Pseudouridine
Names | |
---|---|
IUPAC name
5-(β-D-Ribofuranosyl)pyrimidine-2,4(1H,3H)-dione
| |
Systematic IUPAC name
5-[(2S,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidine-2,4(1H,3H)-dione | |
Other names
psi-Uridine, 5-Ribosyluracil, beta-D-Pseudouridine, 5-(beta-D-Ribofuranosyl)uracil
| |
Identifiers | |
3D model (
JSmol ) |
|
32779 | |
ChEBI | |
ChEMBL | |
ChemSpider | |
KEGG | |
PubChem CID
|
|
UNII | |
CompTox Dashboard (EPA)
|
|
| |
| |
Properties | |
C9H12N2O6 | |
Molar mass | 244.20 g/mol |
Appearance | White granular powder |
Highly soluble in water. | |
Except where otherwise noted, data are given for materials in their standard state (at 25 °C [77 °F], 100 kPa).
|
Pseudouridine (5-ribosyluracil, abbreviated by the Greek letter psi- Ψ)[1] is an isomer of the nucleoside uridine in which the uracil is attached via a carbon-carbon instead of a nitrogen-carbon glycosidic bond.
Pseudouridine is the most abundant
Pseudouridine is a ubiquitous constituent of structural RNA (
Pseudouridine in rRNA and tRNA has been shown to fine-tune and stabilize the regional structure and help maintain their functions in mRNA decoding, ribosome assembly, processing and translation.[4][8][9] Pseudouridine in snRNA has been shown to enhance spliceosomal RNA-pre-mRNA interaction to facilitate splicing regulation.[10]
Effects and modification on different RNA
tRNA
Ψ is ubiquitous in this class of RNAs and facilitates common tRNA structural motifs. One such structural motif is the TΨC stem loop which incorporates Ψ55. Ψ is commonly found in the D stem and anticodon stem and loop of tRNAs from each domain. In each structural motif the unique physicochemical properties of Ψ stabilize structures that would not be possible with the standard U.[4]
During translation Ψ modulates interactions of tRNA molecules with rRNAs and mRNAs. Ψ and other modified nucleotides affect the local structure of the tRNA domains they are found in without impacting the overall fold of the RNA. In the anticodon stem-loop (ASL) Ψ seems critical for proper binding of tRNAs to the ribosome. Ψ stabilizes the dynamic structure of the ASL and promotes stronger binding to the 30S ribosome. The stabilized conformation of the ASL helps maintain correct anticodon-codon pairings during translation. This stability may increase translational accuracy by decreasing the rate of peptide bond formation and allowing for more time for incorrect codon-anticodon pairs to be rejected. Despite Ψ’s role in local structure stabilization, pseudouridylation of tRNA is not essential for cell viability and is not usually required for aminoacylation.[4]
mRNA
Ψ is also found in
rRNA
Ψ is found in the large and small ribosomal subunits of all domains of life and their organelles. In the ribosome Ψ residues cluster in domains II, IV, and V and stabilize RNA-RNA and/or RNA-protein interactions. The stability afforded by Ψ may assist rRNA folding and ribosome assembly. Ψ may also influence the stability of local structures which impact the speed and accuracy of decoding and proofreading during translation.[4]
snRNA
Ψ is found in the major spliceosomal snRNAs of eukaryotes. Ψ residues in snRNA are often phylogenetically conserved, but have some variations across taxa and organisms. The Ψ residues in snRNAs are normally located in regions that participate in RNA-RNA and/or RNA-protein interactions involved in the assembly and function of the spliceosome. Ψ residues in snRNAS contribute to the proper folding and assembly of the spliceosome which is essential for pre-mRNA processing.[4]
Synthases
Pseudouridine are RNA modifications that are done post-transcription, so after the RNA is formed [citation needed]. The proteins that do this modification are called pseudouridine synthases (PUS) and are found in all kingdoms of life. Most research has been done on how PUS modify tRNA, so mechanisms involving snRNA, and mRNA are not clearly defined. PUS can vary on RNA specificity, structure, and isomerization mechanisms. The different structures of PUS are divided into five families which share the active sequence and important structural motifs.[1]
TruA
TruA domain modifies a variety of different places in tRNA, snRNA, and mRNA. The mechanism of isomerization of uridine is still being talked about in this family.[9][13]
PUS 1 is located in the nucleus and modifies tRNA at different locations, U44 of U2 snRNA, and U28 of U6 snRNA. Studies found that PUS 1 expression increased during environmental stress and is important for regulating the splicing of RNA. Also, that PUS 1 is necessary for taking the tRNA made in the nucleus and sending them to the cytoplasm.[9]
PUS 2 is very similar to PUS 1, but located in the mitochondria and only modifies U27 and U28 of mito-tRNA. This protein modifies the mitochondrial tRNA, which has a lesser amount of pseudouridine modifications compared to other tRNAs. Unlike most mitochondria located protein, PUS 2 has not been found to have a mitochondrial targeting signal or MTS.[9]
PUS 3 is a homolog to PUS 1, but modifies different places of the tRNA (U38/39) in the cytoplasm and mitochondrial. This protein is the most conserved of the TruA family. A decrease in modifications made by PUS 3 was found when the tRNA structure of improperly folded. Along with tRNA the protein targets ncRNA and mRNA, further research is still needed as to the importance of this modification. PUS 3 along with PUS 1 modify the steroid activator receptor in humans.[9]
TruB
The TruB family only contains PUS 4 located in the mitochondrial and nucleus. PUS 4 modification is heavily conserved located in the U55 in the elbow of the tRNA. The human form of PUS 4 is actually missing a binding domain called PUA or pseudouridine synthase and archaeosine trans-glycosylase. PUS 4 has a sequence specificity for T-loop part of the tRNA. Preliminary data of PUS4 modifying mRNA, but more research is needed to confirm. Also binds to a specific Brome Mosaic Virus, which is a plant-infecting RNA virus.[9][14]
TruD
TruD is able to modify a variety of RNA, and it is unclear how these different RNA substrates are recognized. PUS 7 modifies U2 snRNA at the position 35 and this modification will increase when the cells are in heat shock. Another modification is cytoplasmic tRNA in position 13, and position 35 in pre-tRNATyr. PUS 7 modifies almost specificity does not depend on the type of RNA as mRNA show pseudouridylated by PUS 7. Recognize this the sequence of the RNA, UGUAR with the second U being the nucleotide that will be modified. The pseudouridylation of mRNA by PUS 7 increases during heat shock, because the protein moves from the nucleus to the cytoplasm. The modification is thought to increase the stability of mRNA during heat shock before the RNA goes to the nucleus or mitochondria, but more studies are needed.[9][13]
RluA
The RluA domain of these proteins can identify the substrate through a different protein binding to the substrate and then particular bonds to the RluA domain.[1][13]
PUS 5 is not well studied and located pseudouridine synthase and similar to Pus 2 does not have a mitochondrial signal targeting sequence. The protein modifies U2819 of mitochondrial 21S rRNA. Also suspected that Pus 5 modifies some uridines in the mRNA, but again more data is needed to confirm.
PUS 6 has one that only modifies U31 of cytoplasmic and mitochondrial tRNA. Pus 6 is also known to modify mRNA.[9]
PUS 8 also known as Rib2 modifies cytoplasmic tRNA at position U32. On the C-terminus there is a DRAP-deaminase domain related to the biosynthesis of riboflavin. The RluA and DRAP or deaminase domain related to riboflavin synthase have completely separate functions in the protein and it is not known whether they interact with each other. PUS 8 is necessary in yeast, but that is suspected to be related to the riboflavin synthesis and not the pseudouridine modification.[9]
PUS 9 and PUS 8 catalyze the same position in mitochondrial tRNA instead of cytoplasmic. It is the only PUS protein that contains a mitochondrial targeting signal domain on the N-terminus. Studies suggest that PUS 9 can modify mRNAs, which would mean less substrate specificity.[9]
RsuA
This section is empty. You can help by adding to it. (July 2022) |
Techniques in genome sequencing for pseudouridine
Pseudouridine can be identified through a multitude of different techniques. A common technique to identify modifications in RNA and DNA is Liquid Chromatography with Mass Spectrometry or LC-MS. Mass spectrometry separates molecules by the mass and charge. While uridine and pseudouridine have the same mass, they have different charges. Liquid chromatography works by retention time, which has to do with leaving the column.[15] A chemical way to identify pseudouridine uses a compound called CMC or N-cyclohexyl-N′-β-(4-methylmorpholinium) ethylcarbodiimide to specifically label and distinguish uridine from pseudouridine.[16] CMC will bond both with pseudouridine and uridine, but holds tighter to the former, because of the third nitrogen able to form hydrogen bond. CMC bound to pseudouridine can then be imaged by tagging a signaling molecule. This method is still being worked on to become high-throughput.[17]
Medical relevance of pseudouridine
Pseudouridine exerts a subtle but significant influence on the nearby sugar-phosphate backbone and also enhances base stacking. These effects may underlie the biological role of most, but perhaps not all of the pseudouridine residues in RNA. Certain genetic mutants lacking specific pseudouridine residues in tRNA or rRNA exhibit difficulties in translation, display slow growth rates, and fail to compete effectively with wild-type strains in mixed culture. Pseudouridine modifications are also implicated in human diseases such as
Vaccines
When pseudouridine is used in place of uridine in synthetic mRNA, the modified mRNA molecule arouses less response from
N1-Methylpseudouridine provides even less innate immune response than Ψ, as well as improving translation capacity.[21] Both Pfizer-BioNTech and Moderna mRNA vaccines therefore use N1-Methylpseudouridine rather than Ψ.[21]
See also
- Pseudouridine kinase
- TRNA-pseudouridine synthase
- PUS1
References
- ^ PMID 17113994.
- PMID 29104216.
- PMID 34556550.
- ^ S2CID 20561376.)
{{cite journal}}
: CS1 maint: multiple names: authors list (link - PMID 8559660.
- PMID 9047361.
- PMID 34903666.
- PMID 23391857.
- ^ PMID 28045575.
- PMID 27268497.
- PMID 30414851.
- ^ "European medicines Agency Assessment report on Comirnaty (Common name: COVID-19 mRNA vaccine) (nucleoside-modified) Procedure No. EMEA/H/C/005735/0000" (PDF). 2021-02-19.
- ^ PMID 29104216.
- PMID 27849601.
- PMID 28872587.
- PMID 8373778.
- )
- ^ PMID 27558685.
- ^ Dolgin, Elie (September 14, 2021). "The tangled history of mRNA vaccines". Nature.
- ^ "The Nobel Prize in Physiology or Medicine 2023". NobelPrize.org. Retrieved 2023-10-02.
- ^ PMID 34805188.