Partial digestion of a yeast lysine transfer ribonucleic acid and reconstruction of the nucleotide sequence

Madison, James T.; Boguslawski, Sophia J.

doi:10.1021/bi00700a019

Cited by 20 publications

(3 citation statements)

References 32 publications

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“…Thus the consensus sequence which is absolutely necessary for *35 synthesis comprises at least the four nucleosides stretching from U33 to A36. This strict sequence specificity explains the fact that uridine 35 in yeast tRNALyS with UU35U anticodon is not modified to *35 (Madison and Boguslawski, 1974) although this pre-tRNA contains an intron (Ogden et al, 1984), one of the prerequisites for I35 synthesis. A comparison of the nucleotide sequence in this region of tRNATYr and tRNALYS reveals that the only difference lies in the presence or absence of A36.…”

Section: Discussionmentioning

confidence: 99%

Sequence and structure requirements for the biosynthesis of pseudouridine (psi 35) in plant pre-tRNA(Tyr).

Szweykowska-Kulinska

Beier

1992

The EMBO Journal

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All eukaryotic cytoplasmic tRNAs(Tyr) contain pseudouridine in the centre of the anticodon (psi 35). Recently, it has been shown that the formation of psi 35 is dependent on the presence of introns in tRNA(Tyr) genes. Furthermore, we have investigated the structural and sequence requirements for the biosynthesis of psi 35. A number of mutant genes were constructed by oligonucleotide‐directed mutagenesis of a cloned Arabidopsis tRNA(Tyr) gene. Nucleotide exchanges were produced in the first and third positions of the anticodon and at positions adjacent to the anticodon. Moreover, insertion and deletion mutations were made in the anticodon stem and in the intron. The mutant genes were transcribed in HeLa cell extract and the pre‐tRNAs(Tyr) were used for studying psi 35 biosynthesis in HeLa cell and wheat germ extracts. We have made the following observations about the specificity of plant and vertebrate psi 35 syntheses: (i) insertion or deletion of one base pair in the anticodon stem does not influence the efficiency and accuracy of the psi 35 synthase; (ii) the presence of U35 in a stable double‐stranded region prevents its modification to psi 35; and (iii) the consensus sequence U33N34U35A36Pu37 in the anticodon loop is an absolute requirement for psi 35 synthesis. Thus, psi 35 synthases recognize both tRNA tertiary structure and specific sequences surrounding the nucleotide to be modified.

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Section: Discussionmentioning

confidence: 99%

Sequence and structure requirements for the biosynthesis of pseudouridine (psi 35) in plant pre-tRNA(Tyr).

Szweykowska-Kulinska

Beier

1992

The EMBO Journal

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“…This confirms the strict dependence on the wild-type sequence and/or structure of pre-tRNAIle intron for U34 G u ! U and U36 conversions and explains why the UUU anticodon YI of yeast pre-tRNALYs containing a 23 base intron is not 1 modified into TUT (Madison and Boguslawski, 1974;Culbertson and Winey, 1989). Also, T34 has not been found in yeast pre-tRNAPro (UGC anticodon) (Winey et al, 1986) or in pre-tRNALeu (UAG anticodon; Randerath -34 et al, 1979), although both pre-tRNAs contain introns.…”

Section: Ggmentioning

confidence: 99%

Intron-dependent formation of pseudouridines in the anticodon of Saccharomyces cerevisiae minor tRNA(Ile).

et al. 1994

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We have isolated and sequenced the minor species of tRNA(Ile) from Saccharomyces cerevisiae. This tRNA contains two unusual pseudouridines (psi s) in the first and third positions of the anticodon. As shown earlier by others, this tRNA derives from two genes having an identical 60 nt intron. We used in vitro procedures to study the structural requirements for the conversion of the anticodon uridines to psi 34 and psi 36. We show here that psi 34/psi 36 modifications require the presence of the pre‐tRNA(Ile) intron but are not dependent upon the particular base at any single position of the anticodon. The conversion of U34 to psi 34 occurs independently from psi 36 synthesis and vice versa. However, psi 34 is not formed when the middle and the third anticodon bases of pre‐tRNA(Ile) are both substituted to yield ochre anticodon UUA. This ochre pre‐tRNA(Ile) mutant has the central anticodon uridine modified to psi 35 as is the case for S.cerevisiae SUP6 tyrosine‐inserting ochre suppressor tRNA. In contrast, neither the first nor the third anticodon pseudouridine is formed, when the ochre (UUA) anticodon in the pre‐tRNA(Tyr) is substituted with the isoleucine UAU anticodon. A synthetic mini‐substrate consisting of the anticodon stem and loop and the wild‐type intron of pre‐tRNA(Ile) is sufficient to fully modify the anticodon U34 and U36 into psi s. This is the first example of the tRNA intron sequence, rather than the whole tRNA or pre‐tRNA domain, being the main determinant of nucleoside modification.

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“…The mPus1p activity was tested in Dpus1 cells and compared with in vitro results. Modification of both tRNAs and U2 snRNA was tested and we investigated whether scPus1p and mPus1p exhibit one or both of the yet unidentified yeast tRNA:C-synthase activities, namely, pseudouridylation at position 1 in the cytoplasmic tRNA Arg (ACG) and tRNA Lys (UUU) (Madison and Boguslawski 1974;Weissenbach et al 1975) and pseudouridylation FIGURE 1. Sequences and secondary structures of the S. cerevisiae tRNA substrates used in this work.…”

Section: Introductionmentioning

confidence: 99%

A previously unidentified activity of yeast and mouse RNA:pseudouridine synthases 1 (Pus1p) on tRNAs

Behm‐Ansmant

Massenet²,

Immel³

et al. 2006

RNA

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Mouse pseudouridine synthase 1 (mPus1p) was the first vertebrate RNA:pseudouridine synthase that was cloned and characterized biochemically. The mPus1p was previously found to catalyze C formation at positions 27, 28, 34, and 36 in in vitro produced yeast and human tRNAs. On the other hand, the homologous Saccharomyces cerevisiae scPus1p protein was shown to modify seven uridine residues in tRNAs (26, 27, 28, 34, 36, 65, and 67) and U44 in U2 snRNA. In this work, we expressed mPus1p in yeast cells lacking scPus1p and studied modification of U2 snRNA and several yeast tRNAs. Our data showed that, in these in vivo conditions, the mouse enzyme efficiently modifies yeast U2 snRNA at position 44 and tRNAs at positions 27, 28, 34, and 36. However, a tRNA:C26-synthase activity of mPus1p was not observed. Furthermore, we found that both scPus1p and mPus1p, in vivo and in vitro, have a previously unidentified activity at position 1 in cytoplasmic tRNA Arg (ACG). This modification can take place in mature tRNA, as well as in pre-tRNAs with 59 and/or 39 extensions. Thus, we identified the protein carrying one of the last missing yeast tRNA:C synthase activities. In addition, our results reveal an additional activity of mPus1p at position 30 in tRNA that scPus1p does not possess.

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Partial digestion of a yeast lysine transfer ribonucleic acid and reconstruction of the nucleotide sequence

Abstract: The production, isolation, and analysis of the large oligonucleotides that were used to reconstruct the nucleotide sequence of a yeast lysine transfer RNA are described. Since

Cited by 20 publications

References 32 publications

Sequence and structure requirements for the biosynthesis of pseudouridine (psi 35) in plant pre-tRNA(Tyr).

Sequence and structure requirements for the biosynthesis of pseudouridine (psi 35) in plant pre-tRNA(Tyr).

Intron-dependent formation of pseudouridines in the anticodon of Saccharomyces cerevisiae minor tRNA(Ile).

A previously unidentified activity of yeast and mouse RNA:pseudouridine synthases 1 (Pus1p) on tRNAs

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