Inhibition of leucyl-RNA synthetase by periodate-oxidized transfer RNA modified by hydroxylamine.
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Hydroxylamines↗
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Results for “RNA, Transfer”
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Conformational change of tyrosyl-RNA synthetase induced by its specific transfer RNA.
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Carbon Isotopes↗
Tertiary core rearrangements in a tight binding transfer RNA aptamer.
Guided by an in vitro selection experiment designed to obtain tight binding aptamers of Escherichia coli glutamine specific tRNA (tRNAGln) for glutaminyl-tRNA synthetase (GlnRS), we have engineered a tRNA mutant in which the five-nucleotide variable loop sequence 5'-44CAUUC48-3' is replaced by 5'-44AGGU48-3'. This mutant tRNA binds to GlnRS with 30-fold improved affinity compared to the wild type. The 2.7 A cocrystal structure of the RNA aptamer-GlnRS complex reveals major rearrangements in the central tertiary core of the tRNA, while maintaining an RNA-protein interface identical to the wild type. The repacked RNA core features a novel hydrogen bonding arrangement of the trans Levitt pair G15-U48, a new sulfate binding pocket in the major groove, and increased hydrophobic stacking interactions among the bases. These data suggest that enhanced protein binding to a mutant globular RNA can arise from stabilization of RNA tertiary interactions rather than optimization of RNA-protein contacts.
Amino Acyl-tRNA Synthetases↗
RNA quality control: degradation of defective transfer RNA.
The distinction between stable (tRNA and rRNA) and unstable (mRNA) RNA has been considered an important feature of bacterial RNA metabolism. One factor thought to contribute to the difference between these RNA populations is polyadenylation, which promotes degradation of unstable RNA. However, the recent discovery that polyadenylation also occurs on stable RNA led us to examine whether poly(A) might serve as a signal for eliminating defective stable RNAs, and thus play a role in RNA quality control. Here we show that a readily denaturable, mutant tRNA(Trp) does not accumulate to normal levels in Escherichia coli because its precursor is rapidly degraded. Degradation is largely dependent on polyadenylation of the precursor by poly(A) polymerase and on its removal by polynucleotide phosphorylase. Thus, in the absence of these two enzymes large amounts of tRNA(Trp) precursor accumulate. We propose that defective stable RNA precursors that are poorly converted to their mature forms may be polyadenylated and subsequently degraded. These data indicate that quality control of stable RNA metabolism in many ways resembles normal turnover of unstable RNA.
Escherichia coli↗
Participation by Drosophila transfer RNA in protein synthesis in an E. coli protein synthesizing system.
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Animals↗
In vitro O2'-methylation of sugars in E. coli RNA. II. Methylation of ribosomal and transfer RNA by homologous methylases in crude cell-free extracts and particulate suspensions from a relaxed mutant of E. coli.
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Carbon Isotopes↗
In vitro O 2 '-methylation of sugars in E. coli RNA. 3. Methylation of E. coli transfer RNA by heterologous methylases in particulate-free extracts of wheat embryo.
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Base Sequence↗
[Total chemical synthesis of natural transfer RNA].
New improvements in the chemical synthesis of oligoribonucleotides are reported and they are applied to the first total chemical synthesis of a natural RNA. This E. coli K12 alanine tRNA contains in its sequence dihydrouridine, ribothymidine and pseudo-uridine. The synthetic tRNA was fully sequenced and showed a 42% aminoacyl acceptance activity. When tRNA was used as a template, reverse transcriptase directed the incorporation of adenine opposite dihydrouridine, ribothymidine and pseudouridine.
Base Sequence↗
Mapping of mutation tsm-8 with respect to transfer RNA genes on the mitochondrial DNA of Saccharomyces cerevisiae.
A precise localization of the tsm-8 mutation in relation to the transfer RNA genes has been attempted by rho- deletion analysis. The data show that the tsm-8 mutation is in close proximity to the isoleucyl transfer RNA gene. However, it is not yet possible to decide whether the tsm-8 mutation is within this transfer RNA gene.
DNA, Mitochondrial↗
Codon and amino-acid specificities of a transfer RNA are both converted by a single post-transcriptional modification.
An Escherichia coli isoleucine transfer RNA specific for the codon AUA (tRNA(2Ile) or tRNA(minorIle] has a novel modified nucleoside, lysidine in the first position of the anticodon (position 34), which is essential for the specific recognition of the codon AUA. We isolated the gene for tRNA(2Ile) (ileX) and found that the anticodon is CAT, which is characteristic of the methionine tRNA gene. Replacement of L(34) of tRNA(2Ile) molecule enzymatically with unmodified C(34) resulted in a marked reduction of the isoleucine-accepting activity and, surprisingly, in the appearance of methionine-accepting activity. Thus, both the codon and amino-acid specificity of this tRNA are converted by a single post-transcriptional modification of the first position of the anticodon during tRNA maturation.
Anticodon↗
Genomic organization of the human asparagine transfer RNA genes: localization to the U1 RNA gene and class I pseudogene repeat units.
Previously isolated human DNA clones containing asparagine transfer RNA (tRNAAsn) genes have been used to determine the genomic organization of this multigene family in man. One clone also contained a gene for U1 RNA, and so the organization of the two multigene families could be directly compared. The majority, and perhaps all, of the human tRNAAsn genes map to the same chromosome bands as do the U1 RNA true genes and class I pseudogenes located on the short and long arms, respectively, of chromosome 1. These two gene clusters were independently isolated using a somatic-cell hybrid minipanel, and use of repeat-unit DNA polymorphisms showed that one tRNA gene clone maps to the short-arm gene cluster and the other to the long-arm gene cluster. Electron microscopy of heteroduplexes between these two clones showed duplex formation along the proposed region of overlap between them, indicating that the short- and long-arm gene clusters are structurally related. I suggest that the split into two distinct loci was facilitated by a pericentric chromosome inversion. This would have had the effect of positioning the genes currently on the long arm adjacent to the centromeric heterochromatin, perhaps resulting in a "position effect" on transcription of these genes. Restriction fragments of different sizes were found that were common to a majority of repeat units, depending on the restriction enzyme being used. Pulsed-field electrophoresis revealed that fragments of molecular weight of 180 kb were common to each unit (or multiples of units). These fragments also contained U1 RNA gene sequences. I therefore propose that these two gene families are closely linked on repeat units (or multiples of units) of 180 kb in size, which are probably organized in tandem arrays.
Chromosome Inversion↗
Characterization of phage-specific transfer RNA molecules coded by Vibrio eltor phage e4.
Transfer RNAs were isolated from phage e4-infected Vibrio eltor Mak 757 cells. These were aminoacylated with 14 individual 3H-labeled L-amino acids. Hybridization of these [3H]aminoacyl-tRNAs with phage e4 DNA revealed that the phage e4 encodes tRNAs for arginine, tryptophan, tyrosine, leucine, and isoleucine. Direct aminoacylation of phage-coded tRNA molecules isolated from phage DNA-RNA hybrids also confirmed this observation.
Bacteriophages↗
Hydration of transfer RNA molecules: a crystallographic study.
Four crystal structures of transfer RNA molecules were refined at 3 A resolution with the inclusion of the solvent molecules found in the difference maps: yeast tRNA-phe in the orthorhombic form, yeast tRNA-phe in the monoclinic form and yeast tRNA-asp in the A and B forms. Over 100 solvent molecules were located in each tRNA crystal. Several hydration schemes are found repeatedly in the 4 crystals. The tertiary interactions in the corner of the L-shaped molecule attract numerous solvent molecules which bridge the ribose hydroxyl O(2') atoms, base exocyclic atoms and phosphate anionic oxygen atoms. Conservation of bases leads to conservative localized hydration patterns. Several solvent molecules are found stabilizing unusual base pairs like the G-U pairs and those involving the pseudouridine base. Water bridges between the O(2') and the exocyclic atom O2 of pyrimidines or the N3 atom of purines are common. Water bridges occur frequently between successive anionic oxygen atoms of each strand as well as between N7 or other exocyclic atoms of successive bases in the major groove. Magnesium ions or spermine molecules are found to bind in the major groove of tRNA helices without specific interactions.
Crystallography↗
Organothallium(III) reagents for modification of biomacromolecules: interaction of thallium derivatives with transfer RNA.
As an extension of work on the inhibition of enzymes by arylthallium(III) reagents, the thallium analogues of the organomercurials, we have studied the interactions of these molecules with transfer RNA. In contrast to thallous acetate, thallium(III) derivatives (thallic trifluoroacetate, p-methylphenylthallium(III) bis-trifluoroacetate (MPT) and o-carboxyphenylthallium(III) bis-trifluoroacetate) bound to Escherichia coli tRNA. The interaction was fully reversible upon Sephadex G-25 gel filtration, and binding constants and stoichiometries were evaluated by a number of procedures. The likely site of interaction was shown to be the thiouridine residue (s4U8) based on changes induced by MPT on the absorbance around 330 nm. No changes in stacking interactions could be detected from the absorption or circular dichroic spectra. The detailed structure of the groups on thallium(III) affected the interaction with tRNA. Thalliation at s4U8 affects the absorbance at 335 nm and the amino-acid uptake capacity of E. coli tRNAPhe in parallel, the latter being progressively inhibited by increasing amounts of MPT. In a model nucleoside system, uridine disulphide is probably formed from reduced thiouridine by the oxidative action of the Tl(III) reagents. No evidence of cross-linking of E. coli tRNA molecules under gel electrophoretic conditions was obtained in contrast to the model nucleoside. The easily reversible interaction of MPT with sulphur sites in E. coli tRNA contrasts with the stable (to gel filtration) bonds formed between MPT and (thiol) sites in enzymes.
Chromatography, Gel↗
Primary structure of wheat germ phenylalanine transfer RNA.
The complete nucleotide sequence of wheat germ phenylalanine transfer RNA (tRNA(Phe)) is presented. This RNA, which is an acceptable substrate for yeast phenylalanine tRNA synthetase, has a structure very similar to that of yeast tRNA(Phe). Only 16 of the 76 nucleotides are different, and all but two of the nucleotide changes are located in regions that are doublestranded in the cloverleaf model. The two changes in single-stranded regions involve minor modifications of the same nucleotide. The dihydrouridine loop and its supporting stem are completely free of nucleotide changes.
Amino Acid Sequence↗
A mammalian mitochondrial serine transfer RNA lacking the "dihydrouridine" loop and stem.
A unique transfer RNA has been identified in human and bovine mitochondria that lacks the "dihydrouridine" loop and stem structure. This tRNA is mitochondrially coded as shown by DNA sequence analysis of the human and bovine mitochondrial DNA. Sequence analysis of the RNA shows that it is post-transcriptionally modified by the addition of CCA at the 3' terminus and that at least one base is modified. As predicted by its anticodon (GCU, corresponding to the serine codons AGU/C) this tRNA can be aminoacylated with serine when purified mitochondria are incubated in a medium containing 3H-serine.
Animals↗
Photo-induced crosslinking between phenylalanine transfer RNA and messenger RNA on the Escherichia coli ribosome.
Crosslinking between phenylalanyl transfer RNA from brewer's yeast and poly(U) can be obtained when ribosomal complexes are irradiated at > 300 nm; the ribosomal complexes were formed by enzymatic binding of the tRNA. The crosslinked product was isolated on oligo(dA)-cellulose columns. The experiments suggest that the photo-crosslinking occurs via the wybutine in the anticodon loop of the tRNA. This system can be used to study interactions between tRNA and messenger RNA on the ribosome.
Escherichia coli↗
An NAD derivative produced during transfer RNA splicing: ADP-ribose 1"-2" cyclic phosphate.
Transfer RNA (tRNA) splicing is essential in Saccharomyces cerevisiae as well as in humans, and many of its features are the same in both. In yeast, the final step of this process is removal of the 2' phosphate generated at the splice junction during ligation. A nicotinamide adenine dinucleotide (NAD)-dependent phosphotransferase catalyzes removal of the 2' phosphate and produces a small molecule. It is shown here that this small molecule is an NAD derivative: adenosine diphosphate (ADP)-ribose 1"-2" cyclic phosphate. Evidence is also presented that this molecule is produced in Xenopus laevis oocytes as a result of dephosphorylation of ligated tRNA.
Adenosine Diphosphate Ribose↗