Pseudouridine formation in small nuclear RNAs

Pleiotropic effects and compensation mechanisms determine tissue specificity in mitochondrial myopathy and sideroblastic anemia (MLASA)

The tissue specificity of mitochondrial diseases is poorly understood. Recently, tissue-specific quantitative differences of the components of the mitochondrial translation system have been found to correlate with disease presentation in fatal hepatopathy caused by mutations in mitochondrial translation factor EFG1. MLASA is an autosomal recessive inherited progressive oxidative phosphorylation disorder that affects muscle and erythroid cells. The disease is caused by the homozygous point mutation C656T (R116W) in the catalytic domain of the pseudouridylate synthase 1 (PUS1) gene, which leads to a complete lack of pseudouridylation at the expected sites in mitochondrial and cytoplasmic tRNAs. Despite the presence of these altered tRNAs, most tissues are unaffected, and even in muscle and erythroid cells the disease phenotype only slowly emerges over the course of years. In order to elucidate intracellular pathways through which the homozygous mutation leads to tissue-restricted phenotype, we performed microarray expression analysis of EBV-transformed lymphoblasts from MLASA patients, heterozygous parents, and controls using human Beadchip microarray with 47,296 transcripts. Genes coding for proteins involved in DNA transcription and its regulation, and metal binding proteins, demonstrated major differences in expression between patients and all other individuals with normal phenotype. Genes coding for ribosomal proteins differed significantly between individual with at least one copy of the mutated PUS1 gene and controls. These findings indicate that the lack of tRNA pseudouridylation can be overcome by compensatory changes in levels of ribosomal proteins, and that the disease phenotype in affected tissues is likely due to pleiotropic effects of PUS1p on non-tRNA molecules involved in DNA transcription and iron metabolism. Similar combinations of mechanisms may play a role in the tissue specificity of other mitochondrial disorders.

Immunopurified small nucleolar ribonucleoprotein particles pseudouridylate rRNA independently of their association with phosphorylated Nopp140

The isomerization of up to 100 uridines to pseudouridines (Psis) in eukaryotic rRNA is guided by a similar number of box H/ACA small nucleolar RNAs (snoRNAs), each forming a unique small nucleolar ribonucleoprotein particle (snoRNP) with the same four core proteins, NAP57 (also known as dyskerin or Cbf5p), GAR1, NHP2, and NOP10. Additionally, the nucleolar and Cajal body protein Nopp140 (Srp40p) associates with the snoRNPs. To understand the role of these factors in pseudouridylation, we established an in vitro assay system. Short site-specifically (32)P-labeled rRNA substrates were incubated with subcellular fractions, and the conversion of uridine to Psi was monitored by thin-layer chromatography after digestion to single nucleotides. Immunopurified box H/ACA core particles were sufficient for the reaction. SnoRNPs associated quantitatively and reversibly with Nopp140. However, pseudouridylation activity was independent of Nopp140, consistent with a chaperoning role for this highly phosphorylated protein. Although up to 14 bp between the snoRNA and rRNA were required for the in vitro reaction, rRNA pseudouridylation and release occurred in the absence of ATP and magnesium. These data suggest that substrate release takes place without RNA helicase activity but may be aided by the snoRNP core proteins.

Pseudouridine mapping in the Saccharomyces cerevisiae spliceosomal U small nuclear RNAs (snRNAs) reveals that pseudouridine synthase pus1p exhibits a dual substrate specificity for U2 snRNA and tRNA

Pseudouridine (Psi) residues were localized in the Saccharomyces cerevisiae spliceosomal U small nuclear RNAs (UsnRNAs) by using the chemical mapping method. In contrast to vertebrate UsnRNAs, S. cerevisiae UsnRNAs contain only a few Psi residues, which are located in segments involved in intermolecular RNA-RNA or RNA-protein interactions. At these positions, UsnRNAs are universally modified. When yeast mutants disrupted for one of the several pseudouridine synthase genes (PUS1, PUS2, PUS3, and PUS4) or depleted in rRNA-pseudouridine synthase Cbf5p were tested for UsnRNA Psi content, only the loss of the Pus1p activity was found to affect Psi formation in spliceosomal UsnRNAs. Indeed, Psi44 formation in U2 snRNA was abolished. By using purified Pus1p enzyme and in vitro-produced U2 snRNA, Pus1p is shown here to catalyze Psi44 formation in the S. cerevisiae U2 snRNA. Thus, Pus1p is the first UsnRNA pseudouridine synthase characterized so far which exhibits a dual substrate specificity, acting on both tRNAs and U2 snRNA. As depletion of rRNA-pseudouridine synthase Cbf5p had no effect on UsnRNA Psi content, formation of Psi residues in S. cerevisiae UsnRNAs is not dependent on the Cbf5p-snoRNA guided mechanism.

Characterization of yeast protein Deg1 as pseudouridine synthase (Pus3) catalyzing the formation of psi 38 and psi 39 in tRNA anticodon loop

The enzymatic activity of yeast gene product Deg1 was identified using both disrupted yeast strain and cloned recombinant protein expressed in yeast and in Escherichia coli. The results show that the DEG1-disrupted yeast strain lacks synthase activity for the formation of pseudouridines psi 38 and psi 39 in tRNA whereas the other activities, specific for psi formation at positions 13, 27, 28, 32, 34, 35, 36, and 55 in tRNA, remain unaffected. Also, the His6-tagged recombinant yeast Deg1p expressed in E. coli as well as a protein fusion with protein A in yeast display the enzymatic activity only toward psi 38 and psi 39 formation in different tRNA substrates. Therefore, Deg1p is the third tRNA:pseudouridine synthase (Pus3p) characterized so far in yeast. Disruption of the DEG1 gene is not lethal but reduces considerably the yeast growth rate, especially at an elevated temperature (37 degrees C). Deg1p localizes both in the nucleus and in the cytoplasm, as shown by immunofluorescence microscopy. Identification of the pseudouridine residues present (or absent) in selected naturally occurring cytoplasmic and mitochondrial tRNAs from DEG1-disrupted strain points out a common origin of psi 38- and psi 39-synthesizing activity in both of these two cellular compartments. The sensitivity of Pus3p (Deg1p) activity to overall three-dimensional tRNA architecture and to a few individual mutations in tRNA was also studied. The results indicate the existence of subtle differences in the tRNA recognition by yeast Pus3p and by its homologous tRNA:pseudouridine synthase truA from E. coli (initially called hisT or PSU-I gene product).

Small nucleolar RNAs direct site-specific synthesis of pseudouridine in ribosomal RNA

Ten ACA yeast small nucleolar RNAs (snoRNAs) were shown to be required for site-specific synthesis of pseudouridine psi in ribosomal RNA. A common secondary folding motif for the snoRNAs and rRNA target segments predicts that site selection involves: (1) base pairing of the snoRNA with complementary rRNA elements flanking the site of modification, and (2) identification of a uridine located at a near-constant distance from the snoRNA ACA box. The model is supported by mutations showing that: (1) reducing the complementarity between the snoRNA and rRNA disrupts psi formation, and (2) altering the distance between the ACA box and target uridine causes an adjacent uridine to be modified. This discovery implies that most snoRNAs function in targeting nucleotide modification in rRNA: ribose methylation for the box C/D snoRNAs and psi formation for the ACA snoRNAs.