PseudoUridine 5'-monophosphate

Higher enzymatic hydrolysis stability of pseudoUridine

In general, the heterocyclic moiety is linked to the ribose portion through its nitrogen atom forming a C-N bond to product nucleoside, which could be called N-nucleoside. Differently, C-nucleosides is referred non-canonical nucleosides where the heterocycle combine with ribose via a C-C bond. These C-nucleosides are naturally occurring and endowed with a higher enzymatic hydrolysis stability of the C-C glycosidic bond compared with the C-N bond of N-nucleosides.

pseudoUridine (Ψ) is an isomer of uridine and belong to the non-canonical C-nucleoside, which is the most abundant modified nucleoside in noncoding RNAs (ncRNAs). Introducing the Ψ into both single-stranded and double-stranded RNAs to provide structural rigidity enhancement, because of an appropriate setting for the co-ordination of a water molecule between the Ψ free imino proton and the 5'-phosphate backbone of the preceding residue when incorporation of Ψ in oligonucleotides. To lead a reduced backbone mobility and a restricted base conformation inducing enhanced bases stacking which is perhaps the major contribution of Ψ toward stabilizing the RNA structure.

Catabolism of pseudoUridine

In Ψ biosynthesis, pseudoUridine synthases introduce Ψ through the isomerization of specific uridine residues via the post-transcriptional modification of the RNA. As early as 1970, it was found that in Escherichia coli, pseudoUridine added to the growth medium could be used as the sole pyrimidine source by pyrimidine auxotrophic mutants. This was later shown to be achieved through the catabolism of pseudoUridine. A metabolic process has been acknowledged for pseudoUridine, and it involves the pseudoUridine phosphorylation to generate pseudoUridine 5^'-monophosphate (ΨMP) catalyzed by the enzyme pseudoUridine kinase and thereafter the C-C glycosidic bond cleavage to give uracil and ribose 5-phosphate which mediated by the pseudoUridine 5ʹ-monophosphate glycosidase.

Study reported the crystal structure of pseudoUridine 5^'-monophosphate glycosidase, the proposed mechanism of pseudoUridine cleavage contemplates the acid catalyzed ribose ring opening followed by a covalent linkage between the ribose C1^' and a pseudoUridine 5^'-monophosphate glycosidase active site lysine amino group. This modification leads to a facile C-C glycosidic bond fragmentation following a novel retro aldol-type mechanism. These above two enzymes responsible for pseudoUridine degradation were identified in the uropathogenic Escherichia coli, the principal agent of urinary tract infections in humans, while the genes encoding these enzymes are absent from the genomes of man and other mammals.

pseudoUridine 5^'-monophosphate in plant

PseudoUridine is a common nucleoside modification found in ncRNAs and mRNAs. RNA undergoes constant turnover, releasing free pseudoUridine, but the metabolism of pseudoUridine in eukaryotes has not been studied enough. Recently, one research showed that pseudoUridine is catabolized in the peroxisome by a pseudoUridine kinase from the PfkB family that generates ΨMP and a ΨMP glycosylase that hydrolyzes ΨMP to uracil and ribose-5-phosphate in Arabidopsis thaliana. Disruption of pseudoUridine catabolism leads to strong pseudoUridine accumulation and increased ΨMP content. It is worth noting that ΨMP is toxic to this plant, causing delayed germination and growth inhibition. However, experiments have shown that impairing pseudoUridine catabolism does not affect the Ψ/U ratio in RNA. The bipartite peroxisomal pseudoUridine kinase and ΨMP glycosylase are conserved in plants and algae, whereas some fungi and most animals (except mammals) possess a ΨMP glycosylase - pseudoUridine kinase fusion protein, likely in mitochondria.