Compilation of tRNA sequences and sequences of tRNA genes

Sprinzl, Mathias; Hartmann, Tom; Weber, Jérémie; Blank, Jutta; Zeidler, Reinhard

doi:10.1093/nar/17.suppl.r1

Cited by 370 publications

(265 citation statements)

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“…This will depend in part upon how close the fold-back and the extended conformations are energetically to the conformation of tRNA required for aminoacylation. Cysteine and glycine tRNAs of E. coli and glutamine tRNAs of eukaryotic cytoplasm contain U73 (36). The first four base pairs in the acceptor stem of E. coli tRNACYs are, in fact, identical to those of the U19 variant studied here.…”

Section: Discussionmentioning

confidence: 50%

NMR analysis of tRNA acceptor stem microhelices: discriminator base change affects tRNA conformation at the 3' end.

Puglisi

Williamson

et al. 1994

Proc. Natl. Acad. Sci. U.S.A.

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An important step in initiation of protein synthesis in Escherichia col is the specific formylation of the initiator methionyl-tRNA (Met-tRNA) by Met-tRNA transformylase. The deterinants for formylation are clustered mostly in the acceptor stem of the initiator tRNA. Here we use NMR spectroscopy to characterize the conformation of two RNA microhelces, which correspond to the acceptor stem of mutants of E. coUi initator tRNA and which differ only at the position corresponding to the "discriminator base" in tRNAs.One of the mutant tRNAs is an extremely poor substrate for Met-tRNA trausformylase, whereas the other one is a much better substrate. We show that one microhelix forms a struchire in which its 3'-ACCA sequence extends the tacklng of the acceptor stem. The other microhelix forms a structure in which its 3'-UCCA sequence folds back such that the 3'-terminal A22 is in dose proximity to GI. These results highiight the importance of the discriminator base in determining tRNA conformation at the 3' end. They also suggest a correlation between tRNA structure at the 3' end and its recognition by Met-tRNA trandormylase.Protein synthesis in Escherichia coli is initiated with formylmethionyl-tRNA (tMet-tRNA). A crucial step in this process is the specific formylation of methionine attached to tRNAfmet by Met-tRNA transformylase (EC 2.1.2.9) (1, 2). We showed previously that the major determinants for formylation are clustered in the acceptor stem of tRNA (3). One of these determinants is a mismatch (as found in tRNAfmet) or a weak base pair at the end of the acceptor stem. tRNAs carrying the wild-type ClxA72 or virtually any other mismatch are good substrates, whereas those carrying stable base pairs such as ClG72 or GlFC72 are extremely poor substrates (4-6). These results suggest a requirement for nucleotides 1 and 72 to be unpaired during formylation.The strong negative effect of ClG72 or G1C72 base pairs on formylation can be compensated for by an additional mutation of A73, the discriminator base, which precedes the CCA sequence common to all tRNAs, to a pyrimidine such as U73 (4). For example, in contrast to the ClG72 mutant, which is a very poor substrate (V 1/K aPP down by a factor of495 compared to wild-type tRNA), the ClG72/U73 mutant is almost as good a substrate as wild-type tRNA (V./KIPP down only by a factor of 3.7). Similarly, compared to the G1*C72 mutant, the G1'C72/U73 mutant is a better substrate for Met-tRNA transformylase (V./KIPP down by a factor of 60, while the factor is 1035 for the G1-C72 mutant). On the basis of these results, we proposed that the discriminator base influences the stability of the terminal base pair in the acceptor stem and/or structure of tRNA at the 3' end (4, 6).In this paper, we use NMR spectroscopy (7) to study the effect of the discriminator base (8) on tRNA conformation at the 3' end. Two RNA oligonucleotides that correspond to variants of the acceptor stem of initiator tRNAfmet were designed for NMR study (Fig. 1A). These oligonucleotides contain the seven ...

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Section: Discussionmentioning

confidence: 50%

NMR analysis of tRNA acceptor stem microhelices: discriminator base change affects tRNA conformation at the 3' end.

Puglisi

Williamson

et al. 1994

Proc. Natl. Acad. Sci. U.S.A.

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“…The central one of the CpGs in the sequence TTCGA is of special interest because this sequence is conserved in 65% of the eukaryotic tRNA genes. Another 9% of tRNA genes have the closely related sequence ATCGA at this position [30].…”

Section: Discussionmentioning

confidence: 99%

DNA methylation inhibits transcription by RNA polymerase III of a tRNA gene, but not of a 5S rRNA gene

et al. 1990

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Methylation of cytosine in the DNA inhibits the transcription by RNA polymerase II in higher eukaryotes, but has no infhtence on RNA polymerase I transcription. The effect on RNA polymerase III was unknown, so far. Two polymerase III genes: a type 1 5s rRNA gene and a type 2 tRNA gene were methylated in vitro with a purified eukaryotic DNA methyltransferase (EC2.1.1.37) and their transcription was analyzed in Xenopus oocytes. The 5s rRNA gene, an oocyte 5s rRNA gene from X. luevis which is subject to developmental inactivation, was not alfected by methylation. Conversely, transcription of the tRNA gene was 8m inhibited by methylation with the eukaryotic methyltransferase. H/au1 and HpaII methylation left its transcription unaffected.

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“…This A is conserved in all known valylatable tRNAs [46] and tRNA-like structures [31]. The C54 mutant showed a moderately decreased relative specificity constant (10-fold), indicating that this position should be included in the set of valylation determinants, although the contribution is minor compared to that of N56 in the anticodon itself.…”

Section: Role Of Other Nucleotidesmentioning

confidence: 99%

“…In the latter case, substituting at position 34 and 36 of the anticodon of tRNAM" (CAU) to create a UAC valine anticodon resulted in a 20000-fold increase in relative valine specificity ( Vmax/Km). Since the 5'-wobble position is less likely to contribute significantly to specificity due to the variable sequence present among different tRNAVa' species [46] and valylatable tymoviral RNAs [31], the valylation of the modified tRNAM"' is probably due to a single substitution at the 3'-anticodon position. However, the separate contribution of each anticodon base in the E. coli system has not yet been tested.…”

Section: What Determines the Valine Identity For Yeast Valyl-trna Synmentioning

confidence: 99%

Specific valylation identity of turnip yellow mosaic virus RNA by yeast valyl‐tRNA synthetase is directed by the anticodon in a kinetic rather than affinity‐based discrimination

Florentz

Dreher

Rudinger

et al. 1991

European Journal of Biochemistry

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Variants with mutations in three parts of the tRNA-like structure of turnip yellow mosaic virus RNA (the anticodon, the discriminator position in the amino acid acceptor stem, and in the variable loop) were created via site-directed mutagenesis of a cDNA clone and transcription with T7 RNA polymerase. The valylation properties of transcripts were studied in the presence of pure yeast valyl-tRNA synthetase. Mutation of the central position of the anticodon triplet resulted in a quasi-total loss of valylation activity, indicating that the anticodon is a principal determinant for valylation of the turnip yellow mosaic virus tRNA-like structure. These anticodon mutants interacted with yeast valyl-tRNA synthetase with affinities comparable to those of the wild-type RNA and behaved as competitive inhibitors in the valylation reaction of yeast tRNAVal. The defective aminoacylation of these mutants therefore results from kinetic rather than affinity effects. Minor negative effects on valylation efficiency were observed for mutants with substitutions at the two other sites studied, suggesting a structural role or a limited contribution to the valine identity of the tRNA-like molecule.Turnip yellow mosaic virus (TYMV) is one of several RNA plant viruses whose genomic RNA has a 3'-terminal region that resembles and mimics transfer RNAs [l, 21. This region of the RNA, which contains no known modified bases, can be specifically and efficiently valylated by valyl-tRNA synthetases from prokaryotic or eukaryotic sources [3 -51. The 3' 82 nucleotides fold into an L-shaped structure with strong analogies to canonical tRNA structure and to the sequence of tRNAVal, including the presence of a CAC valine anticodon [6 -81. Our interests in the properties of the tRNAlike structure are twofold: firstly since TYMV RNA can be considered as a variant of tRNAVa', it is useful in the study of tRNA function and specificity; secondly, by analogy with the brome mosaic virus system [9 -111, the tRNA-like structure may play an important role in viral replication. We describe here experiments investigating the determinants within the 3'tRNA-like structure of TYMV RNA that direct its specific charging by purified yeast valyl-tRNA synthetase. Such information would extend our understanding of aminoacylation determinants in eukaryotic tRNAs, as well as assist in identifying the role of aminoacylation in the viral life cycle.There has recently been rapid progress in identifying the specificity determinants of a number of tRNAs. mostly from Escherichia coli. These studies were made possible by new Ahhreviutions. TYMV, turnip yellow mosaic virus; BMV, brome mosaic virus; tRNA""', transfer ribonucleic acid specific for valine.Enzymes. Valyl-tRNA synthetase (EC 6.1.1.9); T7 RNA polymerase (EC 2.7.7.6).techniques permitting the synthesis of tRNA variants in vitro (e.g. [12 -151) and the assessment of the activity of specifically constructed suppressor tRNAs in protein synthesis in vivo ( e g [16]). The locations and complexity of the set of specificitydet...

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Compilation of tRNA sequences and sequences of tRNA genes

Cited by 370 publications

References 0 publications

NMR analysis of tRNA acceptor stem microhelices: discriminator base change affects tRNA conformation at the 3' end.

NMR analysis of tRNA acceptor stem microhelices: discriminator base change affects tRNA conformation at the 3' end.

DNA methylation inhibits transcription by RNA polymerase III of a tRNA gene, but not of a 5S rRNA gene

Specific valylation identity of turnip yellow mosaic virus RNA by yeast valyl‐tRNA synthetase is directed by the anticodon in a kinetic rather than affinity‐based discrimination

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