Compilation of tRNA sequences

Sprinzl, Mathias; Moll, J.; Meissner, Felix; Hartmann, Tom

doi:10.1093/nar/13.suppl.r1

Cited by 383 publications

(99 citation statements)

References 18 publications

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“…The replacement of residue US by another nucleoside has not been found in any other mt tRNA species from yeast, and it occurs only in some other mt tRNAs of fungal and animal origins and in TS coded tRNAAsp [19]. In the tertiary structure of yeast cytoplasmic tRNAPhe [20] and tRNAASp [211, Azi is involved in an interaction with Us by base-backbone interactions, whereas Py48 interacts with PUNS by 'transpairing'.…”

Section: Structural Featuresmentioning

confidence: 99%

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Codon reading patterns in Saccharomyces cerevisiae mitochondria based on sequences of mitochondrial tRNAs

1986

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The sequences of Saccharomyces cerevisiae mitochondrial tRNA1 Arg, tRNA2 Arg, tRNAGly, tRNA2 Lys tRNALeu and tRNAPro are reported. Special structural features were found in tRNAPro, which has A8, C21, A48 instead of the constant residues U8, A21 and pyrimidine 48, and in tRNA2 Lys, which has a U excluded from basepairing and bulging out from the TΨC stem. The tRNA1 Arg, tRNA2 Lys and tRNALeu, which belong to two‐codon families ending in a purine, have a modified uridine in the wobble position, which prevents misreading of C and U. It is likely to be 5‐carboxymethylaminomethyluridine. tRNAGly and tRNAPro have an unmodified uridine in the wobble position allowing the reading of all four codons of a four‐codon family. However, tRNA2 Arg, which is a minor species and belongs to the CGN four‐codon family, has an unmodified A in the wobble position. This very unusual feature raises the problem of the mechanism by which the codons CGA, CGG and CGC are recognized.

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Section: Structural Featuresmentioning

confidence: 99%

“…The presence of an unmodified A in this position has never been found in any sequenced tRNA. In fact, A is always modified to inosine [19], except in E. coli tRNA%ZA where its modification is of unknown structure [33]. In the wobble hypothesis [l], inosine pairs with A, U and C, whereas an unmodified A pairs with U.…”

Section: Codon Recognition Patternsmentioning

confidence: 99%

Codon reading patterns in Saccharomyces cerevisiae mitochondria based on sequences of mitochondrial tRNAs

1986

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“…The developed architecture of tRNA exhibits a seven-membered anticodon loop with only three bases sufficiently exposed to interact with the mRNA. This structure is only possible because of invariant or semiinvariant nucleotides in positions 32, 33, 37 and 38 [40] (numbering system according to [41]) and it is possible because of nucleotide modifications, especially those in position 37. Presuppositions for these structural features of tRNA are therefore conservation of information by a genetic apparatus and existence of post-transcriptional tRNA-modifying enzymes. Both phenomena are thought to occur at a much later stage than emergence of primitive hairpin adaptors, the size as well as detailed loop structure of which deviates hence from those of tRNA.…”

Section: Implications For the Model Of Primordial Translationmentioning

confidence: 99%

Complexes of DNA hairpins and a single‐stranded oligonucleotide detected by affinity chromatography and mung bean nuclease cleavage

Baumann

Lehmann

Schwellnus³

et al. 1987

European Journal of Biochemistry

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The emergence of a simple translation device consisting of an assembler strand (primordial mRNA) and RNA hairpins (primordial tRNA) is presumed to be an important step leading to the origin of life. The assumption of a non-enzymatic interaction of primordial tRNA and mRNA is experimentally approached. DNA hairpins containing five or more adenosine residues in the loop are able to bind to complementary oligonucleotides covalently bound to cellulose. The exact number of base pairs formed between the hairpins and the assembler strand is determined by two methods applied to DNA hairpin/assembler complexes. The melting temperature of a complex is measured and the cleavage pattern by nuclease from mung bean is determined. The loop of the smallest hairpin able to bind consists of five adenosine residues and only three base pairs are formed. This supports the idea of a primordial recognition similar to the contemporary codon-anticodon interaction.The emergence of a simple translation device is a crucial step in the process leading to the origin of life. A proposed translation device [l] consists of interacting oligoribonucleotides. The occurrence of short oligoribonucleotides seems reasonable, since the synthesis of chemically activated ribonucleotides under almost primordial conditions [2], their oligomerisation [3] and their template-directed enzyme-free polymerisation [4, 51 have been demonstrated. The model for self-organisation of matter needs oligoribonucleotides with a hairpin structure acting as primeval tRNA and a singlestranded polynucleotide functioning as primeval mRNA. This single-stranded assembler is thought to bind the hairpin molecules by formation of three base pairs with the loop nucleosides thus arranging the hairpins in a distinct sequence. The base-pairing interactions are thought to be stabilized additionally by lateral forces between the helical parts of the hairpin oligonucleotides occurring at a high Mg2 + concentration. The search for conditions leading to stable binding of hairpins to single strands by base triplets is of interest and a presupposition for intended formation of the peptide bond.In order to investigate the proposed base-pairing ability, two sets of molecules containing either thymidine or deoxyadenosine in the loop region both with an identical helical region as shown in Fig. 1 were synthesized 16 size of the loop was varied with regard to a possible primordial codon-anticodon interaction. The binding ability of the hairpins to complementary homooligonucleotides chemically bound to a solid support was investigated. This method had been originally used for the study of complexes of singlestranded oligonucleotides [8, 91. In order to investigate the steric arrangement of the particular loop nucleosides in free and complexed hairpin oligonucleotides, the single-strandspecific nuclease from mung bean was used as a structural probe [lo, 111. The best known similar nuclease S1 from Aspergillus oryzae had been used as a structural tool to reveal special features of tRNA [12, 131. MAT...

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“…Thus, the hypermodified nucleoside t6A, N-[N-(9-P-~-ribofuranosylpurine-6-yl)carbamoyl]threonine, or a derivative thereof is located in position 37 of tRNAs having anticodons terminating in a uridine. One enigmatic exception is the initiator methionine tRNA of Escherichia coli, for most other tRNAs including the eubacterial elongator Met-tRNA, which has the same anticodon sequence, and the eukaryotic initiator tRNA contain the A-37 modification [3].To study the effect of structural modifications in the anticodon loop on the modification of A-37, we have turned to recombinant RNA methods based on T4 RNA ligase. These techniques are particularly well-suited to the preparation of related tRNA chimera, which have substitutions in or near the anticodon, since fragments serving as starting material for the tRNA variant can be readily obtained from controlled…”

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confidence: 99%

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The in vivo stability, maturation and aminoacylation of anticodon-substituted Escherichia coli initiator methionine tRNAs

et al. 1987

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We have constructed eight anticodon-modified Escherichia coli initiator methionine (Met) tRNAs by insertion of synthetic ribotrinucleotides between two fragments ('half molecules') derived from the initiator tRNA. The trinucleotides, namely CAU (the normal anticodon), CAA, CAC, CAG, GAA, GAC, GAG and GAU, were joined to the 5' and 3' tRNA fragments with T4 RNA ligase. The strategy of reconstruction permitted the insertion of radioactive 32P label between nucleotides 36 and 37. tRNAs were microinjected into the cytoplasm of Xenopus laevis oocytes, and the following properties were evaluated: (a) the stability of these eubacterial tRNA variants in the eukaryotic oocytes; (b) the enzymatic modification of the adenosine at position 37 (3' adjacent to the anticodon) and (c) aminoacylation of the chimeric tRNAs by endogenous oocyte aminoacyl-tRNA synthetases.In contrast to other variants, the two RNAs having CAU and GAU anticodons were stable and underwent quantitative modification at A-37. These results show that the enzyme responsible for the modification of A-37 to N-[N-(9-~-~-ribofuranosylpurine-6-yl)carbamoy~]threonine (t6A) is present in the cytoplasm of oocytes and is very sensitive to the anticodon environment of the tRNA. Also, these same GAU and CAU anticodon-containing tRNAs are fully aminoacylated with the heterologous oocyte aminoacyl-tRNA synthetases in vivo. During the course of this work we developed a generally applicable assay for the aminoacylation of femtomole amounts of labelled tRNAs.Some time ago a correlation between the anticodon sequence of a tRNA and the identity of neighbouring modified nucleosides was noted [l] (reviewed in [2]). Thus, the hypermodified nucleoside t6A, N-[N-(9-P-~-ribofuranosylpurine-6-yl)carbamoyl]threonine, or a derivative thereof is located in position 37 of tRNAs having anticodons terminating in a uridine. One enigmatic exception is the initiator methionine tRNA of Escherichia coli, for most other tRNAs including the eubacterial elongator Met-tRNA, which has the same anticodon sequence, and the eukaryotic initiator tRNA contain the A-37 modification [3].To study the effect of structural modifications in the anticodon loop on the modification of A-37, we have turned to recombinant RNA methods based on T4 RNA ligase. These techniques are particularly well-suited to the preparation of related tRNA chimera, which have substitutions in or near the anticodon, since fragments serving as starting material for the tRNA variant can be readily obtained from controlled

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Compilation of tRNA sequences

Cited by 383 publications

References 18 publications

Codon reading patterns in Saccharomyces cerevisiae mitochondria based on sequences of mitochondrial tRNAs

Codon reading patterns in Saccharomyces cerevisiae mitochondria based on sequences of mitochondrial tRNAs

Complexes of DNA hairpins and a single‐stranded oligonucleotide detected by affinity chromatography and mung bean nuclease cleavage

The in vivo stability, maturation and aminoacylation of anticodon-substituted Escherichia coli initiator methionine tRNAs

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