Spb1p-Directed Formation of Gm2922 in the Ribosome Catalytic Center Occurs at a Late Processing Stage

Lapeyre, Bruno; Purushothaman, Suresh K.

doi:10.1016/j.molcel.2004.10.022

Cited by 100 publications

(118 citation statements)

References 36 publications

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“…This information is now fully integrated into the database. Presently, 76 snoRNA species have been identified, and essentially all of the 100 known Nm and C modifications in yeast rRNA have been assigned to a specific guide snoRNA-with experimental validation-or to proteins, in two cases (Lowe and Eddy 1999;Lapeyre and Purushothaman 2004;Schattner et al 2004;Torchet et al 2005;W.A. Decatur and M.J. Fournier, unpubl.…”

Section: Upgrading Of the Yeast Snorna Databasementioning

confidence: 99%

New bioinformatic tools for analysis of nucleotide modifications in eukaryotic rRNA

Piekna‐Przybylska

Decatur²,

Fournier³

2007

RNA

115

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This report presents a valuable new bioinformatics package for research on rRNA nucleotide modifications in the ribosome, especially those created by small nucleolar RNA:protein complexes (snoRNPs). The interactive service, which is not available elsewhere, enables a user to visualize the positions of pseudouridines, 29-O-methylations, and base methylations in threedimensional space in the ribosome and also in linear and secondary structure formats of ribosomal RNA. Our tools provide additional perspective on where the modifications occur relative to functional regions within the rRNA and relative to other nearby modifications. This package of new tools is presented as a major enhancement of an existing but significantly upgraded yeast snoRNA database available publicly at http://people.biochem.umass.edu/sfournier/fournierlab/snornadb/. The other key features of the enhanced database include details of the base pairing of snoRNAs with target RNAs, genomic organization of the yeast snoRNA genes, and information on corresponding snoRNAs and modifications in other model organisms.

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Section: Upgrading Of the Yeast Snorna Databasementioning

confidence: 99%

New bioinformatic tools for analysis of nucleotide modifications in eukaryotic rRNA

Piekna‐Przybylska

Decatur²,

Fournier³

2007

RNA

115

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“…There is no obvious homology with other methyltransferases, based on BLAST search. Moreover, there is little, if any, similarity between Trm13 protein and other tRNA 29-O-methyltransferases identified in yeast (Cavaille et al 1999;Pintard et al 2002a,b;Lapeyre and Purushothaman 2004), as determined by pairwise BLAST, or with the RrmJ/fibrillarin superfamily of 29-Omethyltransferases (Feder et al 2003). Since Trm13 protein is described in the PFAM database as a domain of unknown function (DUF 715) and all of the putative Trm13 protein homologs are annotated as novel or hypothetical proteins, the Trm13 family might represent an additional family of methyltransferase proteins, although the low degree of similarity among methyltransferases within the family precludes a definitive statement in this regard (Schubert et al 2003).…”

Section: Trm13 Protein Is Highly Conserved Within Eukaryotes and Is Nmentioning

confidence: 99%

The 2′-O-methyltransferase responsible for modification of yeast tRNA at position 4

Wilkinson¹,

Crary²,

Jackman³

et al. 2007

RNA

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The methylation of the ribose 29-OH of RNA occurs widely in nature and in all stable RNAs and occurs at five positions in yeast tRNA. 29-O-methylation of tRNA at position 4 is interesting because it occurs in the acceptor stem (which is normally undermodified), it is the only 29-O-methylation that occurs in the middle of a duplex region in tRNA, the modification is conserved in eukaryotes, and the features of the tRNA necessary for substrate recognition are poorly defined. We show here that Saccharomyces cerevisiae ORF YOL125w (TRM13) is necessary and sufficient for 29-O-methylation at position 4 of yeast tRNA. Biochemical analysis of the S. cerevisiae proteome shows that Trm13 copurifies with 29-O-methylation activity, using tRNA Gly(GCC) as a substrate, and extracts made from a trm13-D strain have undetectable levels of this activity. Trm13 is necessary for activity in vivo because tRNAs isolated from a trm13-D strain lack the corresponding 29-O-methylated residue for each of the three known tRNAs with this modification. Trm13 is sufficient for 29-O-methylation at position 4 in vitro since yeast Trm13 protein purified after expression in Escherichia coli has the same activity as that produced in yeast. Trm13 protein binds substrates tRNA His and tRNA Gly(GCC) with K D values of 85 6 8 and 100 6 14 nM, respectively, and has a K M for tRNA His of 10 nM, but binds nonsubstrate tRNAs very poorly (K D > 1 mM). Trm13 is conserved in eukaryotes, but there is no sequence similarity between Trm13 and other known methyltransferases.

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“…In a wildtype context, Um2921 is RNA-guided by a C/D snoRNA (snR52), whereas the neighbor Gm2922 is enzymatically modified by Sbp1 at a later stage of 60S maturation. In a context of snR52 depletion, however, Um2921 may also be performed by Sbp1 described as a ''region'' specific enzyme (Lapeyre and Purushothaman 2004).…”

Section: Site-specific Mtase or C/d Srnp: Which Came First?mentioning

confidence: 99%

The Cm56 tRNA modification in archaea is catalyzed either by a specific 2′-O-methylase, or a C/D sRNP

Renalier¹,

Joseph²,

Gaspin³

et al. 2005

RNA

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We identified the first archaeal tRNA ribose 2 0 -O-methylase, aTrm56, belonging to the Cluster of Orthologous Groups (COG) 1303 that contains archaeal genes only. The corresponding protein exhibits a SPOUT S-adenosylmethionine (AdoMet)-dependent methyltransferase domain found in bacterial and yeast G18 tRNA 2 0 -O-methylases (SpoU, Trm3). We cloned the Pyrococcus abyssi PAB1040 gene belonging to this COG, expressed and purified the corresponding protein, and showed that in vitro, it specifically catalyzes the AdoMet-dependent 2 0 -O-ribose methylation of C at position 56 in tRNA transcripts. This tRNA methylation is present only in archaea, and the gene for this enzyme is present in all the archaeal genomes sequenced up to now, except in the crenarchaeon Pyrobaculum aerophilum. In this archaea, the C56 2 0 -O-methylation is provided by a C/D sRNP. Our work is the first demonstration that, within the same kingdom, two different mechanisms are used to modify the same nucleoside in tRNAs.

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Spb1p-Directed Formation of Gm2922 in the Ribosome Catalytic Center Occurs at a Late Processing Stage

Cited by 100 publications

References 36 publications

New bioinformatic tools for analysis of nucleotide modifications in eukaryotic rRNA

New bioinformatic tools for analysis of nucleotide modifications in eukaryotic rRNA

The 2′-O-methyltransferase responsible for modification of yeast tRNA at position 4

The Cm56 tRNA modification in archaea is catalyzed either by a specific 2′-O-methylase, or a C/D sRNP

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