Pseudouridine, in RNA

Methylpseudouridine (m vj/) has been synthesised and incorporated into RNA where it was found to be slightly destabilising compared to pseudouridine.Psuedouridine can be selectively cyanoethylated with acrylonitrile, aiding its detection in tRNA by MALDI mass spectrometry. The presence of pseudouridine in RNA has also been detected by NMR using chemical exchange spectroscopy as pseudouridine has an additional Another... 

Patteson, K.G., Rodicio, L.P., and limbach, P.A. (2001) Identification of the mass-silent post-transcriptionally modified nucleoside pseudouridine in RNA by matrix-assisted laser desorption/ ionization mass spectrometry. Nucleic Acids Res., 29 (10), E49-9. 

Increased levels of pseudouridine have been reported to be present in the urine of patients with various types of cancer (Al, M20, Wl, W2). Since pseudouridine is only found in RNA, Kuo et al. (K38) developed a sensitive RPLC method for the rapid determination of urine pseudouridine levels. In a study of 10 colon cancer patients, they reported that 9 exhibited higher than normal pseudouridine-to-creatinine ratios. Davis et al. (D2) have also investigated urine ribonucleoside distribution patterns in patients with advanced colon cancer and report increased levels of I-methylinosine, 1-methylguanosine, 2-methyIguanosine, adenosine, and N. N -dimethylguanosine when compared to normal urine controls. Figure 17 illustrates the advanced colon cancer and normal urine chromatographic profiles. 

Figure 24 Transglycosylase reactions. The four known transglycosylation reactions involved in RNA modification generating in archaea, archaeosine (G+) in eubacteria and eukarya, queuosine (Q) and across the three kingdoms, pseudouridine ( ).

Pseudouridine ( j/, pseudoU) is the most abundant modified nucleoside in RNA and has been referred to as the fifth nucleoside . PseudoU is found in a plethora of positions within tRNAs as well as in a number of positions in rRNAs and in snRNAs. It is quite likely that the true extent of pseudoU occurrence in RNA species will not be fully understood for some time. One of the difficulties in detecting RNA base modifications is the relatively low abundance of many RNA species in vivo. Unlike queuine and archaeosine, where one could theoretically synthesize radiolabeled forms of the modified base and use this to probe for RNA species that are substrates for TGT, less direct and possibly less sensitive methods must be used to detect pseudoU formation. ... 

THioUridine synthases, RNA Methyltransferases, and Pseudouridine synthases RNA-binding motif originally characterized in TRM2 and miaB... 

Examples of A -amino-carboxy-propylation are mainly observed in RNA modifications, such as 3-(3-amino-3-carboxypropyl)uridine [9] or l-methyl-3-(3-amino-3-carboxypropyl)pseudouridine [10, 11]. Another 7V-ACP-transfer reaction was also observed in the biosynthesis of 2-(3-amino-3-carboxypropyl)-isoxazolin-5-one (neurotoxic amino acid fxoraLathyrus odoratus) (Figure 1.8) [12]. 

The diester of phosphoric acid constitutes the link betwc en the individual ribose units. The 3 -5 -type linkage is found in RNA. The bases are arranged like side chains of the sugar-phosphate chain. Some RNAs, in addition to the usual bases adenine, guanine, uracil, and cytosine, contain trace amounts of other bases. Among the latter pseudouridine is the most interesting it is a uracil which carries its ribosyl residue on C atom 5 in a C—bond (not glycosidic). 

Identification of the component pentose sugar confirms whether the polynucleotide chain is RNA or DNA. Both RNA and DNA contain the same two purine bases, adenine (A) and guanine (G) whereas they differ in their content of the pyrimidine bases. RNA contains cytosine (C) and uracil (U) but DNA contains cytosine and the 5-methyl derivative of uracil called thymine (T). In addition to these bases, called major bases, DNA and RNA also contain altered or less common bases called minor bases. In DNA, the minor bases are usually methylated derivatives of the major bases which play a special role in the functioning of the polynucleotide. RNAs, especially transfer RNAs, also contain minor bases, e.g. inosine, pseudouridine (in which uracil is linked through C-5, not N-1, to ribose), dihydrouridine, ribosylthymine and methylated derivatives of nucleosides (Figure 7.2). Minor bases are mainly modified versions of major bases. 

Ribosomal RNAs characteristically contain a number of specially modified nucleotides, including pseudouridine residues, ribothymidylic acid, and methylated bases (Figure 11.26). The central role of ribosomes in the biosynthesis of proteins is treated in detail in Chapter 33. Here we briefly note the significant point that genetic information in the nucleotide sequence of an mRNA is translated into the amino acid sequence of a polypeptide chain by ribosomes. 

PUA Putative RNA-binding domain in PseudoUridine synthase and Archaeosine transglycosylase E(MFP)AB 5(5) 3(3) ... 

Pseudouridine is formed by enzymatic rearrangement of uridine in the original transcript (Eq. 28-3). It can form a base pair with adenine in the same manner as does uracil. Pseudouridine is found not only in tRNA but also in several places in both large and small ribo-somal RNA subunits. For example, it is present at position 516 in the E. coli 16S RNA,364 at a specific position in the 23S RNA, and at many more locations in eukaryotic rRNA. 

The sequences of all three pieces of RNA in the E. coli ribosomes are known as are those from many other species. These include eukaryotic mitochondrial, plas-tid, and cytosolic rRNA. From the sequences alone, it was clear that these long molecules could fold into a complex series of hairpin loops resembling those in tRNA. For example, the 16S rRNA of E. coli can fold as in Fig. 29-2A and eukaryotic 18S RNA in a similar way (Fig. 29-4).38/39/67 69 The actual secondary structures of 16S and 18S RNAs, within the folded molecules revealed by X-ray crystallography, are very similar to that shown in Fig. 29-2A. Ribosomal RNAs undergo many posttranscriptional alterations. Methylation of 2 -hydroxyls and of the nucleic acid bases as well as conversion to pseudouridines (pp. 1638-1641) predominate over 200 modifications, principally in functionally important locations that have been found in human rRNA.69a... 

Transfer RNA (Mr s= 25,000) functions as an adapter in polypeptide chain synthesis. It comprises 10-20 percent of the total RNA in a cell, and there is at least one type of tRNA for each type of amino acid. Transfer RNAs are unique in that they contain a relatively high proportion of nucleosides of unusual structure (e.g., pseudouridine, inosine, and 2 -0-methylnucleosides) and many types of modified bases (e.g., methylated or acetylated adenine, cytosine, guanine, and uracil). As examples, the structures of pseudouridine and inosine are shown below. Inosine has an important role in codon-anticodon pairing (Chap. 17). 

Modified nucleosides incorporated into small RNA model systems can also be used to investigate the global versus individual effects of modified nucleotides on natural RNAs, such as rRNA or tRNA. For example, in some early studies, Yarian et al. (44) demonstrated that pseudouridine (Table 1) leads to increased thermal stability of the tRNA anticodon stem-loop region. Later, Meroueh et al. (45) demonstrated that pseudouridines have opposing effects on rRNA helix 69 stability, which depends on their specific locations and sequence contexts. These effects on stability may be important for conformational switching mechanisms in functional RNAs (46, 47). 

Newby MI, Greenbaum NL. A conserved pseudouridine modification in eukaryotic U2 snRNA induces a change in branch-site architecture. RNA 2001 7 833-845. 

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