contrast to the formation of several other types of modifications where moieties are added covalently to the bases or backbone, the formation of pseudouridine from uridine is mechanistically rather complex. In order to form this modified nucleotide, the base has to be removed from the uridine monophospate, rotated, and covalently rebonded to form pseudouridine.
In contrast to the formation of several other types of modifications where moieties are added covalently to the bases or backbone, the formation of pseudouridine from uridine is mechanistically rather complex. In order to form this modified nucleotide, the base has to be removed from the uridine monophospate, rotated, and covalently rebonded to form pseudouridine.


Most tRNAs contain modified nucleotides, [[TRNA|tRNAs]] are well-known to feature this modification<ref>PMID:20459084</ref>, and [[TRNA|tRNAs]] are well-known to feature this modification, which are added post-transcriptionally by specific enzymes. Archaeal and Eukaryotic rRNAs are well known to be targets of guided pseudouridine formation by protein-small RNA complexes. However, recent studies have revealed many more pseudouridines exist in messenger RNA in humans than appreciated before<ref>PMID: 25192136</ref><ref>PMID: 25367125</ref><ref>PMID: 30414851</ref>.
Most [[TRNA|transfer RNAs(tRNAs)]] contain modified nucleotides<ref>PMID:20459084</ref>, which are generated post-transcriptionally by specific enzymes. Archaeal and eukaryotic rRNAs are well known to be targets of guided pseudouridine formation by protein-small RNA complexes. However, recent studies have revealed many more pseudouridines exist in messenger RNA in humans than appreciated before<ref>PMID: 25192136</ref><ref>PMID: 25367125</ref><ref>PMID: 30414851</ref>.


== Representation ==
== Representation ==


An uppercase greek character <code>'''Ψ'''</code>, name 'Psi', is often used to represent [[Pseudouridine|pseudouridine]] along with the single characters A,C,G, and U for the standard ribonucleotides.
An uppercase greek character <code>'''Ψ'''</code>, known as 'Psi', is often used to symbolically represent '[[pseudouridine]]' or its monophosphate as a single character, especially when using it along with 'A', 'C', 'G' and 'U' for the standard ribonucleotides.
 
{| class="wikitable" style="margin-left: auto; margin-right: auto;"
|-
! base
! nucleoside
! nucleotide
|-
| adenine, Ade, A
| adenosine, Ado, A
| adenylate, adenosine monophosphate, AMP, A
|-
| guanine, Gua, G
| guanosine, Guo, G
| guanylate, guanosine monophosphate, GMP, G
|-
| cytosine, Cyt, C
| cytidine, Cyd, C
| cytidylate, cytidine monophosphate, CMP, C
|-
| thymine, Thy, T
| thymidine, Thd, T
| thymidylate, thymidine monophosphate, TMP, T
|-
| uracyl, Ura, U
| uridine, Urd, U
pseudouridine, Ψrd, Ψ
| uridylate, uridine monophosphate, UMP, U
pseudouridylate, pseudouridine monophosphate, Ψ
|-
| hypoxanthine, Hyp
| inosine, Ino, I
| inosinate, inosine monophosphate, IMP, I
|}
(Similarly for deoxynucleosides and deoxynucleotides. The 3-letter abbreviations are those recommended by IUBMB and IUPAC<ref>PMID: 5502660</ref><ref>PMID: 2417239</ref>)


== Enzymatic Synthesis ==
== Enzymatic Synthesis ==
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==See also==
==See also==
*[[Transfer RNA (tRNA)]]
* [[Ribosome]]
* [[Ribosome]]


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Wayne Decatur, Angel Herraez
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