Location of Repository

Pseudouridine synthase 1: a site-specific synthase without strict sequence recognition requirements

By Bryan S. Sibert and Jeffrey R. Patton

Abstract

Pseudouridine synthase 1 (Pus1p) is an unusual site-specific modification enzyme in that it can modify a number of positions in tRNAs and can recognize several other types of RNA. No consensus recognition sequence or structure has been identified for Pus1p. Human Pus1p was used to determine which structural or sequence elements of human tRNASer are necessary for pseudouridine (Ψ) formation at position 28 in the anticodon stem-loop (ASL). Some point mutations in the ASL stem of tRNASer had significant effects on the levels of modification and compensatory mutation, to reform the base pair, restored a wild-type level of Ψ formation. Deletion analysis showed that the tRNASer TΨC stem-loop was a determinant for modification in the ASL. A mini-substrate composed of the ASL and TΨC stem-loop exhibited significant Ψ formation at position 28 and a number of mutants were tested. Substantial base pairing in the ASL stem (3 out of 5 bp) is required, but the sequence of the TΨC loop is not required for modification. When all nucleotides in the ASL stem other than U28 were changed in a single mutant, but base pairing was retained, a near wild-type level of modification was observed

Topics: Nucleic Acid Enzymes
Publisher: Oxford University Press
OAI identifier: oai:pubmedcentral.nih.gov:3299991
Provided by: PubMed Central
Download PDF:
Sorry, we are unable to provide the full text but you may find it at the following location(s):
  • http://www.pubmedcentral.nih.g... (external link)
  • Suggested articles

    Preview

    Citations

    1. (2001). A conserved pseudouridine modification in eukaryotic U2 snRNA induces a change in branch-site architecture.
    2. (2006). A previously unidentified activity of yeast and mouse RNA:pseudouridine synthases 1 (Pus1p) on tRNAs.
    3. (2001). A small nucleolar guide RNA functions both in 2’-O-ribose methylation and pseudouridylation of the U5 spliceosomal RNA.
    4. (2002). An H/ACA guide RNA directs U2 pseudouridylation at two different sites in the branch point recognition region in Xenopus oocytes.
    5. (1998). An RNA model system for investigation of pseudouridine stabilization of the codon-anticodon interaction in tRNALys, tRNAHis and tRNATyr.
    6. (1974). Biosynthesis of pseudouridine in transfer ribonucleic acid.
    7. (2003). Caenorhabditis elegans pseudouridine synthase 1 activity in vivo: tRNA is a substrate but not U2 small nuclear RNA.
    8. (2002). Cajal body-specific small nuclear RNAs: a novel class of 2’-O-methylation and pseudouridylation guide RNAs.
    9. (1998). Characterization of yeast protein Deg1 as pseudouridine synthase (Pus3) catalyzing the formation of psi 38 and psi 39 in tRNA anticodon loop.
    10. (1999). Cloning and characterization of a mammalian pseudouridine synthase.
    11. (2001). Cocrystal structure of a tRNA Psi55 pseudouridine synthase: nucleotide flipping by an RNA-modifying enzyme.
    12. (1998). Compilation of tRNA sequences and sequences of tRNA genes.
    13. (1984). Efficient in vitro synthesis of biologically active RNA and RNA hybridization probes from plasmids containing a bacteriophage SP6 promoter.
    14. (2006). Formation of the conserved pseudouridine at position 55 in archaeal tRNA.
    15. (2007). How U38, 39, and 40 of many tRNAs become the targets for pseudouridylation by TruA.
    16. (2004). Human box H/ACA pseudouridylation guide RNA machinery.
    17. (2001). Identification and characterization of the tRNA:Psi 31-synthase (Pus6p) of Saccharomyces cerevisiae.
    18. (1995). In vitro reconstitution of mammalian U2 and U5 snRNPs active in splicing: Sm proteins are functionally interchangeable and are essential for the formation of functional U2 and U5 snRNPs.
    19. (1997). Intron-dependent enzymatic formation of modified nucleosides in eukaryotic tRNAs: a review.
    20. (2002). Lack of pseudouridine 38/39 in the anticodon arm of yeast cytoplasmic tRNA decreases in vivo recoding efficiency.
    21. (2004). Missense mutation in pseudouridine synthase 1 (PUS1) causes mitochondrial myopathy and sideroblastic anemia (MLASA).
    22. (2005). Mitochondrial myopathy and sideroblastic anemia (MLASA): missense mutation in the pseudouridine synthase 1 (PUS1) gene is associated with the loss of tRNA pseudouridylation.
    23. (2005). Mitochondrial myopathy, sideroblastic anemia, and lactic acidosis: an autosomal recessive syndrome in Persian Jews caused by a mutation in the PUS1 gene.
    24. (1998). Modification and Editing of RNA.
    25. (1998). Modifications of U2 snRNA are required for snRNP assembly and pre-mRNA splicing.
    26. (2004). Modified nucleotides at the 5’ end of human U2 snRNA are required for spliceosomal E-complex formation.
    27. (2000). Mouse pseudouridine synthase 1: gene structure and alternative splicing of pre-mRNA.
    28. (2007). Nonsense mutation in pseudouridylate synthase 1 (PUS1) in two brothers affected by myopathy, lactic acidosis and sideroblastic anaemia (MLASA).
    29. (1996). Nuclear pore proteins are involved in the biogenesis of functional tRNA.
    30. (1987). Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates.
    31. (2008). Partial activity is seen with many substitutions of highly conserved active site residues in human Pseudouridine synthase 1.
    32. (1999). Point mutations in yeast CBF5 can abolish in vivo pseudouridylation of rRNA.
    33. (2004). Pseudouridine in and near the branch site recognition region of U2 snRNA are required for snRNP biogenesis and pre-mRNA splicing in Xenopus oocytes.
    34. (1992). Pseudouridine in the anticodon G psi A of plant cytoplasmic tRNA(Tyr) is required for UAG and UAA suppression in the TMV-specific context.
    35. (1999). 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.
    36. (2005). Pseudouridine modification in Caenorhabditis elegans spliceosomal snRNAs: unique modifications are found in regions involved in snRNA-snRNA interactions.
    37. (2000). Pseudouridine Synthase 3 from Mouse Modifies the Anticodon Loop of tRNA.
    38. (2006). Pseudouridine synthases.
    39. (1999). Pseudouridine synthetase Pus1 of Saccharomyces cerevisiae: kinetic characterisation, tRNA structural requirement and real-time analysis of its complex with tRNA.
    40. (2004). Pseudouridylation at position 32 of mitochondrial and cytoplasmic tRNAs requires two distinct enzymes in Saccharomyces cerevisiae.
    41. (2007). Pus3p- and Pus1p-dependent pseudouridylation of steroid receptor RNA activator controls a functional switch that regulates nuclear receptor signaling.
    42. (2004). Regulation of nuclear receptor activity by a pseudouridine synthase through posttranscriptional modification of Steriod Receptor
    43. (1990). Relaxation of a transfer RNA specificity by removal of modified nucleotides.
    44. (2009). RNA sequence and two-dimensional structure features required for efficient substrate modification by the Saccharomyces cerevisiae RNA:{Psi}-synthase Pus7p.
    45. (1999). RNA:pseudouridine synthetase Pus1 from Saccharomyces cerevisiae: oligomerization property and stoichiometry of the complex with yeast tRNA(Phe).
    46. (1997). Site-specific pseudouridine formation in preribosomal RNA is guided by small nucleolar RNAs.
    47. (2001). Small nucleolar RNA-guided post-transcriptional modification of cellular RNAs.
    48. (1997). Small nucleolar RNAs direct site-specific synthesis of pseudouridine in ribosomal RNA.
    49. (1995). Stabilization of RNA stacking by pseudouridine.
    50. (1999). Stabilization of the anticodon stem-loop of tRNALys,3 by an A+-C base- pair and by pseudouridine.
    51. (2003). Structure of tRNA pseudouridine synthase TruB and its RNA complex: RNA recognition through a combination of rigid docking and induced fit.
    52. (1989). Synthesis of small RNAs using T7 RNA polymerase.
    53. (1997). The effect of pseudouridine and pH on the structure and dynamics of the anticodon stem-loop of tRNA(Lys,3).
    54. (1993). The long extra arms of human tRNA((Ser)Sec) and tRNA(Ser) function as major identify elements for serylation in an orientation-dependent, but not sequence-specific manner.
    55. (2000). The structural basis for tRNA recognition and pseudouridine formation by pseudouridine synthase I.
    56. (1997). The yeast gene YNL292w encodes a pseudouridine synthase (Pus4) catalyzing the formation of psi55 in both mitochondrial and cytoplasmic tRNAs.
    57. (1998). The yeast tRNA:pseudouridine synthase Pus1p displays a multisite substrate specificity.
    58. (1998). Transfer RNA-pseudouridine synthetase Pus1 of Saccharomyces cerevisiae contains one atom of zinc essential for its native conformation and tRNA recognition.
    59. (2009). tRNAdb 2009: compilation of tRNA sequences and tRNA genes.
    60. (1997). tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.

    To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.