Transfer Rna Modification

Björk, Glenn R.; Sollid, Johanna U. Ericson; Gustafsson, Claes; Hagervall, Tord G.; Jonsson, Yvonne; Wikström, P. Mikael

doi:10.1146/annurev.bi.56.070187.001403

Cited by 330 publications

(189 citation statements)

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“…Surprisingly, neither of the two major Tyr isoacceptor tRNAs isolated from calf liver displays UAG suppressor activity: both possess a Q nucleoside in the anticodon, thus confirming again the role of the level of base modifica-tion on the codon reading pattern of tRNAs (review [28]). Yet, amber suppressor tRNAs have been purified from calf liver: they are Leu-tRNAs harbouring a 5 ' -CAA-3 ' and a 5 ' -CAG-3 ' anticodon, respectively.…”

Section: Nonsense Suppression Via Misreadingmentioning

confidence: 67%

Stop making sense or Regulation at the level of termination in eukaryotic protein synthesis

Valle

Morch

1988

FEBS Letters

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Section: Nonsense Suppression Via Misreadingmentioning

confidence: 67%

Stop making sense or Regulation at the level of termination in eukaryotic protein synthesis

Valle

Morch

1988

FEBS Letters

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“…In at least some animal mitochondria, it is thought that post-transcriptional modification of the first position of the anticodon to 5-formylcytidine may allow the tRNA Met to read both AUG and AUA codons [36,37]. Our data clearly establish that there are no modified residues in the anticodon of T. pyriformis mitochondrial tRNAMet; however, the two ~ residues close to the 3'-end of the anticodon are expected to have considerable effect on the structure of this region of the tRNA [32] and therefore may influence codon reading [27,38]. Another possibility is that T. pyriformis mitochondrial mRNAs undergo RNA editing as in some other mitochondrial systems [39,40], thereby acquiring the necessary AUG start codons in the appropriate positions.…”

Section: Discussionmentioning

confidence: 67%

“…The 3'-CCA sequence is a universal feature of all tRNAs and is important in many aspects of tRNA function [22], including aminoacylation [23,24] and interaction with large subunit rRNA [25]. This tRNA also contains several modified nucleosides that are highly conserved among tRNAs and are thought to be important for tRNA structure and function [26][27][28][29][30][31][32][33].…”

Section: Discussionmentioning

confidence: 99%

Primary sequence and post‐transcriptional modification pattern of an unusual mitochondrial tRNA^Met from Tetrahymena pyriformis

1995

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We have now isolated and characterized the smallest T. pyriformis mitochondrial tRNA and we show here that it has the primary sequence that we had predicted from the trnM sequence. The transcript also contains a Y-terminal CCA sequence, not encoded in the mtDNA, as well as several modified nucleosides characteristic of known functional tRNAs. Materials and methodsT. pyriformis, amicronucleate strain ST (obtained from Y. Suyama, Department of Biology, University of Pennsylvania), was grown at 28°C with constant shaking in 500 ml NeWs medium [9]. The culture was chilled on ice for 10 15 min, following which cells were collected by centrifugation at 2000 rpm for 5 min, resuspended, and centrifuged at 2000 rpm for 5 min through a layer of ice-cold homogenizing medium (0.35 M sucrose, 10 mM Tris-HC1, pH 7.2, 2 mM EDTA) [10]. Resuspended cells in 50 ml homogenizing medium were disrupted by three passages through a hand emulsifier (nozzle unscrewed 2.5 turns) [11]. Unbroken cells and debris were removed by centrifugation at 3000 rpm (IEC) for 5 min. A mitochondrial pellet was recovered from the resulting supernatant by centrifugation at 8000 rpm for 5 min and washed twice by resuspension in 50 ml homogenizing medium followed by centrifugation (5 min, 8000 rpm). The final mitochondrial pellet was resuspended in 10 ml 0.15 M NaC1, 0.1 M EDTA (pH 9.0) [12] at room temperature. Ten ml of 4% SDS in the same buffer were added and the mitochondrial lysate was then extracted three times with phenol/cresol [13] at room temperature. Nucleic acids were precipitated by addition of 2 vols. of 95% ethanol. For preparation of a post-ribosomal supernatant [14], purified mitochondria were resuspended in buffer (100 mM KC1, 10 mM MgCI 2, 10 mM Tris-HCl, pH 7.4) and lysed at a final concentration of 2% Triton X-100. After removal of membrane fragments by centrifugation at 10,000 rpm for 10 rain (IEC), the clarified mitochondrial lysate was centrifuged at 42,000 rpm for 90 min in a Ti50 rotor to sediment ribosomes. Transfer RNA was isolated from the supernatant by detergent phenol/cresol extraction.Nucleic acid samples were either used directly for 3'-end-labeling or, alternatively, the RNA samples (5 ~tg post-ribosomal supernatant RNA or 20/lg total nucleic acid) were dissolved in 7.5/11 NMF/urea loading buffer [15] containing 0.1% (w/v) xylene cyanol or Bromophenol blue and heated to 65°C for 5 min. After electrophoresis in a thin (0.5 ram) 6% polyacrylamide gel containing 7 M urea, the smallest tRNA was visualized by ethidium bromide staining and eluted [16] in the presence of 20 gtg linear polyacrylamide carrier (prepared as in [17], extracted with phenol, precipitated with ethanol and re-dissolved at 2.5 flg//.tl). The unlabeled tRNA was either re-purified by gel-electrophoresis and then subjected to modified nucleotide analysis [16] or used directly for end-labeling. 3'-End-labeled tRNA [18] was purified by gel-electrophoresis and used for chemical sequence analysis [18]; both 3'-and 5'-endlabeled tRNAs were subjected to enzymatic s...

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“…Their function and kind of modification (methylation, desaminization, conversion of uridine to pseuduridine etc.) depend on their location in the tRNA chain [1,3]. After having performed their task, the tRNA molecules are cleaved to nucleosides.…”

mentioning

confidence: 99%

“…After having performed their task, the tRNA molecules are cleaved to nucleosides. Unmodified nucleosides are recycled for biosynthesis of new RNA, while modified ones are not substrates to the salvage enzymes and thus are set free in the blood circulation and excreted with urine [1,3]. In the meantime, 79 different modified nucleosides have been isolated from tRNA and have been characterized, all of which are derivatives of the nucleosides adenosine, guanosine, uridine, and cytosine [4].…”

mentioning

confidence: 99%

MALDI-TOF MS analysis of urinary nucleosides

Kammerer¹,

Frickenschmidt²,

Gleiter³

et al. 2005

J. Am. Soc. Mass Spectrom.

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As RNA turnover seems to be impaired in cancer patients, modified nucleosides have been evaluated as potential tumor markers. Modified nucleosides are mainly formed posttranscriptionally in tRNA, set free during RNA metabolism, and excreted in urine. Especially methylated nucleosides play an important role, as their levels are higher in urine from cancer patients. For structural elucidation of known and unknown nucleosides from urine samples of cancer patients, MALDI-TOF MS and MALDI-PSD were used for the first time. This technique generally ensures high sensitivity, mass resolution, and accuracy. In our analytical approach we prepurified nucleosides from urine by affinity chromatography and subsequently separated them by semipreparative high performance liquid chromatography. The different fractions were collected separately and analyzed by MALDI-TOF MS and PSD-MALDI using a mixture of six low molecular weight calibrants for internal or external calibration. The molecular totals formulas based on a mass accuracy of 10 ppm and below were calculated and a systematic data base search was performed. The inherent problem of the MALDI-technique, the reduced sensitivity for low molecular weight substances caused by matrix suppression effects, was reduced by our technique. We identified several nucleosides in urine, which were previously identified via retention times and UV spectra of standards after HPLC analysis. Eight further nucleosides were observed. This work demonstrates for the first time the potential of MALDI-TOF and PSD-MALDI in combination with semipreparative HPLC for assignment of nucleosides in urine. The particularly high mass accuracy of this mass spectrometric method provides opportunities for identifying unknown compounds. (J Am Soc Mass Spectrom 2005, 16, 940 -947)

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Transfer Rna Modification

Cited by 330 publications

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Stop making sense or Regulation at the level of termination in eukaryotic protein synthesis

Stop making sense or Regulation at the level of termination in eukaryotic protein synthesis

Primary sequence and post‐transcriptional modification pattern of an unusual mitochondrial tRNA^Met from Tetrahymena pyriformis

MALDI-TOF MS analysis of urinary nucleosides

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Transfer Rna Modification

Cited by 330 publications

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Stop making sense or Regulation at the level of termination in eukaryotic protein synthesis

Stop making sense or Regulation at the level of termination in eukaryotic protein synthesis

Primary sequence and post‐transcriptional modification pattern of an unusual mitochondrial tRNAMet from Tetrahymena pyriformis

MALDI-TOF MS analysis of urinary nucleosides

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Primary sequence and post‐transcriptional modification pattern of an unusual mitochondrial tRNA^Met from Tetrahymena pyriformis