PseudoUridine
PseudoUridine (abbreviated by Ψ) or 5-ribosyluracil, is an isomer of uridine (U), and unlike uracil in uridine, which is linked to ribose by a carbon-nitrogen bond (C1-N1), uridine and ribose of Ψ are linked by a carbon-carbon bond (C1-C5). Uracil and ribose are connected by a C1-C5 bond in Ψ, so its structure is more flexible and has an additional site for hydrogen bonding than uridine, and the overlap effect in RNA is higher than that of uridine. Ψ was first discovered as early as 1951. It is well known that Ψ is the most common modification in cellular RNA and is found in all domains of organisms. Therefore, Ψ is known as the "fifth nucleoside" in addition to A, U, C and G.
Applications of pseudoUridine
As the most abundant modification of RNA, PseudoUridine may affect the structure, function, location and half-life of RNAs. PseudoUridine modifications have been found in transfer RNA (tRNA), ribosomal RNA (rRNA), small nuclear RNA (snRNA), and have important roles for these abundant non-coding RNAs (ncRNAs). For instance, PseudoUridine in rRNA contributes to rRNA processing and protein synthesis, PseudoUridine in tRNA is critical for local structure and decoding, and PseudoUridine in snRNA affects snRNP splicing that facilitates the cleavage of precursor mRNA by spliceosomes. Because widespread pseudouridylation events have been identified in the transcriptome of yeast, mice and humans, further studies have found PseudoUridine modified RNA species such as messenger RNA (mRNA). It is worth noting that the function of PseudoUridine in mRNA remains to be discovered, but some studies suggested that PseudoUridine in the stop codon may cause translation readthrough. PseudoUridine may also be used by cells as a symbol to recognize their own versus foreign RNAs, for example, innate immune proteins such as RIG-I and protein kinase R could recognize viral RNAs that do not contain PseudoUridine, leading to initiation of an immune response.
PseudoUridine synthase (PUS)
PseudoUridine modification in cells is one of the post-transcriptional RNA modifications. PseudoUridine is converted from uridine catalyzed by pseudoUridine synthase (PUS) via breakage of the glycosidic bond. PUSs can be classified into six families including TruA, TruB, TruD, RsuA, RluA and Pus10p. Human cells contain 13 PUS members that belong to five families except RsuA. Two major classes of PUSs guiding pseudouridylation are either RNA-dependent or RNA-independent. The RNA-dependent PUSs, Cbf5, in yeast and DCK1 in humans, associate with Box H/ACA snoRNPs and recognize their targets through base pairing between the guide snoRNA and substrate RNA. The RNA-independent PUS proteins target site-specific modification of tRNA, snRNA and rRNA by directly recognizing sequence and structural elements within these molecules.
Studies have been reported that PUSs relate to human diseases and important biological processes. For example, mutations in PUS1 from the TruA family lead to mitochondrial myopathy and sideroblastic anemia, and homozygous variants in PUS3 contribute to intellectual disability. A study found that dyskeratosis congenita is caused by mutations in DKC1, an RNA-dependent TruB member. In the TruD family, PUS7 variants are also connected to intellectual disability. PUS7-dependent Ψ modification in tRNA fragments was recently found to impact translation and contributes to tumorigenesis. In conclusion, these researches emphasize that PUSs play an important role in biological processes and human health. Notably, a recent study has shown the differential functions of human PUS10 in nuclear miRNA processing and cytoplasmic tRNA pseudouridylation, which is filling a gap in the field of PUSs research. In this study, PUS10 is demonstrated that it can work on different RNA species either in a catalytically dependent or independent approach.