The mesmerizing world of RNAs is expansive, and so are their modifications and bases. The first notable feature of RNAs is that containing pseudouridine (5-ribosyluracil). This nucleoside is a C5 isomer of uracil base and is present in tRNAs, rRNAs, small nuclear RNAs (snRNAs), small nucleolar RNAs (snoRNAs), and mRNAs1,2.It was found in 1951 as the first modified nucleoside and then took the name of “The fifth nucleoside”. After that ongoing RNA, epigenetics studies helped scientists to understand pseudouridine’s nature and its importance in RNA.1 In this article pseudouridine’s structural aspects, its duty, and biosynthesis will be explained.
Being identified as the first modified nucleoside, pseudouridine has been extensively studied. It comprises 5% of all RNA nucleotides. Furthermore, its modification is the most abundant one in all RNA modifications3.To explain pseudouridine and its features, its structure, and biogenesis should be understood well. In uridine, glycosidic bond forms between C–N, which makes the bond less flexible. In contrast, the glycosidic bond in pseudouridine forms between C–C, and that unusual bond gives enhanced bond flexibility, rotation, and stability2.In Watson-Crick faces of the nucleosides, pseudouridine has an additional H-bond donor (figure 1). To think of the sugar-phosphate backbone of RNAs, this additional H-bond attracts a water molecule by doing so it helps to rigid the backbone and enhances base stacking1,2.

The synthesis of pseudouridine is done by either pseudouridine synthases (PUS) or H/ACA snoRNP complexes. PUSs have been divided into 6 main categories in order TruD, TruA, TruB, RsuA, RluA, and PUS104,5. They can be a part of RNA-guided ribonucleoprotein complexes (RNPs) or can be found as standalone enzymes in eukaryotes. Even though each enzyme has a unique mechanism, PUSs perform the isomerization of uridine to pseudouridine. This isomerization is irreversible and spontaneous5.Any defect in the biosynthesis of pseudouridine results in high-morbidity diseases such as X-linked dyskeratosis congenital (X-DC).1 X-DC is characterized by telomere maintenance. But how is this disease linked to pseudouridine synthesis? The patients who have mutant DKC1 genes are unable to maintain telomerase activity. Therefore, the telomere lengths are getting shorter after each replication. DKC1 gene encodes dyskerin protein. This protein binds the telomerase (hTR) and helps to stabilize the structure. Dyskerin protein has multiple pseudouridylation sites (TruB synthase motifs). Without pseudouridylation, the enzyme activity dramatically decreases. Mutated DKC1 gene also results in defective rRNA pseudouridylation. Eventually, it ends up with decreased translation rates and defaced telomerase activit.1,6.
To sum up, pseudouridine is the fifth RNA nucleoside. Many articles have reported its presence in rRNAs, snRNAs, tRNAs, and others1,2. Lacking pseudouridylation sites has led to the conclusion that its presence is a must. It is vital for cell growth, translation rate and accuracy, and base pairing1,2,6. Having been synthesized by PUSs, pseudouridine occupies 5% of all RNAs in a cell. Considering the fact that the isomerization reaction is irreversible, it can be used as a biomarker for diseases such as cancer and so on3. Moreover, the application of pseudouridine goes beyond the borders. For instance, mRNA vaccines that are being used for the SARS-CoV-2 outbreak contain multiple methylated pseudouridine sites7. The use of pseudouridine in mRNA vaccines is to stabilize the structure and enhance the translation rate. All these postulations, results, and the great spectrum of usage make us think about what else can be done. In the end, pseudouridine is worth more investigation for future aspects, new methodologies, and strategies to overcome diseases.
References:
- Li, X., Ma, S., & Yi, C. (2016). Pseudouridine: the fifth RNA nucleotide with renewed interests. Current Opinion in Chemical Biology, 33(Figure 2), 108–116. https://doi.org/10.1016/j.cbpa.2016.06.014
- Mueller, M. (1990). Critical review. Critical Review, 4(1–2), ebi. https://doi.org/10.1080/08913819008459588
- Stockert, J. A., Weil, R., Yadav, K. K., Kyprianou, N., & Tewari, A. K. (2021). Pseudouridine as a novel biomarker in prostate cancer. Urologic Oncology: Seminars and Original Investigations, 39(1), 63–71. https://doi.org/10.1016/j.urolonc.2020.06.026
- Yu, Y. T., & Meier, U. T. (2014). RNA-guided isomerization of uridine to pseudouridine – Pseudouridylation. RNA Biology, 11(12), 1483–1494. https://doi.org/10.4161/15476286.2014.972855
- Spenkuch, F., Motorin, Y., & Helm, M. (2014). Pseudouridine: Still mysterious, but never a fake (uridine)! RNA Biology, 11(12), 1540–1554. https://doi.org/10.4161/15476286.2014.992278
- Heiss, N., Knight, S., Vulliamy, T. et al. X-linked dyskeratosis congenita is caused by mutations in a highly conserved gene with putative nucleolar functions. Nat Genet 19, 32–38 (1998). https://doi.org/10.1038/ng0598-32
- Morais P, Adachi H, Yu YT. The Critical Contribution of Pseudouridine to mRNA COVID-19 Vaccines. Front Cell Dev Biol. 2021 Nov 4;9:789427. doi: 10.3389/fcell.2021.789427. PMID: 34805188; PMCID: PMC8600071.
Figure reference: Stockert, J. A., Weil, R., Yadav, K. K., Kyprianou, N., & Tewari, A. K. (2021). Pseudouridine as a novel biomarker in prostate cancer. Urologic Oncology: Seminars and Original Investigations, 39(1), 63–71. https://doi.org/10.1016/j.urolonc.2020.06.026
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