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PubMed2003

Biosynthesis of the 7-deazaguanosine hypermodified nucleosides of transfer RNA.

Transfer RNA (tRNA) is structurally unique among nucleic acids in harboring an astonishing diversity of post-transcriptionally modified nucleoside. Two of the most radically modified nucleosides known to occur in tRNA are queuosine and archaeosine, both of which are characterized by a 7-deazaguanosine core structure. In spite of the phylogenetic segregation observed for these nucleosides (queuosine is present in Eukarya and Bacteria, while archaeosine is present only in Archaea), their structural similarity suggested a common biosynthetic origin, and recent biochemical and genetic studies have provided compelling evidence that a significant portion of their biosynthesis may in fact be identical. This review covers current understanding of the physiology and biosynthesis of these remarkable nucleosides, with particular emphasis on the only two enzymes that have been discovered in the pathways: tRNA-guanine transglycosylase (TGT), which catalyzes the insertion of a modified base into the polynucleotide with the concomitant elimination of the genetically encoded guanine in the biosynthesis of both nucleosides, and S-adenosylmethionine:tRNA ribosyltransferase-isomerase (QueA), which catalyzes the penultimate step in the biosynthesis of queuosine, the construction of the carbocyclic side chain.

Catalysis↗
PubMed1969

Cytokinins: distribution in species of yeast transfer RNA.

Transfer RNA fractions from Saccharomyces lactis and Saccharomyces cerevisiae have been tested for cytokinin activity in the tobacco bioassay. Cysteine tRNA has been identified as a cytokinin-containing tRNA species in S. cerevisiae. Acid hydrolysates of S. lactis tRNA fractions (containing arginine tryptophan, and valine acceptor activities) and S. cerevisiae tRNA fractions (containing alanine, asparagine, aspartic acid, glutamic acid, glycine, histidine, tryptophan, and valine acceptor activities) were inactive in the tobacco bioassay. Cytokinins have been found only in those tRNA species corresponding to codons beginning with U.

Biological Assay↗
PubMed1976

Chloroplast DNA codes for transfer RNA.

Transfer RNA's were isolated from Euglena gracilis. Chloroplast cistrons for tRNA were quantitated by hybridizing tRNA to ct DNA. Species of tRNA hybridizing to ct DNA were partially purified by hybridization-chromatography. The tRNA's hybridizing to ct DNA and nuclear DNA appear to be different. Total cellular tRNA was hybridized to ct DNA to an equivalent of approximately 25 cistrons. The total cellular tRNA was also separated into 2 fractions by chromatography on dihydroxyboryl substituted amino ethyl cellulose. Fraction I hybridized to both nuclear and ct DNA. Hybridizations to ct DNA indicated approximately 18 cistrons. Fraction II-tRNA hybridized only to ct DNA, saturating at a level of approximately 7 cistrons. The tRNA from isolated chloroplasts hybridized to both chloroplast and nuclear DNA. The level of hybridization to ct DNA indicated approximately 18 cistrons. Fraction II-type tRNA could not be detected in the isolated chloroplasts.

Amino Acyl-tRNA Synthetases↗
PubMed1987

Interaction of RNA with transformed glucocorticoid receptor. II. Identification of the RNA as transfer RNA.

An endogenous RNA (designated as PIVB RNA), which is capable of associating with the 4 S glucocorticoid receptor (GR) to generate the 6 S form, has been purified from AtT-20 cells (Ali, M., and Vedeckis, W. V. (1987) J. Biol. Chem., 262, 6771-6777). We describe here the physiochemical properties, GR-RNA interaction characteristics, and the chemical identification of PIVB RNA. 32P-Labeled PIVB RNA was similar to transfer RNA (tRNA) in its sedimentation coefficient (4 S) on sucrose gradients, electrophoretic mobility on formaldehyde-agarose gels, and receptor binding characteristics. The amino acid acceptor activity of PIVB RNA displayed a typical tRNA-dependent saturation curve and was 2-3-fold higher than that of homologous rabbit liver tRNA when tested using rabbit liver aminoacyl-tRNA synthetase. The purified [3H] aminoacyl-PIVB complex was also capable of binding to the 4 S GR to generate the 6 S form. The analysis of PIVB RNA on an acrylamide-urea sequencing gel revealed that it contained a major tRNA of 76 nucleotides and other minor tRNA species of 74 and 78 nucleotides. The identity of the tRNA present in the PIVB RNA was indirectly deduced by analyzing the 3H-amino acids, liberated from the [3H]aminoacyl-PIVB RNA (tRNA) complex, and subsequent analysis on an amino acid analyzer. PIVB RNA mainly contained tRNAArg (51.8%), tRNALys (17.1%), and tRNAHis (9.2%) which together accounted for 78% of the total PIVB tRNA. The remaining 22% of tRNA was contributed by threonine, valine, aspartic acid, alanine, and phenylalanine tRNAs. The GR displayed no species specificity, and tRNA samples from mouse, cow, rabbit, yeast, and Escherichia coli can bind to the mouse 4 S GR to generate the 6 S form. However, PIVB RNA did not affect the sedimentation profiles of albumin, chymotrypsinogen, and histone, indicating that PIVB RNA does not bind to all proteins. Thus, there may exist some specificity both at the level of protein (GR) and the selection of RNA (tRNA). The GR binding to PIVB RNA occurred at low (nM) receptor concentration, and PIVB RNA showed limited capacity to shift 4 S GR to the 6 S form. 22.4 X 10(-11) mol of PIVB RNA can completely shift 4.8 X 10(-13) mol of 4 S GR to 6 S. That is, PIVB RNA has to be in a 500-600-fold excess over the amounts of GR to observe a stable 6 S GR X RNA complex on sucrose gradients. These results conclusively demonstrate that the transformed GR specifically binds to endogenous tRNA.

Amino Acids↗
PubMed1976

Transfer RNA and aminoacyl transfer RNA in developing rats.

The total transfer RNA (tRNA) level in the liver, kidney, skeletal muscle and heart muscle of developing rats was determined by purification using (3H)tRNA as an internal standard. Liver and kidney contained almost twice as much tRNA per gram tissue as heart and skeletal muscle. There were no apparent differences between the sexes. The aminoacylation capacities of six tRNA species (alanyl, aspartyl, leucyl, methionyl, phenylalanyl, and tryptophanyl) from rat liver were not different during 3 developmental stages (suckling, weaning and young adult), and there were also no differences noted between males females. The in vivo percent aminoacylation of 4 tRNAs (aspartyl, leucyl, methionyl, and phenylalanyl) was lower during the newborn and suckling periods than in weaning and young adult rat livers. The tRNA of young adults was almost completely aminoacylated in vivo with the exception of alanyl-tRNA.

Acylation↗
PubMed1975

Equilibrium measurements of cognate and noncognate interactions between aminoacyl transfer RNA synthetases and transfer RNA.

The interaction of Escherichia coli isoleucyl-tRNA synthetase with its cognate and five noncognate tRNAs, and of yeast valyl-tRNA synthetase with its cognate and four noncognate tRNAs, has been measured directly by fluorescence quenching. The cognate associations are strongest (association constant of 10(8) M-1 or more at pH 5.5, 17 degrees). A wide variation is found in the strengths of the noncognate interactions; these have association constants smaller than that of these cognate association by a factor of less than 10 to over 10(4), depending on the enzyme-t-RNA pair. A more detailed study of the cognate isoleucyl-tRNA synthetase-tRNAIle association suggests that the strength of the interaction is markedly sensitive to a pH-dependent transition in the enzyme centered at pH 6 on the other hand, Mg2+-induced structural changes in tRNAIle at 17 degrees in low salt do not greatly affect the availability of the nucleic acid's receptor sites for enzyme...

Amino Acyl-tRNA Synthetases↗
PubMed1995

A noncanonical tertiary conformation of a human mitochondrial transfer RNA.

Transfer RNAs possess highly conserved secondary structures, and crystallographic studies suggest a common, L-shaped tertiary conformation in which the anticodon and acceptor stems are disposed at approximately right angles to one another. However, many animal mitochondrial tRNAs possess unusual secondary structures, and little is known regarding their tertiary conformations, in particular, the relative orientations of their acceptor and anticodon stems. To address this issue, we have constructed heteroduplex RNA molecules corresponding to human mitochondrial and cytoplasmic lysyl tRNAs in which the acceptor and anticodon stems of each tRNA have been extended by approximately 70 base pairs. The rotational decay times of the two "extended" tRNA(Lys) species were compared to the decay times of a linear RNA control and to an extended yeast cytoplasmic tRNA(Phe) species whose interstem angle had been reported previously. Whereas the apparent interstem angle of the human cytoplasmic tRNA(Lys) species is essentially identical to that of the yeast tRNA(Phe) heteroduplex, with both conforming to the canonical L-shape, the angle for the mitochondrial tRNA(Lys) construct is much larger (approximately 140 degrees). Thus, the universal L-shape may not be applicable to noncanonical mitochondrial tRNAs, a finding of significance for both tRNA evolution and mitochondrial disease.

Anticodon↗
PubMed1981

Iron-related modification of bacterial transfer RNA.

Transfer RNAs isolated from E. coli grown in media where ferric iron is not freely available show well characterized chromatographic changes due to the absence of the methylthio moiety of ms2i6A. The altered tRNA molecules include tRNA trp tRNA tyr, tRNA phe and two minor tRNA ser species. It has been suggested that methylthiolation of tRNA affects its function in regulation. We now show iron-related changes in tRNA trp from S. typhimurium, Ps. aeruginosa and K. pneumoniae. tRNA trp from S. typhimurium contains ms2i6A and it seems probable that the availability of iron affects the synthesis of ms2i6A-tRNA trp from i6A-tRNA trp in this organism. An iron-related methylthiolating system may also be operative in K. pneumoniae. S. marcescens tRNA trp, however was not affected by the availability of iron. Neither ms2i6A nor i6A was found in S. marcescens tRNA, although an, as yet unidentified, hydrophobic nucleoside was present.

Bacteria↗
PubMed1994

Structural elements that contribute to an unusual tertiary interaction in a transfer RNA.

Transfer RNAs (tRNAs) contain a set of defined tertiary hydrogen-bonding interactions that are established between conserved and semiconserved nucleotides. Although the crystal structures of tRNAs describe each of the tertiary interactions in detailed molecular terms, little is known about the underlying structural parameters that stabilize the tertiary interactions. Escherichia coli (E. coli) tRNA(Cys) has an unusual tertiary interaction between G15 in the dihydrouridine (D) loop and G48 in the variable loop that is critical for cysteine aminoacylation. All other tRNAs have a purine 15 and a complementary pyrimidine 48 that establish a tertiary interaction known as the Levitt base pair [Levitt, M. (1969) Nature 224, 759-763; Klug et al. (1974) J. Mol. Biol. 89, 511-516]. In this study, the G15.G48 tertiary interaction in E. coli tRNA(Cys) was used to investigate the structural elements that contribute to its variation from the Levitt base pair. Analysis with chemical probes showed that substitution of U21 with A21 in the D loop and formation of a Watson-Crick base pair between nucleotides 13 and 22 in the D stem switch the hydrogen-pairing of G15.G48 to a Levitt-like G15.G48 base pair. This switch was accompanied by a decrease of the catalytic efficiency of aminoacylation by 2 orders of magnitude. In contrast, insertion of additional nucleotides in the D or variable loops had little effect.(ABSTRACT TRUNCATED AT 250 WORDS)

Acylation↗
PubMed1976

Aminoacyl transfer RNA formation. Binding of cations to transfer RNA and its role in aminoacyl transfer RNA formation.

The role of cations (polyamines and Mg2+) in isoleucyl-tRNA formation catalyzed by purified isolecuyl-tRNA synthetase [EC 6.1.1.5] from Escherichia coli was studied. It was found that spermine, spermidine, and Mg2+ bind to tRNA and that when bound to these cations, tRNA acts as substrate of aminoacylation without requiring further cations. These findings suggest that the primary function of cations in aminoacyl-tRNA formation is to bind to tRNA to stabilize its structure, not to bind to the enzyme to activate it.

Binding Sites↗
PubMed1980

The binding of T4 gene 32 protein to MS2 virus RNA and transfer RNA.

Fluorescence titrations, absorption spectroscopy and stopped-flow techniques were used to study the interaction of T4 coded 32-protein (P 32) with MS2 RNA and total tRNA from E. coli under different ionic conditions. It is shown that the amount of MS2 RNA and tRNA secondary structure melted by P 32 varies markedly and reversibly within a range of ionic conditions under which the binding constant of P 32 to single-stranded nucleic acids unable to form stable hairpins remains higher than 10(8) M-1. Kinetic experiments suggest that P 32 dissociates from the MS2 RNA rewinding strand with a similar rate constant as calculated for the dissociation from single-stranded regions. Possible in vivo consequences of these findings are discussed.

Bacteriophages↗