Methylated regions of hamster mitochondrial ribosomal RNA: structural and functional correlates

Baer, Richard; Dubin, Donald T.

doi:10.1093/nar/9.2.323

Cited by 68 publications

(69 citation statements)

References 45 publications

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“…Unfortunately, the most obvious way to study this modification by using in vivo methylation with radioactive S-[ H]adenosylmethionine was not practical due to the large quantity of isotopes used in such studies (6) and the limited amount of RNA available from siRNA knockdown specimens.…”

Section: Resultsmentioning

confidence: 99%

Mitochondrial Ribosomal RNA (rRNA) Methyltransferase Family Members Are Positioned to Modify Nascent rRNA in Foci near the Mitochondrial DNA Nucleoid

Lee

Okot-Kotber²,

LaComb

et al. 2013

Journal of Biological Chemistry

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Background: Mitochondrial rRNAs contain site-specific modifications, including methylated residues, but few of the enzymes responsible for these modifications have been found. Results: RNMTL1, MRM1, and MRM2 are methyltransferase family members found associated with the mtDNA nucleoid and with the large ribosomal subunit. Conclusion:The association of putative RNA-modifying enzymes with nucleoids and ribosomes supports the model that assembly of mitochondrial ribosomes begins while rRNA transcription continues. Significance: This work advances understanding of the assembly of mitochondrial ribosomes necessary for biosynthesis of the respiratory chain.

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Section: Resultsmentioning

confidence: 99%

Mitochondrial Ribosomal RNA (rRNA) Methyltransferase Family Members Are Positioned to Modify Nascent rRNA in Foci near the Mitochondrial DNA Nucleoid

Lee

Okot-Kotber²,

LaComb

et al. 2013

Journal of Biological Chemistry

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“…The C1941-methylation is on the ribose, deduced from tandem MS of the unique overlapping RNase A fragment at m/z 1992. 33 Three of the methylated nucleotides could not be assigned to a specific position in the 23 S rRNA, because their sequence contexts were present in numerous copies. These were [Um]GU, [mA]UG, and G[Gm]GGC.…”

Section: Detection Of 23 S Rrna Post-transcriptional Modifications Bymentioning

confidence: 99%

“…However, comparison with modification patterns in other organisms gives suggestions to the location of these modifications. E. coli and a number of other species harbor ribose-methylated uridine at position 2552 (E. coli numbering) in the sequence context [Um]GU, identical to the above (1, 3,4,7,33). Likewise, A2503 (E. coli numbering) in the sequence AUG is methylated in E. coli (3) and in Bacillus megaterium.…”

Section: Detection Of 23 S Rrna Post-transcriptional Modifications Bymentioning

confidence: 99%

Modifications in Thermus thermophilus 23 S Ribosomal RNA Are Centered in Regions of RNA-RNA Contact

Mengel-Jørgensen¹,

Jensen

Rasmussen

et al. 2006

Journal of Biological Chemistry

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Ribosomal RNA from all organisms contains post-transcriptionally modified nucleotides whose function is far from clear. To gain insight into the molecular interactions of modified nucleotides, we investigated the modification status of Thermus thermophilus 5 S and 23 S ribosomal RNA by mass spectrometry and chemical derivatization/primer extension. A total of eleven modified nucleotides was found in 23 S rRNA, of which eight were singly methylated nucleotides and three were pseudouridines. These modified nucleotides were mapped into the published three-dimensional ribosome structure. Seven of the modified nucleotides located to domain IV, and four modified nucleotides located to domain V of the 23 S rRNA. All posttranscriptionally modified nucleotides map in the center of the ribosome, and none of them are in contact with ribosomal proteins. All except one of the modified nucleotides were found in secondary structure elements of the 23 S ribosomal RNA that contact either 16 S ribosomal RNA or transfer RNA, with five of these nucleotides physically involved in intermolecular RNA-RNA bridges. These findings strongly suggest that the posttranscriptional modifications play a role in modulating intermolecular RNA-RNA contacts, which is the first suggestion on a specific function of endogenous ribosomal RNA modifications.All cellular protein synthesis is performed by ribosomes, which are large ribonucleoprotein particles. The prokaryote ribosome consists of two stable and separable entities, a 50 S and a 30 S subunit. The 50 S subunit contains two rRNAs of ϳ3000 and 120 nucleotides (23 S and 5 S rRNA, respectively) and around 35 proteins, whereas the 30 S subunit contains 16 S rRNA of ϳ1600 nucleotides and around 20 proteins; the exact numbers vary with the species. Eukaryotic ribosomes are larger, but structural features are remarkably conserved between the domains of life.rRNAs are post-transcriptionally modified at specific nucleotides, but the number of modified nucleotides varies greatly. The large ribosomal RNA in mitochondria contains just a few modified nucleotides (1), Escherichia coli 23 S rRNA has 25 (2, 3), whereas over 100 are found in vertebrate cytoplasmic 28 S rRNA (4). The function of post-transcriptional rRNA modifications is far from clear, although they have been implicated in various processes. Specific rRNA methylation is used by numerous antibiotics-producing microorganisms as a means of autoprotection (see e.g. Refs. 5 and 6), but only a small fraction of post-transcriptional modifications can be assigned to this well defined function. E. coli 23 S rRNA modifications cluster in functionally principal parts of the ribosome such as the peptidyl transferase center and inter-subunit bridges when modeled into the structure of the Haloarcula marismortui large ribosomal subunit (7). The modified nucleotides in the central domains of 23 S rRNA from H. marismortui itself are all located in regions of intra-or intermolecular RNA-RNA contact (8) suggesting structure stabilization.The post-transcriptionall...

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“…Up to date the complete nucleotide sequences of the large-subunit rRNA genes (rDNA) from Escherichia coli [l] [20] are well conserved among these large-subunit rRNAs.…”

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confidence: 99%

The Complete Nucleotide Sequence of a 23‐S rRNA Gene from Tobacco Chloroplasts

Takaiwa

Sugiura

1982

European Journal of Biochemistry

112

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The nucleotide sequence of a tobacco chloroplast 23-S rRNA gene, including the spacer between it and the 4.5-S rRNA gene, has been determined. The 23-S rRNA coding region is 2804-base-pairs long. A comparison with the 23-S rRNA sequence of Escherichia coli reveals strong homology and further shows a similarity between the chloroplast 4.5-S rRNA and the 3'-terminal region of E. coli 23-S rRNA. However, the 101-base-pair spacer sequence between the 23-S and 4.5-S rRNA genes has little homology with E. coli 23-S rRNA.Elucidation of the structure of ribosomes and the function of large-subunit rRNAs is essentially dependent upon the determination of the primary structure of the rRNA. Up to date the complete nucleotide sequences of the large-subunit rRNA genes (rDNA) from Escherichia coli [l] [20] are well conserved among these large-subunit rRNAs.Tobacco chloroplasts have circular DNAs with molecular weights of around lo8 and their DNAs contain two rDNA clusters, which are located in an inverted order [21-231. We have previously cloned and characterized the rDNAs [24 -271. This rDNA cluster is arranged in the order of genes for 16-S, 23-S, 4.5-S and 5-S rRNAs and these four rDNAs are coded for by the same strand and the transcription proceeds from the 16-S to the 5-S rRNA gene [25,26]. The sequences of the DNAs coding for 4.5-S and 5-S rRNAs and their surrounding regions [28] and that of the 16-S rRNA [29] and its 5'-flanking region [30] have been determined previously. In this paper, we present the nucleotide sequence of a 23-S rRNA gene including the spacer between it and that for 4.5-S rRNA from tobacco chloroplasts and compare it with other large-subunit rDNAs. MATERIALS AND METHODS MaterialsTobacco (Nicotiana tabacum var. Bright Yellow 4) chloroplast 23-S rRNA was prepared as described [24] Preparation of DNA Fragments and Sequencing Recombinant plasmid pTCP243 1261 was propagated in Escherichia coliHBIO1 cells and the plasmid DNA was isolated by the cleared lysate method [33]. The DNA was digested with HindIII, XhoI or EcoRI + HindIII, and the digests were separated on 5 % polyacrylamide gels (14 x 11 x 0.5 cm). The DNA fragments containing the 23-S rRNA gene were recovered from the excised gel pieces by electrophoresis. The fragments were purified by DEAE-Sephacel chromatography [29]. DNA fragments were labeled at the 5' ends with [Y-~'P]ATP and T4 polynucleotide kinase after alkaline phosphatase treatment as described by Maxam and Gilbert [34]. The 3'-terminal labeling was carried out by using [IX-'~P]~CTP and T4 DNA polymerase as described by Challberg and Englund [35]. Labeled fragments were separated on 6 % or 8 polyacrylamide gels (37 x 28 x 0.05 cm). Strand separation was performed on 5 % polyacrylamide gels (52 x 28 x 0.05 cm). DNA fragments were eluted from the polyacrylamide gel by diffusion as described by Maxam and Gilbert [34]. Nucleoside-specific chemical cleavages (dG, dA>dC, dT+dC and dC) were performed according to the method of Maxam and Gilbert [34].Partial cleavage products were analyzed on...

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Methylated regions of hamster mitochondrial ribosomal RNA: structural and functional correlates

Cited by 68 publications

References 45 publications

Mitochondrial Ribosomal RNA (rRNA) Methyltransferase Family Members Are Positioned to Modify Nascent rRNA in Foci near the Mitochondrial DNA Nucleoid

Mitochondrial Ribosomal RNA (rRNA) Methyltransferase Family Members Are Positioned to Modify Nascent rRNA in Foci near the Mitochondrial DNA Nucleoid

Modifications in Thermus thermophilus 23 S Ribosomal RNA Are Centered in Regions of RNA-RNA Contact

The Complete Nucleotide Sequence of a 23‐S rRNA Gene from Tobacco Chloroplasts

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