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PubMed1967

Chemical modification of yeast alanine-tRNA with a radioactive carbodiimide.

Yeast alanine-tRNA was reacted with 1-cyclohexyl-3-[2-morpholinyl-(4)-ethyl] carbodiimide (14)C-methoiodide in the presence of magnesium ion. The carbodiimide formed addition products with bases in the sequences psipGp, UpCp and UpUpIpGpCp. The expected bases in the sequence TppsipCpGpApUp did not react, although this region is postulated to be in a loop that is not hydrogen-bonded. The capacity of the alanine-tRNA to accept amino acids decreased after reaction with the carbodiimide.

Alanine↗
PubMed1988

Reduced leu operon expression in a miaA mutant of Salmonella typhimurium.

Salmonella typhimurium miaA mutants lacking the tRNA base modification cis-2-methylthioribosylzeatin (ms2io6A) were examined and found to be sensitive to a variety of chemical oxidants and unable to grow aerobically at 42 degrees C in a defined medium. Leucine supplementation suppressed both of these phenotypes, suggesting that leucine synthesis was defective. Intracellular levels of leucine decreased 40-fold in mutant strains after a shift from 30 to 42 degrees C during growth, and expression of a leu-lacZ transcriptional fusion ceased. Steady-state levels of leu mRNA were also significantly reduced during growth at elevated temperatures. Failure of miaA mutant leu-lacZ expression to be fully derepressed during L-leucine limitation at 30 degrees C and suppression of the miaA mutation by a mutation in the S. typhimurium leu attenuator suggests that translational control of the transcription termination mechanism regulating leu expression is defective. Since the S. typhimurium miaA mutation was also suppressed by the Escherichia coli leu operon in trans, phenotypic differences between E. coli and S. typhimurium miaA mutants may result from a difference between their respective leu operons.

Genotype↗
PubMed1989

Isolation and characterization of isoprene mutants of Escherichia coli.

Isoprenoid compounds are found in all organisms. In Escherichia coli the isoprene pathway has three distinct branches: the modification of tRNA; the respiratory quinones ubiquinone and menaquinone; and the dolichols, which are long-chain alcohols involved in cell wall biosynthesis. Very little is known about procaryotic isoprene biosynthesis compared with what is known about eucaryote isoprene biosynthesis. This study approached some of the questions about isoprenoid biosynthesis and regulation in procaryotes by isolating and characterizing mutants in E. coli. Mutants were selected by determining their resistance to low levels of aminoglycoside antibiotics, which require an electron transport chain for uptake into bacterial cells. The mutants were characterized with regard to their phenotypes, map positions, enzymatic activities, and total ubiquinone content. In particular, the enzymes studied were isopentenyldiphosphate delta-isomerase (EC 5.3.3.2), farnesyldiphosphate synthetase (EC 2.5.1.1), and higher prenyl transferases.

Butadienes↗
PubMed1988

The nutrient factor queuine: biosynthesis, occurrence in transfer RNA and function.

Queuine, 7-(( (4,5-cis-dihydroxy-2-cyclopenten-1-yl)-amino]-methyl)-7-deazagu ani ne is synthesized de novo only in eubacteria and is preseent in place of guanine 34 in specific tRNAs containing anticodones GUN where N is one of the four canonical nucleotides. The biosynthetic pathway starting with GTP shares common steps with that of pteridines and riboflavin, and involves iron ions and a 'vitamin B12' coenzyme. Lower and higher eukaryotes are supplied with queuine by nutrition or the intestinal flora. The modification of tRNA with queuine is tissue specific and depends on the metabolic state of cells and tissues. Starvation for queuine and/or Q-deficiency in tRNA causes a few specific changes in the pattern of protein synthesis involving lactate dehydrogenases and cytochromes.

Animals↗
PubMedDate not supplied

[Chemical modification of the complex of tRNA Phe with phenylalanyl-tRNA synthetase from Escherichia coli].

Alkylation of E. coli tRNAPhe, bound to the cognate synthetase was investigated. The alkylating reagent is a derivative of 2-chloroethylamine: 2',3'-O-[4(N-2-chloroethyl-N-methylamino)-benzylidene]-uridine-5'-methylphosphate. It was found that the enzyme protects from the reaction D-stem (guanosine G24) and the region of juxtaposition of acceptor stem and D-stem (S4U8 and C13) in the tRNAPhe.

Alkylation↗
PubMedDate not supplied

[Comparative analysis of affinity modification of several aminoacyl-tRNA synthetases with gamma-(p-azidoanilide)-ATP].

The inhibitory action of gamma-(p-azidoanilide)-ATP on the reactions of tRNA aminoacylation catalysed by several aminoacyl-tRNA synthetases was investigated. This compound was shown to be a competitive inhibitor with respect to ATP in the case of arginyl-, valyl-, isoleucyl-, leucyl-, threonyl-, phenylalanyl-tRNA synthetases of E. coli MRE-600 and tryptophanyl-tRNA synthetase of beef pancreas. The Ki value of this analog changes from 3 x 10(-5) up to 4 x 10(-3) M depending on the enzyme specificity. In the case of methionyland lysyl-tRNA synthetases from E. coli the non-competitive and mixed inhibition accordingly was observed. The activity of isoleucyl-, valyl-, leucyl-, threonyl-, phenyl-alanyl- and tryptophanyl-tRNA synthetases in the reaction of tRNA aminoacylation is decreased as a result of UV-irradiation of the enzymes in the presence of gamma-(p-azidoanilide)-ATP. ATP and aminoacids protect these enzymes against irreversible inactivation. These results confirm the affinity labelling of the substrate binding sites of these enzymes. However, the appreciable inactivation of enzymes with UV-irradiation in the presence of gamma-(p-azidoanilide)-ATP was not detected in the cases of hystidyl-, lysyl-, methionyl-, seryl-, tyrosyl- and phenylalanyl-tRNA synthetases of E. coli MRE-600. The data obtained enable one to suggest the difference in the structure of the amino acid activating sites of different aminoacyl-tRNA synthetases.

Adenosine Triphosphate↗
PubMed1994

Altered queuine modification of transfer RNA involved in the differentiation of human K562 erythroleukemia cells in the presence of distinct differentiation inducers.

Altered queuine modification of tRNA has been correlated to neoplasia and cell differentiation, but much of the existing evidence is only circumstantial. In the present study, we used several distinct differentiation inducers to measure changes in Q-family tRNA species during the erythroid differentiation of human K562 erythroleukemia cells. Treatment of K562 cells with 3.6 microM 1-beta-D-arabinofuranosylcytosine (ara-C), 1 mM sodium butyrate, 0.1 mM hemin, or 5 microM 5-azacytidine resulted in growth inhibition, erythroid differentiation, and changes in queuine content of tRNA. In the presence of the irreversible inducer ara-C, the queuine content of tRNA increased markedly when the cells differentiated into benzidine-positive erythroid cells, and cell growth was inhibited. The increase in the queuine content of tRNA in differentiated K562 cells was an irreversible event. In cells incubated with the reversible inducer sodium butyrate, an increase in the queuine content of tRNA was correlated with the increase in benzidine-positive erythroid cells throughout the culturing period. After removal of the drug at 48 h, the queuine content of tRNA decreased concomitant with a decrease in benzidine-positive cells. Treatment with another reversible inducer, hemin, caused only a transient increase in the queuine content of tRNA, which was not correlated with the steady increase in benzidine-positive erythroid cells. The agent 5-azacytidine slightly inhibited cell growth but did not significantly change the percentage of benzidine-positive cells and the queuine content of tRNA. We further clarified the changes in queuine content of tRNA by analyzing the Q-containing isoacceptors of Q-family tRNA species including tRNA(Tyr), tRNA(His), tRNA(Asp), and tRNA(Asn) by RPC-5 chromatography, and found that the change in queuine content of tRNA(Tyr) was greater than the other Q-family tRNA species during induction by ara-C, sodium butyrate, and hemin. Our results indicate that the change in queuine content of tRNA is an irreversible event of terminal differentiation in ara-C induction and is a transient event of reversible differentiation in hemin induction. Sodium butyrate induction might represent a status between irreversible and reversible differentiation. Q-containing isoacceptors of tRNA might potentially play an important biological role during K562 cell differentiation.

Aspartate-tRNA Ligase↗
PubMed1993

Tertiary structures of mitochondrial tRNAs having characteristic secondary structures.

Some of the animal mitochondrial (mt) tRNAs are thought to have unusual secondary structures as inferred from the mt DNA sequence analysis. To obtain information on the relationship between the unusual secondary and tertiary structures and function of these mt tRNAs at the RNA level, we have analyzed the structure of bovine mt serine tRNAs and obtained the following results. 1) Using the novel secondary structure proposed on the basis of enzymatic probing and phylogenetic comparison and the known tertiary structure of yeast tRNA(Phe), a tertiary structural model of tRNA(Ser) specific for UCU/C/A/G codons was constructed by a computer modeling. In the proposed model, one-base-pair elongation of anticodon stem compensated for the deletions in some of the loop regions of this tRNA, and the model maintained the topological relationship between the anticodon and 3'-CCA terminus as nearly the same as that of yeast tRNA(Phe). The results of chemical modification of this tRNA supported the proposed model. 2) For NMR analysis of tRNA(Ser) specific for AGU/C codons and lacking the D stem, a large scale preparation of the unmodified tRNA transcript has been performed by the use of an in vitro T7 transcription system.

Animals↗
PubMed2004

Aminoacyl-tRNA synthesis by pre-translational amino acid modification.

Aminoacyl-tRNAs (aa-tRNAs) are essential substrates for ribosomal translation, and are generally synthesized by aminoacyl-tRNA synthetases (aaRSs). It was expected earlier that every organism would contain a complete set of twenty aaRSs, one for each canonical amino acid. However, analysis of the many known genome sequences and biochemical studies revealed that most organisms lack asparaginyl- and glutaminyl-tRNA synthetases, and thus are unable to attach asparagine and glutamine directly onto their corresponding tRNA. Instead, a pretranslational amino acid modification is required to convert Asp-tRNA(Asn) and Glu-tRNA(Gln) to the correctly charged Asn-tRNA(Asn) and Gln-tRNA(Gln), respectively. This transamidation pathway of amide aa-tRNA synthesis is common in most bacteria and archaea. Unexpected results from biochemical, genetic and genomic studies showed that a large variety of different bacteria rely on tRNA-dependent transamidation for the formation of the amino acid asparagine. Pretranslational modifications are not restricted to asparagine and glutamine but are also found in the biosynthesis of some other aa-tRNAs, such as the initiator tRNA fmet-tRNA(Met)(i) and Sec-tRNA(Sec) specifying selenocysteine, the 21(st) cotranslationally inserted amino acid. tRNA-dependent amino acid modification is also involved in the generation of aminolevulinic acid, the first precursor for porphyrin biosynthesis in many organisms.

Amino Acids↗
PubMed1976

[Conformational heterogeneity of tRNA, detected in the reaction of guanine bases with ketoxal].

The study of kinetic characteristics of the reaction of tRNA guanine bases with kethoxal has shown that temperature, ionic strength and Mg2+ ions, i.e. factors directly affecting the spatial structure of tRNA, influence also on its internal modification. The modification degree under stabilized spatial tRNA structure depends also on the concentration of kethoxal and is expressed in fractional values of the number of modified guanosine residues per tRNA molecule, which indicates the heterogeneity of tRNA for the modification degree. Chromatography of tRNA1 Val preparation on BD cellulose after the exhaustive modification with kethoxal under conditions of stabilized spatial structure has revealed a fraction of molecules completely resistant to the modificator, and a fraction containing differently modified tRNA molecules. tRNA heterogeneity after the reaction with kethoxal (the presence of resistant and reactive forms) indicates conformational heterogeneity of tRNA, expressed in the simultaneous presence of at least two conformer families.

Aldehydes↗
PubMed1990

Modification of the anticodon wobble position of tRNA(Ala) in vitro does not require 5' or 3' processing.

Maturation of eukaryotic tRNA molecules requires nuclear processing as well as nuclear and cytoplasmic modification of specific nucleotides. Nucleotide modifications within the anticodon are found in the majority of all tRNAs and are among the last maturation events to occur in vivo. We show that 5' and 3' processing of SP6 polymerase-generated transcripts are not necessary for the in vitro modification of A----I in the anticodon of tRNA(Ala).

Animals↗
PubMed2005

N6-Acetyladenosine: a new modified nucleoside from Methanopyrus kandleri tRNA.

Post-transcriptionally modified nucleosides are constituents of transfer RNA (tRNA) that are known to influence tertiary structure, stability and coding properties. Modifications in unfractionated tRNA from the phylogenetically unique archaeal methanogen Methanopyrus kandleri (optimal growth temperature 98 degrees C) were studied using liquid chromatography-mass spectrometry to establish the extent to which they might differ from those of other methanogens. The exceptionally diverse population of nucleosides included four new nucleosides of unknown structure, and one that was characterized as N(6)-acetyladenosine, a new RNA constituent. The nucleoside modification pattern in M. kandleri tRNA is notably different from that of other archaeal methanogens, and is closer to that of the thermophilic crenarchaeota.

Adenosine↗
PubMed1989

The selenocysteine-inserting opal suppressor serine tRNA from E. coli is highly unusual in structure and modification.

Selenocysteine is cotranslationally incorporated into selenoproteins in a unique pathway involving tRNA mediated suppression of a UGA nonsense codon (1-3). The DNA sequence of the gene for this suppressor tRNA from Escherichia coli predicts unusual features of the gene product (4). We determined the sequence of this serine tRNA (tRNA(UCASer]. It is the longest tRNA (95 nt) known to date with an acceptor stem of 8 base pairs and lacks some of the 'invariant' nucleotides found in other tRNAs. It is the first E. coli tRNA that contains the hypermodified nucleotide i6A, adjacent to the UGA-recognizing anticodon UCA. The implications of the unusual structure and modification of this tRNA on recognition by seryl-tRNA synthetase, by tRNA modifying enzymes, and on codon recognition are discussed.

Amino Acyl-tRNA Synthetases↗
PubMed2004

Selective rescue of selenoprotein expression in mice lacking a highly specialized methyl group in selenocysteine tRNA.

Selenocysteine (Sec) is the 21st amino acid in the genetic code. Its tRNA is variably methylated on the 2'-O-hydroxyl site of the ribosyl moiety at position 34 (Um34). Herein, we identified a role of Um34 in regulating the expression of some, but not all, selenoproteins. A strain of knock-out transgenic mice was generated, wherein the Sec tRNA gene was replaced with either wild type or mutant Sec tRNA transgenes. The mutant transgene yielded a tRNA that lacked two base modifications, N(6)-isopentenyladenosine at position 37 (i(6)A37) and Um34. Several selenoproteins, including glutathione peroxidases 1 and 3, SelR, and SelT, were not detected in mice rescued with the mutant transgene, whereas other selenoproteins, including thioredoxin reductases 1 and 3 and glutathione peroxidase 4, were expressed in normal or reduced levels. Northern blot analysis suggested that other selenoproteins (e.g. SelW) were also poorly expressed. This novel regulation of protein expression occurred at the level of translation and manifested a tissue-specific pattern. The available data suggest that the Um34 modification has greater influence than the i(6)A37 modification in regulating the expression of various mammalian selenoproteins and Um34 is required for synthesis of several members of this protein class. Many proteins that were poorly rescued appear to be involved in responses to stress, and their expression is also highly dependent on selenium in the diet. Furthermore, their mRNA levels are regulated by selenium and are subject to nonsense-mediated decay. Overall, this study described a novel mechanism of regulation of protein expression by tRNA modification that is in turn regulated by levels of the trace element, selenium.

Animals↗
PubMed2000

Defect in modification at the anticodon wobble nucleotide of mitochondrial tRNA(Lys) with the MERRF encephalomyopathy pathogenic mutation.

A mitochondrial tRNA(Lys) gene mutation at nucleotide position 8344 is responsible for the myoclonus epilepsy associated with ragged-red fibers (MERRF) subgroup of mitochondrial encephalomyopathies. Here, we show that normally modified uridine at the anticodon wobble position remains unmodified in the purified mutant tRNA(Lys). We have reported a similar modification defect at the same position in two mutant mitochondrial tRNAs(Leu)(UUR) in another subgroup, mitochondrial myopathy, encephalopathy, lactic acidosis and stroke-like episodes (MELAS), indicating this defect is common in the two kinds of tRNA molecules with the respective mutations of the two major mitochondrial encephalomyopathies. We therefore suggest the defect in the anticodon is responsible, through the translational process, for the pathogenesis of mitochondrial diseases.

Anticodon↗
PubMed1990

The role of modified purine 64 in initiator/elongator discrimination of tRNA(iMet) from yeast and wheat germ.

The role of 2'-ribosylated adenosine 64 in tRNA(iMet) from yeast in initiation/elongation discrimination was investigated. As measured by in vitro translation in rabbit reticulocyte lysate, the specific removal of the 2'-ribosylphosphate at adenosine 64 via periodate oxidation allows tRNA(iMet) to read internal AUG codons of the globine messenger RNA. Yeast Met-tRNA(iMet) lacking the modification of nucleoside 64 forms ternary complexes with GTP and elongation factor Tu from Escherichia coli. The lack of modification at position 64 does not prevent tRNA(iMet) from participating in the initiation process of in vitro protein synthesis. Wheat germ tRNA(iMet) has a 2'-ribosylated guanosine at position 64. Removal of this modification from the wheat germ tRNA(iMet) enables it to read internal AUG codons of globine and tobacco mosaic virus messenger RNA in reticulocyte and wheat germ translation systems, respectively.

Adenosine↗