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At least 505 records · Page 28Linked to original sources
PubMed1994

Molecular recognition of the identity-determinant set of isoleucine transfer RNA from Escherichia coli.

Molecular recognition of Escherichia coli tRNA(Ile) by the cognate isoleucyl-tRNA synthetase (IleRS) was studied by analyses of chemical footprinting with N-nitroso-N-ethylurea and aminoacylation kinetics of variant tRNA(Ile) transcripts prepared with bacteriophage T7 RNA polymerase. IleRS binds to the acceptor, dihydrouridine (D), and anticodon stems as well as to the anticodon loop. The "complete set" of determinants for the tRNA(Ile) identity consists of most of the nucleotides in the anticodon loop (G34, A35, U36, t6A37 and A38), the discriminator nucleotide (A73), and the base-pairs in the middle of the anticodon, D and acceptor stems (C29.G41, U12.A23 and C4.G69, respectively). As for the tertiary base-pairs, two are indispensable for the isoleucylation activity, whereas the others are dispensable. Correspondingly, some of the phosphate groups of these dispensable tertiary base-pair residues were shown to be exposed to N-nitroso-N-ethylurea when tRNA(Ile) was bound with IleRS. Furthermore, deletion of the T psi C-arm only slightly impaired the tRNA(Ile) activity. Thus, it is proposed that the recognition by IleRS of all the widely distributed identity determinants is coupled with a global conformational change that involves the loosening of a particular set of tertiary base-pairs of tRNA(Ile).

Anticodon↗
PubMed1999

Functional compensation by particular nucleotide substitutions of a critical G*U wobble base-pair during aminoacylation of transfer RNA.

Expression of the genetic code depends on precise tRNA aminoacylation by cognate aminoacyl-tRNA synthetase enzymes. The G.U wobble base-pair in the acceptor helix of Escherichia coli alanine tRNA is the primary aminoacylation determinant of this molecule. Previous work on the process of synthetase recognition of the G.U pair showed that replacing G.U by a G.C Watson-Crick base-pair inactivates alanine acceptance by the tRNA, but that C.A and G.A wobble pair replacements preserve acceptance. Work by another group reported that the effects of a G.C replacement were reversed by a distal wobble base-pair in the anticodon helix. This result is potentially interesting because it suggests that distant regions in alanine tRNA are functionally coupled during synthetase recognition and more generally because recognition determinants of many other tRNAs lie in both the acceptor helix and anticodon helix region. Here, we have conducted an extensive in vivo analysis of the distal wobble pair in alanine tRNA and report that it does not behave like a compensating mutation. Restoration of alanine acceptance was not detected even when the synthetase enzyme was overproduced. We discuss the previous experimental evidence and suggest how the distal wobble pair was incorrectly analyzed. The available data indicate that all principal recognition determinants of alanine tRNA lie in the molecule's acceptor helix.

Acylation↗
PubMed1999

Structural compensation in an archaeal selenocysteine transfer RNA.

A new type of structural compensation between the lengths of two perpendicularly oriented RNA double helices was found in the archaeal selenocysteine tRNA from Methanococcus jannascii. This tRNA contains only four base-pairs in the T-stem, one base-pair less than in all other cytosolic tRNAs. Our analysis shows that such a T-stem in an otherwise normal tRNA cannot guarantee the formation of the normal interactions between the D and T-loops. The absence of these interactions would affect the juxtaposition of the two tRNA helical domains, potentially damaging the tRNA function. In addition to the short T-stem, this tRNA possesses another unprecedented feature, a very long D-stem consisting of seven base-pairs. Taken as such, a seven base-pair D-stem will also disrupt the normal interaction between the D and T-loops. On the other hand, the presence of the universal nucleotides in both the D and T-loops suggests that these loops probably interact with each other in the same way as in other tRNAs. Here, we demonstrate that the short T-stem and the long D-stem can naturally compensate each other, thus providing the normal D/T interactions. Molecular modeling has helped suggest a detailed scheme of mutual compensation between these two unique structural aspects of the archaeal selenocysteine tRNA. In the light of this analysis, other structural and functional characteristics of the selenocysteine tRNAs are discussed.

Base Sequence↗
PubMed1992

Statistical evidence for remnants of the primordial code in the acceptor stem of prokaryotic transfer RNA.

The specificity of interaction of amino acids with triplets in the acceptor helix stem of tRNA was investigated by means of a statistical analysis of 1400 tRNA sequences. The imprint of a prototypic genetic code at position 3-5 of the acceptor helix was detected, but only for those major amino acids, glycine, alanine, aspartic acid, and valine, that are formed by spark discharges of simple gases in the laboratory. Although remnants of the code at position 3-5 are typical for tRNAs of archaebacteria, eubacteria, and chloroplasts, eukaryotes do not seem to contain this code, and mitochondria take up an intermediary position. A duplication mechanism for the transposition of the original 3-5 code toward its present position in the anticodon stem of tRNA is proposed. From this viewpoint, the mode of evolution of mRNA and functional ribosomes becomes more understandable.

Amino Acyl-tRNA Synthetases↗
PubMed1990

Mutant of the glutamine transfer RNA gene as UGA suppressor in Escherichia coli.

A UGA suppressor derived from a glutamine tRNA gene of Escherichia coli K12 was isolated and characterized. Phages carrying the suppressor su+2UGA could be obtained only from a hybrid transducing phage, h80cI857psu+2oc, but not from the original transducing phage lambda cI857psu+2oc. By DNA sequence analysis, it was found that the su+2 UGA suppressor obtained has two mutations; one is in the anticodon (TTA----TCA), as expected, and the other (C----T) is at the 7th position from the 3' end of tRNA(2Gln). The significance of these mutations and the lethal effect on phage lambda of the increased amounts of UGA suppressor tRNAs are discussed.

Bacteriophages↗
PubMed1980

A double base change in alternate base pairs induced by ultraviolet irradiation in a glycine transfer RNA gene.

The glyUsuAGA mutation affects Escherichia coli tRNA Gl y GGG, changing it to an AGA missense suppressor tRNA. Sequence studies have shown that the mutation involves a double base subsitution at the first and third positions of the tRNA anticodon, the result being a change in the anticodon from CCC to UCU. A system has been developed to facilitate the detection of this novel mutation, and we have shown that ultraviolet irradiation and N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) are effective in causing the double base change. A single observation of the mutation occurring spontaneously has been made also. The frequency of MNNG-induced glyUsuAGA mutations is compatible with their being caused by two separate mutagenic events. The frequency of UV-induced glyAGA mutations, however, strongly suggests that the occurrence of one base substitution strongly enhances the chance of finding the second substitution at the alternate position. In addition to the double change in the anticodon, the glyUsuAGA tRNA differs from tRNA Gl y GGG in that it bears a modification of the A adjacent to the 3' position of the anticodon. Most likely, this modified base is N-[9-(beta-D-ribofuranosyl)-purin-6-ylcarbamoyl] threonine.

Base Composition↗
PubMed1991

Nuclear factors which bind to Dictyostelium discoideum transfer RNA genes.

RNA Polymerase III transcription factors from the cellular slime mold Dictyostelium discoideum were characterized, based on their stable binding to isolated tRNA genes. Different protein complexes are sequestered on DNA fragments containing tRNA genes depending on the conditions by which the nuclei were extracted. Binding specificity was determined through competition assays using competitor tRNA genes from the same gene family, from different gene families and from truncated tRNA genes. The complex with the highest multiformity of interdependent proteins is able to assemble with low affinity on a B-block-free tDNA template, whereas most lower molecular weight complexes require the presence of an intact B-block promoter element in order to assemble.

Animals↗
PubMed1975

The selective iodination of yeast phenylalanine transfer RNA with 125-I.

Yeast tRNA-Phe has been labelled with 125-I under conditions which conserve the tertiary structure. Significant labelling was only found to occur on specific cytidines in single stranded regions, while other cytidines in single stranded regions and all those in the double stranded region underwent iodination to a very small extent. The pattern obtained from iodine labelling satisfies the conformation of a model recently proposed for this tRNA.

Binding Sites↗
PubMed1988

Transfer RNA genes and the genetic code in Chlamydomonas reinhardtii mitochondria.

Only three tRNA genes are present within a sequenced 12.35 kbp region of the 15.8 kbp mtDNA of Chlamydomonas reinhardtii, a unicellular green alga. The corresponding tRNAs, whose anticodons are specific for TGG (Trp), CAA/G (Gln) and ATG (Met) codons, all display conventional secondary structures. The tRNA(Met) gene encodes an elongator rather than initiator species. The standard genetic code is used in C. reinhardtii mitochondria, but codon distribution is highly biased: in a collection of six identified protein coding genes, nine codons (including TGA) are not used at all, while four other sense codons occur very infrequently. In spite of the absence of certain codons, a minimum of 23 tRNAs (assuming separate initiator and elongator tRNAs(Met) are used) is needed to translate the C. reinhardtii mitochondrial genetic code. It appears unlikely that this minimal tRNA set is encoded by C. reinhardtii mtDNA.

Base Sequence↗
PubMed1994

Cortical reflex myoclonus in patients with the mitochondrial DNA transfer RNA(Lys)(8344) (MERRF) mutation.

Five patients from three families with the syndrome of myoclonic epilepsy and ragged red fibres (MERRF), associated with the mitochondrial DNA point mutation at position 8344, were studied neurophysiologically to determine the characteristics of their myoclonus. The findings were those of cortical reflex myoclonus, with enlarged cortical somatosensory evoked potentials and late reflex responses to peripheral nerve stimulation. Electroencephalography showed paroxysmal spike and polyspike and wave discharges, with photic sensitivity. This pattern of electrophysiological abnormalities was uniform, despite considerable variation in severity of myoclonus. Although a consistent finding, cortical reflex myoclonus is not specific to MERRF amongst myoclonic syndromes.

Adult↗
PubMed1982

Brain transfer RNA. I. Methylation of newly synthesized tRNA.

Present study demonstrates differences between the labeling patterns of rat cerebral cortex and cerebellum. Although the initial rates of synthesis and methylation of tRNA from these two regions of brain are different, their final degree of methylation is the same in both the cases. Differences in the rates of incorporation of radioactivities in both the tissues can be explained by the differences in the rates of equilibrium of the labeled precursors with the pools. Increased incorporation of labeled uridine into cerebral cortical tRNA following dibutyryl cAMP treatment probably resulted from higher uptake of the labeled precursor due to permeability changes.

Animals↗
PubMedDate not supplied

Transfer RNA gene organization and RNase P.

Mature tRNAs are remarkably similar in all cells. However, the primary transcripts from tRNA genes can vary considerably due to differences in gene organization. RNase P must be able to recognize the elements that are common to all tRNA precursors to accurately remove the 5'-leader sequences.

Bacteria↗
PubMed1981

Transfer-RNA, an early gene?

The theory of self-reproductive molecular systems involves the consequence that translation must have started from a selected distribution of RNA molecules, that comprised GC-rich sequences of a length less than 100 nucleotides. This implies a joint function of messenger and adaptor, which both had to be recruited from the same mutant distribution. The reconstruction of tRNA precursors yields such a molecule showing some reverberation of a codon pattern GNC. These findings suggest that tRNA has been the earliest component of the translation machinery.

Base Sequence↗