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At least 253 records · Page 14Linked to original sources
PubMed1990

Comparative study of the phenylalanyl-tRNA synthetases from Escherichia coli and Thermus thermophlus by the tritium topography method.

A comparative study of thermostability and aminoacid composition of the phenylalanyl-tRNA synthetases from E. coli and Thermus thermophilus HB8 has been carried out. Compared with the mesophilic enzyme, a considerable increase of Pro, Leu, Phe, Arg and decrease of Asx, Ile, Ser, Thr and Lys content have been revealed in the thermophilic protein. Using tritium topography, Pro, (Leu + Ile) and Gly were found to be the most accessible on the surfaces of both the enzymes. In the E. coli enzyme, Thr residues were also easy to access while on the surface of the thermophilic enzyme there were more Arg residues. The quantitative assay of the surface compositions revealed the increased exposure of the (Leu + Ile) residues on the thermophilic protein as well as of the charged Asx and Arg residues. A possible correlation of the observed effects with thermostability is discussed.

Amino Acids↗
PubMed1975

Fluorescence polarization studies on the local conformation of yeast tRNA.

The effects of temperature and guanidine hydrochloride (GuHC1) on the fluorescence polarization of Y base in partially purified yeast phenylalanine tRNA (p.p.tRNAPhe) and in acriflavine conjugates of crude yeast tRNA were investigated to elucidate the stability of the conformation at the 3'-CpCpA terminus and the anticodon loop of tRNA. The results can be summarized as follows: (1) The kinetic unit of the internal rotational motion near Y base in the anticodon loop of p.p.tRNAPhe seems to be independent of the temperature over the range 5--60degrees. Accelerated depolarization is observed in the 3'-CpCpA terminus at temperatures over 30degrees. This suggests that a change occurs in the native conformation of the 3'-CpCpA-acriflavine terminus at temperatures over 30degrees. (2) The fluorescence polarization of Y base in p.p.t-RNAPhe is not affected by the addition of GuHC1 up to 6 M, while that of acriflavine conjugated to the 3'-CpCpA terminus decreases markedly in the presence of 0.8 M GuHC1 reflecting the disruption of the native conformation. These results indicate that the local conformation near Y base is stable, but that of the amino acid acceptor terminus is not.

Binding Sites↗
PubMed1994

Crystal structure of a prokaryotic aspartyl tRNA-synthetase.

The crystal structure of Thermus thermophilus aspartyl tRNA-synthetase (AspRS) refined at 2.5 A resolution is described. This molecular structure is a textbook illustration of the modular organization of aminoacyl-tRNA synthetases. In addition to the three domains found in yeast AspRS, each monomer exhibits a module specific to prokaryotic enzymes, which corresponds to a helix-turn-helix motif in yeast AspRS, a domain implicated in the stabilization of the complex with tRNA. Its topology matches that of the histidine-containing phosphocarrier HPr which has been linked recently to another group of proteins containing the ferredoxin fold. We propose a more extensive alignment of these folds, which involves a circular permutation of the sequences and changes the point of entry of the whole domain. The C-terminal extension, another prokaryotic characteristic, leads to a significant increase in the network of interaction at the dimer interface. Some potential communication pathways suggest how a transfer of information between the two active sites of the homodimer might occur. Most of the residues involved belong to the class II-specific motifs in correlation with the dimeric state of nearly all class II enzymes. The T. thermophilus enzyme exhibits some features not found in any of the six other known AspRSs from mesophilic organisms.

Amino Acid Sequence↗
PubMed1989

Structure of E. coli glutaminyl-tRNA synthetase complexed with tRNA(Gln) and ATP at 2.8 A resolution.

The crystal structure of Escherichia coli glutaminyl-tRNA synthetase (GlnRS) complexed with its cognate glutaminyl transfer RNA (tRNA(Gln] and adenosine triphosphate (ATP) has been derived from a 2.8 angstrom resolution electron density map and the known protein and tRNA sequences. The 63.4-kilodalton monomeric enzyme consists of four domains arranged to give an elongated molecule with an axial ratio greater than 3 to 1. Its interactions with the tRNA extend from the anticodon to the acceptor stem along the entire inside of the L of the tRNA. The complexed tRNA retains the overall conformation of the yeast phenylalanine tRNA (tRNA(Phe] with two major differences: the 3' acceptor strand of tRNA(Gln) makes a hairpin turn toward the inside of the L, with the disruption of the final base pair of the acceptor stem, and the anticodon loop adopts a conformation not seen in any of the previously determined tRNA structures. Specific recognition elements identified so far include (i) enzyme contacts with the 2-amino groups of guanine via the tRNA minor groove in the acceptor stem at G2 and G3; (ii) interactions between the enzyme and the anticodon nucleotides; and (iii) the ability of the nucleotides G73 and U1.A72 of the cognate tRNA to assume a conformation stabilized by the protein at a lower free energy cost than noncognate sequences. The central domain of this synthetase binds ATP, glutamine, and the acceptor end of the tRNA as well as making specific interactions with the acceptor stem.2+t is

Adenosine Triphosphate↗
PubMed2004

The natural intron sequence of human tyrosine pre-transfer RNA is not a temporal stabilizer for cloverleaf structure.

We have developed the hyperprocessing technique to evaluate the stability of the cloverleaf shape of pre-transfer RNA (pre-tRNA). Application of this strategy to hyperprocessible human tyrosine pre-tRNA indicated that the natural intron sequence did not contribute to stabilization of the cloverleaf shape of this pre-tRNA, while the artificial intron with elongated anticodon-stem completely inhibited hyperprocessing of it. Our data suggested that the contemporary intron sequence may be a vestige of the ancient pre-biotic world, but not has been retained as a temporal stabilizer of the pre-tRNA before the base modifications.

Base Sequence↗
PubMed1980

Transfer ribonucleic acid genes in the chloroplast deoxyribonucleic acid of pea leaves.

The saturation hybridization between pea ctDNA and 125I-labeled pea ct-tRNAs has shown that 1.2% of the peak ctDNA codes for tRNA genes. The observed level of hybridization has been found to result from specific base pairings between ctDNA and ct-RNA as shown by competition hybridization experiments and thermal stability studies on DNA-tRNA hybrids. The level of hybridization obtained in this study amounts to the presence of approximately 40 tRNA genes in pea ctDNA. The tRNAs from the cytoplasm of the pea leaves, Escherichia coli, yeast, and calf thymus did not compete with the pea ct-tRNAs for the common base sequences in pea ctDNA. The presence of 17 aminoacyl-tRNA synthetases and their corresponding tRNAs was demonstrated in chloroplast. The acylation of ct-tRNAs proceeds with the same rate whether the partially purified tRNA synthetases from chloroplasts of E. coli are used. The aminoacylation of the three amino acids glutamic acid, glutamine, and cysteine proceeded very slowly in chloroplasts. The individually labeled aminoacyl-tRNAs hybridized with pea ctDNA. The hybridization follows true saturation rates, and the melting profiles of aminoacyl-tRNA-ctDNA indicate the formation of specific base pairs between the ctDNA and tRNA. Seventeen aminoacyl-tRNA genes have been identified in the pea ctDNA.

Chloroplasts↗
PubMed1999

CHOP/GADD153 and methionyl-tRNA synthetase (MetRS) genes overlap in a conserved region that controls mRNA stability.

The transcription factor CHOP is involved in the regulation of the cell division cycle and the control of programmed cell death in response to cellular stress. CHOP expression has been linked with several forms of cancer. A reciprocal translocation between the CHOP and TLS RNA-binding protein gene results in myxoid liposarcoma and amplifications of the CHOP gene are associated with solid tumors including several types of sarcomas. Here we report the mapping of the methionyl tRNA synthetase (MetRS) gene to the identical 12q13 locus where the CHOP gene had previously been mapped. PCR analysis demonstrates a tail-to-tail overlap of both genes over a 55-bp region. As a result the two mRNAs share a 3' UTR complementary sequence allowing an in vivo interaction between the two mRNAs. An AU-rich regulatory element (ARE) known to control mRNA stability resides in the overlapping sequence. To test for functional significance of the ARE a luciferase reporter plasmid containing the 3'UTR of CHOP was constructed. Transfection experiments in NIH-3T3 cells show that CHOP 3'UTR confers a significantly lower activity than a control reporter or a reporter in which the region overlapping the MetRS mRNA is deleted. The conservation of this overlapping of the CHOP and MetRS genes and the role of their complementary sequence in the control of mRNA stability suggest the existence of a functional link between the expression of these two genes.

3' Untranslated Regions↗
PubMed2000

Identity of tRNA for yeast tyrosyl-tRNA synthetase: tyrosylation is more sensitive to identity nucleotides than to structural features.

The specific aminoacylation of tRNA by yeast tyrosyl-tRNA synthetase does not rely on the presence of modified residues in tRNA(Tyr), although such residues stabilize its structure. Thus, the major tyrosine identity determinants were searched by the in vitro approach using unmodified transcripts produced by T7 RNA polymerase. On the basis of the tyrosylation efficiency of tRNA variants, the strongest determinants are base pair C1-G72 and discriminator residue A73 (the 5'-phosphoryl group on C1, however, is unimportant for tyrosylation). The three anticodon bases G34, U35, and A36 contribute also to the tyrosine identity, but to a lesser extent, with G34 having the most pronounced effect. Mutation of the GUA tyrosine anticodon into a CAU methionine anticodon, however, leads to a loss of tyrosylation efficiency similar to that obtained after mutation of the C1-G72 or A73 determinants. Transplantation of the six determinants into four different tRNA frameworks and activity assays on heterologous Escherichia coli and Methanococcus jannaschii tRNA(Tyr) confirmed the completeness of the tyrosine set and the eukaryotic character of the C1-G72 base pair. On the other hand, it was found that tyrosine identity in yeast does not rely on fine architectural features of the tRNA, in particular the size and sequence of the D-loop. Noticeable, yeast TyrRS efficiently charges a variant of E. coli tRNA(Tyr) with a large extra-region provided its G1-C72 base pair is changed to a C1-G72 base pair. Finally, tyrosylation activity is compatible with a +1 shift of the anticodon in the 3'-direction but is strongly inhibited if this shift occurs in the opposite 5'-direction.

Acylation↗
PubMed1995

Structural and functional accommodation of nucleotide variations at a conserved tRNA tertiary base pair.

The U8:A14 tertiary base pair of transfer RNAs (tRNAs) stabilizes the sharp turn from the acceptor stem to the dihydrouridine stem. This tertiary base pair is important for the overall L-shaped tRNA structure. Inspection of tRNA sequences shows that U8:A14 is highly conserved. However, variations of U8:A14 are found in natural sequences. This raises the question of whether all 16 permutations of U8:A14 can be accommodated by a single tRNA sequence framework and by the bacterial translational apparatus. Here we expressed the wild type and 15 variants of U8:A14 of an alanine tRNA amber suppressor in Escherichia coli and tested the ability of each to suppress an amber mutation. We showed that 12 of the 15 variants are functional suppressors (sup+) and 3 are nonfunctional (sup-). Of the 12 functional suppressors, the G8:G14 variant is the most efficient suppressor, whose suppression efficiency is indistinguishable from that of the wild type. Analysis of tRNA structure with chemical probes and the lead-cleavage reaction, however, showed a distinct difference between the G8:G14 variant and the wild type. Thus, two different structures of E. coli tRNAAla/CUA share an identical functional phenotype in protein synthesis. The remaining 11 sup+ variants with reduced suppression efficiencies are likely to have other structural variations. We suggest that the variations of these sup+ mutants are structurally and functionally accommodated by the bacterial translational apparatus. In contrast, the three sup- mutants harbor variations that alter the backbone structure in the corner of the L. These variations are likely to reduce the stability of the tRNA inside the cell or, among others, to interfere with the ability of the tRNA to functionally interact with elongation factor Tu and with the ribosome.

Bacterial Proteins↗
PubMed2004

A pathogenesis-associated mutation in human mitochondrial tRNALeu(UUR) leads to reduced 3'-end processing and CCA addition.

Point mutations in mitochondrial tRNAs can cause severe multisystemic disorders such as mitochondrial encephalomyopathy with lactic acidosis and stroke-like episodes (MELAS) and myoclonus epilepsy with ragged-red fibers (MERRF). Some of these mutations impair one or more steps of tRNA maturation and protein biosynthesis including 5'-end-processing, post-transcriptional base modification, structural stability, aminoacylation, and formation of tRNA-ribosomal complexes. tRNALeu(UUR), an etiologic hot spot for such diseases, harbors 20 of more than 90 disease-associated mutations described to date. Here, the pathogenesis-associated base substitutions A3243G, T3250C, T3271C, A3302G and C3303T within this tRNA were tested for their effects on endonucleolytic 3'-end processing and CCA addition at the tRNA 3'-terminus. Whereas mutations A3243G, A3302G and C3303T reduced the efficiency of 3'-end cleavage, only the C3303T substitution was a less efficient substrate for CCA addition. These results support the view that pathogenesis may be elicited through cumulative effects of tRNA mutations: a mutation can impede several pre-tRNA processing steps, with each such reduction contributing to the overall impairment of tRNA function.

Humans↗
PubMed1970

The effect of hypermethylation on the functional properties of transfer ribonucleic acid. Ribosome-binding and polypeptide synthesis.

1. Phenylalanyl-tRNA formed after chemical hypermethylation of Escherichia coli B tRNA was able to bind to ribosomes with the same efficiency as normal phenylalanyl-tRNA. 2. Under incubation conditions used in the ribosome-binding assay, hypermethylation of tRNA did not measurably decrease the stability of either inter-nucleotide phosphodiester bonds or the covalent bond between amino acid and tRNA in phenylalanyl-tRNA. 3. The ability of hypermethylated tRNA to take part in polyphenylalanine synthesis was inhibited progressively as the degree of hypermethylation increased. 4. Hypermethylation of tRNA affected polyphenylalanine synthesis at the stage of amino acid recognition and at a further point in the synthesis but not at the level of codon-anticodon recognition. 5. The formation of polylysine was more seriously affected by hypermethylation of tRNA than would be accounted for by inhibition of amino acid acceptance alone. 6. Polyproline formation was completely inhibited by the presence of 7mol% excess of methyl groups in tRNA. 7. The possibility of a link between amino acid acceptance and ribosome-binding was suggested for phenylalanyl-tRNA, but not for lysyl- or prolyl-tRNA.

Binding Sites↗
PubMed1983

Formation and properties of a covalent complex between elongation factor Tu and Phe-tRNA bearing a photoaffinity probe on its 3-(3-amino-3-carboxypropyl)uridine residue.

Escherichia coli Phe-tRNA, modified with the photoaffinity reagent 6-(2-nitro-4-azidophenylamino)caproate on the 3-(3-amino-3-carboxypropyl)uridine residue, was crosslinked to E. coli EFTu Section upon irradiation at 0 degree C with visible light at wavelengths greater than 400 nm. Crosslinking was dependent on irradiation, the photoaffinity probe, and was blocked by pre-photolysis. 1 mM-dithiothreitol completely quenched crosslinking. Binding of the tRNA to EFTu was a prerequisite for crosslinking, because neither EFTu . GDP nor AcPhe-tRNA could substitute; EFTu . GDPCP, however, was almost as active as EFTu . GTP. Crosslinking was complete in less than five minutes and was stable to at least 20 minutes of irradiation with a single 650 W tungsten lamp 4 cm away. The crosslinking yield ranged from 15% to 25%. The crosslinked complex possessed several remarkable properties. At 0.5 mM-Mg2+, the complex protected the AA-tRNA link to chemical hydrolysis, stabilized the bound GTP to dissociation or exchange, and was not adsorbed to cellulose nitrate filters. The purified crosslinked complex could be bound to ribosomes with concomitant hydrolysis of GTP. Extensive peptide bond formation with AcPhe-tRNA in the P site occurred despite the presence of the crosslinked EFTu. We conclude that hydrolysis of GTP is sufficient to release the 3' end of the Phe-tRNA from complexation with EFTu. Translocation of the A site bound complex did not occur. The crosslink site on EFTu is probably near the periphery of the molecule, because shortening the probe from 20 A to 14 A completely blocked crosslinking. A similar but shorter 8 A probe, p-azidophenacyl-4-thiouridine located on the opposite face of the tRNA, did not crosslink.

Affinity Labels↗
PubMed1991

Two essential components of the Saccharomyces cerevisiae transcription factor TFIIIB: transcription and DNA-binding properties.

RNA polymerase III transcription factor TFIIIB from Saccharomyces cerevisiae contains at least two polypeptides, with apparent masses of 90 and 70 kDa, that were previously identified by photocrosslinking to DNA. It is shown here that TFIIIB can be chromatographically separated into two components, each of which is required for efficient tRNA gene transcription. DNA-protein photocrosslinking experiments show these two components separately contain the 90- and 70-kDa TFIIIB-specific polypeptides. The 70-kDa component forms a heparin-sensitive complex with transcription factor TFIIIC and DNA, stabilizes TFIIIC interaction with the tRNA gene promoter elements, and protects against DNase I digestion in the 3' portion of the upstream DNA sequence that is occupied by TFIIIB. The 90-kDa component of TFIIIB, which only detectably interacts with the TFIIIC-DNA complex when the 70-kDa component is also present, generates the complete DNase I protection pattern of TFIIIB and bestows heparin-insensitivity on the TFIIIB-DNA complex. The resolution of TFIIIB into two functional components further defines the probable steps and interactions involved in the formation of stable transcription complexes.

Chromatography, Ion Exchange↗
PubMed2004

P-site tRNA is a crucial initiator of ribosomal frameshifting.

The expression of some genes requires a high proportion of ribosomes to shift at a specific site into one of the two alternative frames. This utilized frameshifting provides a unique tool for studying reading frame control. Peptidyl-tRNA slippage has been invoked to explain many cases of programmed frameshifting. The present work extends this to other cases. When the A-site is unoccupied, the P-site tRNA can be repositioned forward with respect to mRNA (although repositioning in the minus direction is also possible). A kinetic model is presented for the influence of both, the cognate tRNAs competing for overlapping codons in A-site, and the stabilities of P-site tRNA:mRNA complexes in the initial and new frames. When the A-site is occupied, the P-site tRNA can be repositioned backward. Whether frameshifting will happen depends on the ability of the A-site tRNA to subsequently be repositioned to maintain physical proximity of the tRNAs. This model offers an alternative explanation to previously published mechanisms of programmed frameshifting, such as out-of-frame tRNA binding, and a different perspective on simultaneous tandem tRNA slippage.

Animals↗
PubMed2001

Identity elements in tRNA-mediated transcription antitermination: implication of tRNA D- and T-arms in mRNA recognition.

tRNA-mediated transcription antitermination has been shown to control the expression of several amino acid biosynthesis operons and aminoacyl-tRNA-synthetase-encoding genes in Gram-positive bacteria. A model originally put forward by Grundy & Henkin describes the conserved structural features of the leader sequences of these operons and genes. Two sequences of 3 and 4 nt, respectively, take a central position in this model and are thought to be responsible for the binding of the system-specific uncharged tRNA, an interaction which would stabilize the antiterminator conformation of the leader. Here a further evolution of this model is presented based on an analysis of trp regulation in Lactococcus lactis in which a function is assigned to hitherto unexplained conserved structures in the leader sequence. It is postulated that the mRNA-tRNA interaction involves various parts of the tRNA in addition to the anticodon and the acceptor in the original model and that these additional interactions contribute to the recognition of a specific tRNA, and hence to the specificity and efficacy of the regulatory response.

5' Untranslated Regions↗
PubMed1982

Mechanism of translocation. Binding equilibria between the ribosome, mRNA analogues, and cognate tRNAs.

The translocation of the mRNA in relation to the ribosome during peptide synthesis represents an example for a mechanochemical reaction in which the chemical bond energy of GTP is transformed into coordinated motion. We demonstrate here that translocation can be explained simply by binding equilibria between the tRNA, the mRNA, and their binding sites on the ribosome. The presence of two cognate tRNAs shifts the association constant for the 70 S ribosome . AUGU3 complex from 6.8 x 10(5) to 2.2 x 10(8) M-1. The elongation factor G and GTP or guanosine-5'-(beta,gamma-methylene)triphosphate GMP-PCP) displace the methionine tRNAs which can be formylated (tRNAfMet) from the quaternary complex 70 S . AUGU3 . tRNAfMet . tRNAPhe. Only the ternary complex Phe-tRNAPhe . elongation factor Tu . GMP-PCP shows an absolute preference for the aminoacyl-tRNA binding site (A site) (K a = 6.6 x 10(6) M-1). AcPhe-tRNAPhe, (N alpha-acetylphenylalanyl-tRNA) an analogue of a peptidyl-tRNA exhibits a 20-fold higher affinity to the peptidyl-tRNA binding site (P site) (K a = 3.5 x 10(6) M-1) as against the A site (K a = 1.8 x 10(6) M-1) at 8 mM Mg2+. Compared to aminoacyl-tRNA and tRNA, peptidyl-tRNA shows a 3- to 15-fold higher affinity toward complementary oligonucleotides both in the binary complex and in the presence of 70 S ribosomes (UUCA . AcPhe-tRNAPhe: K a = 1.9 x 10(5) M-1), UUCA . tRNAPhe:K a = 3.2 x 10(4) M-1). This indicates a stabilization of the peptidyl-tRNA . mRNA complex during translocation. Our data support a concept of mRNA translocation in which the removal of the deacylated tRNA from the P site requires GTP energy and a peptidyl-tRNA . mRNA complex diffuses from its low affinity site (A) to its high affinity binding site (P).

Biological Transport↗
PubMed2003

3'-processing of yeast tRNATrp precedes 5'-processing.

Previous analyses of eukaryotic pre-tRNAs processing have reported that 5'-cleavage by RNase P precedes 3'-maturation. Here we report that in contrast to all other yeast tRNAs analyzed to date, tRNA(Trp) undergoes 3'-maturation prior to 5'-cleavage. Despite its unusual processing pathway, pre-tRNA(Trp) resembles other pre-tRNAs, showing dependence on the essential Lsm proteins for normal processing and efficient association with the yeast La homolog, Lhp1p. tRNA(Trp) is also unusual in not requiring Lhp1p for 3' processing and stability. However, other Lhp1p-independent tRNAs, tRNA(2)(Lys) and tRNA(1)(Ile), follow the normal pathway of 5'-processing prior to 3-processing.

N-Terminal Acetyltransferase C↗
PubMed2002

Synthesis of the tRNA(Lys,3) anticodon stem-loop domain containing the hypermodified ms2t6A nucleoside.

The synthesis of a protected form of the hypermodified nucleoside, N-[(9-beta-D-ribofuranosyl-2-methylthiopurin-6-yl)carbamoyl]threonine, (ms2t6A) is reported. The hypermodified nucleoside was subsequently elaborated to the protected nucleoside phosphophoramidite using a protecting group strategy compatible with standard RNA oligonucleotide chemistry. The phosphoramidite reagent was then used to synthesize the 17-nucleotide RNA hairpin having the sequence of the anticodon stem-loop (ASL) domain of human tRNA(Lys,3), the primer for HIV-1 reverse transcriptase. Introduction of the modification at position 37 of the tRNA ASL modestly decreases the thermodynamic stability of the RNA hairpin as has been seen previously for the prokaryotic t6A nucleoside lacking the 2-methylthio substituent. 2D NOESY NMR spectra of the ms2t6A containing tRNA ASL indicate that the threonyl side chain adopts a conformation similar to that seen in the solution structure of the analogous t6A containing E. coli tRNA(Lys), despite the presence of the bulky methylthio group. This synthetic approach allows for site-specific incorporation of the hypermodified nucleoside and should facilitate future studies directed at understanding the roles of nucleoside modification in modulating the stability and specificity of biologically important RNA-RNA interactions. Our synthesis of the ms2t6A containing RNAs demonstrates that this methodology is suitable for obtaining quantities of RNA required for structural studies of the HIV primer tRNA.

Anticodon↗