Compilation of tRNA sequences and sequences of tRNA genes

Sprinzl, Mathias

doi:10.1093/nar/24.1.68

Cited by 307 publications

(444 citation statements)

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“…More than 80 different nucleotide modifications are listed in the "Compilation of tRNA sequences and sequences of tRNA genes" 5 of various organisms [380,379,381]. These are achieved by a large family of often highly conserved enzymes, see [262] and [169] for reviews.…”

Section: Modifications Of Ncrnasmentioning

confidence: 99%

Evolutionary patterns of non-coding RNAs

Bompfünewerer

Flamm

Fried

et al. 2005

Theory in Biosciences

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A plethora of new functions of non-coding RNAs have been discovered in past few years. In fact, RNA is emerging as the central player in cellular regulation, taking on active roles in multiple regulatory layers from transcription, RNA maturation, and Manuscript January 2005RNA modification to translational regulation. Nevertheless, very little is known about the evolution of this "Modern RNA World" and its components. In this contribution we attempt to provide at least a cursory overview of the diversity of non-coding RNAs and functional RNA motifs in non-translated regions of regular messenger RNAs (mRNAs) with an emphasis on evolutionary questions. This survey is complemented by an in-depth analysis of examples from different classes of RNAs focusing mostly on their evolution in the vertebrate lineage. We present a survey of Y RNA genes in vertebrates, studies of the molecular evolution of the U7 snRNA, the snoRNAs E1/U17, E2, and E3, the Y RNA family, the let-7 microRNA family, and the mRNA-like evf-1 gene. We furthermore discuss the statistical distribution of microRNAs in metazoans, which suggests an explosive increase in the microRNA repertoire in vertebrates. The analysis of the transcription of non-coding RNAs (ncRNAs) suggests that small RNAs in general are genetically mobile in the sense that their association with a hostgene (e.g. when transcribed from introns of a mRNA) can change on evolutionary time scales. The let-7 family demonstrates, that even the mode of transcription (as intron or as exon) can change among paralogous ncRNA.

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Section: Modifications Of Ncrnasmentioning

confidence: 99%

Evolutionary patterns of non-coding RNAs

Bompfünewerer

Flamm

Fried

et al. 2005

Theory in Biosciences

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“…thermophilus, particularly the nucleotides of the D stem, the anticodon arm, and the variable loop ( Fig. 1) [22].…”

Section: Pi1s0014-5793(96)01094-0mentioning

confidence: 99%

“…Analysis of the available tRNA and tRNA gene sequences indicates that the discriminator bases of many tRNA species N. Nameki et al/FEBS Letters 396 (1996) [201][202][203][204][205][206][207] are phylogenetically well conserved among prokaryotes and/or eukaryotes [22]. However, the discriminator base in the threonine system was not regularly conserved.…”

Section: Discriminator Basementioning

confidence: 99%

“…The first and second base pairs are completely conserved among prokaryotic tRNAThrs [22]. Despite the complete conservation within prokaryotes, the second base pair plays an important role on the aminoacylation function for E. coli ThrRS, but not for the T. thermophilus counterpart.…”

Section: Acceptor Stemmentioning

confidence: 99%

“…For 72 thermophilus tRNA Thr, two genes are known but the RNA sequence is not [28]. Numbering is according to [22]. Left, tRNA xhr isoacceptor with the GGU anticodon.…”

Section: Acceptor Stemmentioning

confidence: 99%

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Identity elements of Thermus thermophilus tRNA^Thr

1996

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In this study, we identified nucleotides that specify aminoacylation of tRNA TM by Thermus thermophilus threonyltRNA synthetase (ThrRS) using in vitro transcripts. Mutation studies showed that the first base pair in the acceptor stem as well as the second and third positions of the anticodon are major identity elements of T. thermophilus tRNA TM, which are essentially the same as those of Escherichia coli tRNA TM. The discriminator base, U73, also contributed to the specific aminoacylation, but not the second base pair in the acceptor stem. These findings are in contrast to E. coli tRNA TM, where the second base pair is required for threonylation, with the discriminator base, A73, playing no roles. In addition, among several mutations at the third base pair in the acceptor stem, only the G3-U70 mutant was a poor substrate for ThrRS, suggesting that the G3-UTo wobble pair, which is the identity determinant of tRNA Aj", acts as a negative element for ThrRS. Similar results were obtained in E. coli and yeast. Thus, this manner of rejection of tRNA Ala is also likely to have been retained in the threonine system throughout evolution.

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