Specific Transfer Ribonucleic Acids Research Articles

Degradation of host translational machinery drives tRNA acquisition in viruses.

Viruses are traditionally thought to be under selective pressure to maintain compact genomes and thus depend on host cell translational machinery for reproduction. However, some viruses encode abundant tRNA and other translation-related genes, potentially optimizing for codon usage differences between phage and host. Here, we systematically interrogate selective advantages that carrying 18 tRNAs may convey to a T4-like Vibriophage. Host DNA and RNA degrade upon infection, including host tRNAs, which are replaced by those of the phage. These tRNAs are expressed at levels slightly better adapted to phage codon usage, especially that of late genes. The phage is unlikely to randomly acquire as diverse an array of tRNAs as observed (p= 0.0017). Together, our results support that the main driver behind phage tRNA acquisition is pressure to sustain translation as host machinery degrades, a process resulting in a dynamically adapted codon usage strategy during the course of infection.

Editing Mischarged Amino Acids: the Work of Paul R. Schimmel

RNA Determinants for Translational Editing: Mischarging a Minihelix Substrate by a tRNA Synthetase (Nordin, B. E., and Schimmel, P. (1999) J. Biol. Chem. 274, 6835–6838) Structure-specific tRNA Determinants for Editing a Mischarged Amino Acid (Beebe, K., Merriman, E., and Schimmel, P. (2003) J. Biol. Chem. 278, 45056–45061)

Specific incorporation of glycine into bacterial lipopolysaccharide. Novel function of specific transfer ribonucleic acids

It has been found that the bacterial endotoxins (lipopolysaccharides, LPSs) contain some amino acids and glycine is the most abundant amino acid in the polysaccharide core preparations of LPSs of gram-negative bacteria. Until now nothing was known about the mechanism of amino acid incorporation into the lipopolysaccharide core. We found that one out of three glycyl-tRNAs(Gly) from Escherichia coli is the donor of amino acid and is the substrate for a putative aminoacyl-tRNA:LPS transferase. We have isolated, purified this tRNA and determined its nucleotide sequence to be major E.coli tRNA(3Gly). This tRNA(Gly) (anticodon GCC) conserved the tRNA structural features. The assay for determination of the specific incorporation of glycine into the lipopolysaccharide was also invented and described.

Specific mistranslation in hisT mutants of Escherichia coli.

Certain strains of Escherichia coli mistranslate at very high frequencies when starved for asparagine or histidine. This mistranslation is the result of misreading events on the ribosome. The introduction of a hisT mutation into such a strain decreases the frequency of mistranslation during histidine starvation but not during asparagine starvation. The most likely explanation is that the replacement of the pseudouridine residue in the anticodon loop of glutamine specific transfer ribonucleic acid by uridine in hisT mutants leads to an increase in fidelity of transfer ribonucleic acid function. The hisT gene in Escherichia coli has also been more accurately mapped, giving the gene order purF-hisT-aroC-fadL-dsdA.

Inhibition of yeast tRNATrp aminoacylation by 4-methyltryptophan

The effect of the tryptophan analogue 4-methyltryptophan in Saccharomyces cerevisiae has been investigated. 4-Methyltryptophan inhibits the aminoacylation of tryptophan specific transfer ribonucleic acid (tRNATrp). The mode of inhibition is competitive and the analogue is not charged onto tRNATrp. Thus 4-methyltryptophan application depletes the cells from charged tRNATrp. As a consequence cell growth and protein synthesis are strongly reduced. 4-Methyltryptophan is degraded efficiently in culture media inoculated with the wild type strain; the effects of 4-methyltryptophan were therefore found to be transient.

Arangement of transfer-RNA -genes in yeast.

The redundancy and the arrangement of the genes for specific transfer ribonucleic acids in yeast were studied by the hybridization techniques developed by Birnstiel et al., e.g.[1]. The redundancy was found to be in the order of 10 genes for tRNA1Met, tRNA3Met, tRNA2Ser, and tRNA-Pro. High molecular weight yeast DNA was fractionated by density gradient centrifugation in cesium chloride and the [32p]tRNAs were hybridized to the single fractions. The results together with earlier findings [2] suggest that the cistrons for these tRNAs are arranged in tandem interspersed by 6 to 10 times longer segments of spacer DNA which varies in (G+C) content for the different tRNA species.

Leucine specific transfer ribonucleic acids and synthetases in the cotyledons of mature and germinating pea seeds

Changes in isoaccepting species of tRNA Leu were determined in germinating pea seedlings and in developing pods. Leucine specific transfer ribonucleic acids of pea cotyledons can be fractionated into four isoaccepting species by reversed-phase chromatography (RPC-5) on a Plaskon column. In contrast, only two species of tRNA Leu were observed in developing seed pods. Leucyl- tRNA synthetase purified by ammonium sulfate precipitation and DEAE cellulose column chromatography retained the full range of specificity towards all four tRNA Leu species of pea cotyledons. This partially purified pea cotyledon enzyme could be further separated on a hydroxylapatite (HA) column into two peaks of leucyl- tRNA synthetase activity. Enzyme 1 is dominant in seed pods while 2 is predominant in cotyledons. Enzymes 1 and 2 from cotyledons were examined for the amino acid acceptor activity of twelve different amino acids. Both these fractions showed less than 3% acceptor activity for eleven other amino acids as compared to leucine- tRNA synthetase activity. Preliminary characterization of enzyme 2 from cotyledon, by isoelectric focusing and polyacrylamide gel electrophoresis indicates at least three subspecies.

Three photo-cross-linked complexes of yeast phenylalanine specific transfer ribonucleic acid with aminoacyl transfer ribonucleic acid synthetases.

Yeast tRNA-Phe has been cross-linked photochemically to three aminoacyl-tRNA synthetases, yeast phenylalanyl-tRNA synthetase, Escherichia coli isoleucyl-tRNA synthetase, and E. coli valyl-tRNA synthetase. The two non-cognate enzymes are known to interact with tRNA-Phe. In each complex, three regions on the tRNA are found to cross-link. Two of these are common to all of the complexes, while the third is unique to each. Thus, the cognate and non-cognate complexes bear considerable similarity to each other in the way in which the respective enzyme orients on tRNA-Phe, a result which was also established for the complexes of E. coli tRNA-Ile (BUDZIK, G.P., LAM, S.M., SCHOEMAKER, H.J.P., and SCHIMMEL, P.R. (1975) J. Biol. Chem. 250, 4433-4439). The common regions include a piece extending from the 5'-side of the acceptor stem to the beginning of the dihydrouridine helix, and a segment running from the 3' side of the extra loop into the TpsiC helix. These two regions overlap with and include some of the homologous bases found in eight tRNAs aminoacylated by yeast phenylalanyl-tRNA synthetase (ROE, B., SIROVER, M., and DUDOCK, B. (1973) Biochemistry 12, 4146-4153). Although well separated in the primary and secondary structure, these two segments are in close proximity in the crystallographic tertiary structure. In two of the complexes, the third cross-linked fragment is near to the two common ones. The picture which emerges is that the enzymes all interact with the general area in which the two helical branches of the L-shaped tertiary structure fuse together, with additional interactions on other parts of the tRNAas well.

Two photo-cross-linked complexes of isoleucine specific transfer ribonucleic acid with aminoacyl transfer ribonucleic acid synthetases.

Escherichia coli Ile-tRNA synthetase and tRNA-Ile have been cross-linked photochemically by the direct action of ultraviolet light. In addition, photo-induced joining of tRNA-Ile E. coli to Val-tRNA synthetase from yeast has also been achieved. This yeast enzyme is known to mischarge E. coli tRNA-Ile with valine. Regions on tRNA-Ile involved in cross-linking have been determined for both complexes. In each case, three distinct parts of the nucleic acid are found cross-linked. Two of these are the same in both complexes and involve the dihydrouridine stem and loop region. The third part is unique for each complex. It involves the 3' terminus in the cognate one and the 3' side of the anticodon in the non-cognate case. When the cross-linked regions are projected onto a model of the three-dimensional structure of tRNA, it is clear that these and other data are consistent with having each enzyme bound in a similar orientation across tRNA-Ile. The enzymes are viewed as spanning the distance from the anticodon to the 3' terminus and making extensive contact with the area in which the two helical branches of the L-shape tRNA structure come together.

A calorimetric study of the thermal transitions of three specific transfer ribonucleic acids.

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCalorimetric study of the thermal transitions of three specific transfer ribonucleic acidsJohn F. Brandts, William M. Jackson, and Thomas Y. C. TingCite this: Biochemistry 1974, 13, 17, 3595–3600Publication Date (Print):August 1, 1974Publication History Published online1 May 2002Published inissue 1 August 1974https://doi.org/10.1021/bi00714a030RIGHTS & PERMISSIONSArticle Views29Altmetric-Citations25LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (643 KB) Get e-Alerts Get e-Alerts

Ultra-rapid quantitative isolation of specific transfer ribonucleic acids a solid-phase method

Summary The following procedure is used in a rapid isolation of a specific (isoacceptor) tRNA from a mixture of deacylated tRNAs: (1) Acylation with the amino acid corresponding to the desired specific tRNA (2) Reaction of the specifically acylated tRNA with a new bi-functional reagent (PAMBSYL) (3) Binding of the pambsylated tRNA to a sulfhydryl-containing resin (4) Release of the specific tRNA from the resin after removal of the non-reacted tRNA. Steps 3 and 4 can be carried out in 20 min. One ml of the resin can bind approximately 200 mg of reacted tRNA.

Purification and characterization of AUA specific isoleucine transfer ribonucleic acid from Escherichia coli B.

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPurification and characterization of AUA specific isoleucine transfer ribonucleic acid from Escherichia coli BFumio Harada and Susumu NishimuraCite this: Biochemistry 1974, 13, 2, 300–307Publication Date (Print):January 15, 1974Publication History Published online1 May 2002Published inissue 15 January 1974https://doi.org/10.1021/bi00699a011RIGHTS & PERMISSIONSArticle Views112Altmetric-Citations76LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (873 KB) Get e-Alerts Get e-Alerts

Initiation of protein synthesis: The interaction of methionine specific transfer ribonucleic acids with rabbit reticulocyte ribosomes

The binding of Met-tRNA Met m and the initiator tRNA, Met-tRNA Met f, to rabbit reticulocyte ribosomes in the presence of various oligoribonucleotides containing the methionine codon, AUG, was studied in an in vitro system. 1. 1. At low concentrations of Mg 2+, optimum binding of Met-tRNA Met in response to AUG was observed in the concentration range of 1.5–4 M potassium acetate. 2. 2. Triplet specificity between other aminoacyl-tRNAs and their codons was retained under these ionic conditions. 3. 3. Met-tRNA Met f was shown to have a much higher affinity for ribosomes in response to AUG than Met-tRNA Met m. 4. 4. The binding of Met-tRNA Met f was specific for the 40-S ribosomal subunit. 5. 5. Met-tRNA Met f appeared to set the proper reading frame for the specific binding of a second aminoacyl-tRNA molecule to the 40-S ribosomal subunit.

Synthesis of specific transfer ribonucleic acids during methionine starvation in Escherichia coli 113-3

Escherichia coli mutant 113-3, derived from strain W, requires either vitamin B 12 or methionine for growth. Ribonucleic acids are synthesized without concomitant protein synthesis and cell multiplication when a culture of this mutant is incubated in the absence of methionine. The amounts of RNA and transfer RNA synthesized during methionine starvation depended on the duration of incubation. The co-ordination ratio of tRNA to total RNA indicated that synthesis of tRNA is regulated non-co-ordinately with reference to total RNA during methionine starvation. It is proposed that all classes of RNA are regulated non-co-ordinately in the absence of methionine in this strain. Reverse-phase chromatography revealed two peaks for valyl-tRNA under normal conditions, while under conditions of methionine deprivation an additional peak was found. These observations indicate the synthesis of a new species of undermethylated tRNA which is charged by valyl-tRNA synthetase. The possibility is discussed that this new undermethylated sub-species of valyl-tRNA synthesized in the absence of methionine is a “pre-tRNA”.

Studies on Rat Liver Phenylalanyl Transfer Ribonucleic Acid Synthetase: I. PURIFICATION, STABILIZATION, AND COMPLEX FORMATION

Abstract The phenylalanyl-tRNA synthetase (l-phenylalanine: tRNA ligase [AMP] EC 6.1.1.6) from rat liver was purified 500-fold by phosphocellulose and Sephadex G-100 chromatography. The behavior of this enzyme during purification suggests that intracellularly it exists as a complex with its specific transfer ribonucleic acid (tRNAphe). The sedimentation coefficient in sucrose gradients of the purified enzyme is 7.7 S while that of the complex with yeast tRNAphe is 11.6 S. This change in sedimentation coefficient is most compatible with the binding of 4 tRNAphe molecules to a synthetase of about 180,000 molecular weight although alternative explanations cannot be fully discounted. Similar changes in sedimentation coefficient were observed on binding rat liver tRNAphe and yeast tRNAphe from which the Y base had been removed. Heat inactivation of the synthetase, as measured by its decrease in ability to aminoacylate yeast tRNAphe, proceeds with apparent first order kinetics between pH 6 and pH 8. At pH 6.3 the rate constant for inactivation, ki, increases markedly with increasing ionic strength. However, at pH 7.5, ki decreases somewhat with increasing ionic strength. An inflection point in the plot of ki in 0.2 m KCl versus pH occurs at pH 6.4 and corresponds to the known pK of histidyl residues. Glycerol substantially protects against heat inactivation under all conditions of ionic strength and pH examined.

Alterations in specific transfer ribonucleic acids in a spectrum of hepatomas.

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAlterations in specific transfer ribonucleic acids in a spectrum of hepatomasDorothy Srinivasan, P. R. Srinivasan, Dezider Grunberger, I. Bernard Weinstein, and Harold Paul MorrisCite this: Biochemistry 1971, 10, 11, 1966–1973Publication Date (Print):May 1, 1971Publication History Published online1 May 2002Published inissue 1 May 1971https://doi.org/10.1021/bi00787a002RIGHTS & PERMISSIONSArticle Views15Altmetric-Citations19LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (781 KB) Get e-Alerts Get e-Alerts

A program of statistical designs for optimizing specific transfer ribonucleic acid assay conditions.

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTProgram of statistical designs for optimizing specific transfer ribonucleic acid assay conditionsIra B. Rubin, Toby J. Mitchell, and Gerald. GoldsteinCite this: Anal. Chem. 1971, 43, 6, 717–721Publication Date (Print):May 1, 1971Publication History Published online1 May 2002Published inissue 1 May 1971https://doi.org/10.1021/ac60301a003RIGHTS & PERMISSIONSArticle Views46Altmetric-Citations15LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (624 KB) Get e-Alerts Get e-Alerts

Polymorphism of serine specific transfer ribonucleic acid.

A method is described for the crystallizatino of serine specific transfer ribonucleic acid (tRNAI+IISer) in the prsence of magnesium as a divalent counter ion. The crystallization conditions in relation to different temperatures and various tRNA concentrations were investigated in detail were and three crystal forms were found. Tentative values for the unit cell parameters for two forms determined from X‐ray powder photographs. For the first form a= 120.3 Å, b= 54.2 Å and c= 68.6 Å and the space group is probably P222; for the second form a= 213.2 Å and c= 115.7 Å and the space group is either P6 or P622. From the thrid crystal form a still X‐ray photograph with reflections out to 3.5 Å from a single crystal was obtained using a precession camera. This phtograph together with a precession photograph suggests monolinic symmetry with the cell dimensions of a= 63 Å, b= 41 Å, c= 112 Å and β= 102.30, with the possible space group P21.

Methionine specific transferribonucleic acids from brewer's yeast and a haploid yeast strain.

Methionine specific transferribonucleic acids from brewer's yeast and a haploid yeast strain.

Genetic mapping and dominance of the amber suppressor, Su1 (supD), in Escherichia coli K-12.

In this report Su1 (supD), which is known to suppress "amber" mutations by means of a specific transfer ribonucleic acid, has been mapped relative to his and uvrC and has been found to be located at about 37.5 min on the Taylor and Trotter genetic map of the Escherichia coli K-12 chromosome. In addition, Su1(+) has been shown to be dominant over Su1(-), which supports the idea that Su1 is the structural gene for the suppressing transfer ribonucleic acid.