The structures and functions of transfer RNA

Identity Elements of tRNA as Derived from Information Analysis

The decipherment of the tRNA's operational code, known as the identity problem, requires the location of the sites in the tRNA structure that are involved in their correct recognition by the corresponding aminoacyl-tRNA synthetase. In this work, we determine the identity elements of each tRNA isoacceptor by means of the variation of information measure from information theory. We show that all isoacceptors exhibit sites associated with some bases of the anticodon. These sites form clusters that are scattered along the tRNA structure. The clusters determine the identity elements of each tRNA. We derive a catalogue of clustered sites for each tRNA that expands previously reported elements.

Molecular aspects on the interaction of protoberberine, benzophenanthridine, and aristolochia group of alkaloids with nucleic acid structures and biological perspectives

Alkaloids occupy an important position in chemistry and pharmacology. Among the various alkaloids, berberine and coralyne of the protoberberine group, sanguinarine of the benzophenanthridine group, and aristololactam-beta-d-glucoside of the aristolochia group have potential to form molecular complexes with nucleic acid structures and have attracted recent attention for their prospective clinical and pharmacological utility. This review highlights (i) the physicochemical properties of these alkaloids under various environmental conditions, (ii) the structure and functional aspects of various forms of deoxyribonucleic acid (DNA) (B-form, Z-form, H(L)-form, protonated form, and triple helical form) and ribonucleic acid (RNA) (A-form, protonated form, and triple helical form), and (iii) the interaction of these alkaloids with various polymorphic DNA and RNA structures reported by several research groups employing various analytical techniques like absorbance, fluorescence, circular dichroism, and NMR spectroscopy; electrospray ionization mass spectrometry, thermal melting, viscosity, and DNase footprinting as well as molecular modeling and thermodynamic studies to provide detailed binding mechanism at the molecular level for structure-activity relationship. Nucleic acids binding properties of these alkaloids are interpreted in relation to their biological activity.

The frameshift signal of HIV-1 involves a potential intramolecular triplex RNA structure

The cis-acting mRNA elements that promote programmed -1 ribosomal frameshifting present a natural target for the rational design of antiretroviral chemotherapies. It has been commonly accepted that the HIV-1 frameshifting signal is special, because its downstream enhancer element consists of a simple mRNA stem loop rather than a more complex secondary structure such as a pseudoknot. Here we present three lines of evidence, bioinformatic, structural, and genetic, showing that the biologically relevant HIV-1 frameshift signal contains a complex RNA structure that likely includes an extended RNA triple-helix region. We suggest that the potential intramolecular triplex structure is essential for viral propagation and viability, and that small molecules targeted to this RNA structure may possess antiretroviral activities.

The mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episode syndrome-associated human mitochondrial tRNALeu(UUR) mutation causes aminoacylation deficiency and concomitant reduced association of mRNA with ribosomes

The pathogenetic mechanism of the mitochondrial tRNA(Leu(UUR)) A3243G transition associated with the mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes (MELAS) syndrome has been investigated in transmitochondrial cell lines constructed by transfer of mutant mitochondrial DNA (mtDNA)-carrying mitochondria from three genetically unrelated MELAS patients or of isogenic wild-type mtDNA-carrying organelles into human mtDNA-less cells. An in vivo footprinting analysis of the mtDNA segment within the tRNA(Leu(UUR)) gene that binds the transcription termination factor failed to reveal any difference in occupancy of sites or qualitative interaction with the protein between mutant and wild-type mtDNAs. Cell lines nearly homoplasmic for the mutation exhibited a strong (70-75%) reduction in the level of aminoacylated tRNA(Leu(UUR)) and a decrease in mitochondrial protein synthesis rate. The latter, however, did not show any significant correlation between synthesis defect of the individual polypeptides and number or proportion of UUR codons in their mRNAs, suggesting that another step, other than elongation, may be affected. Sedimentation analysis in sucrose gradient showed a reduction in size of the mitochondrial polysomes, while the distribution of the two rRNA components and of the mRNAs revealed decreased association of mRNA with ribosomes and, in the most affected cell line, pronounced degradation of the mRNA associated with slowly sedimenting structures. Therefore, several lines of evidence indicate that the protein synthesis defect in A3243G MELAS mutation-carrying cells is mainly due to a reduced association of mRNA with ribosomes, possibly as a consequence of the tRNA(Leu(UUR)) aminoacylation defect.

Impairment of tRNA processing by point mutations in mitochondrial tRNA(Leu)(UUR) associated with mitochondrial diseases

Several point mutations in mitochondrial tRNA genes have been linked to distinct clinical subgroups of mitochondrial diseases. A particularly large number of different mutations is found in the tRNA(Leu)(UUR) gene. We show that base substitutions at nucleotide position 3256, 3260, and 3271 of the mitochondrial genome, located in the D and anticodon stem of this tRNA, and mutation 3243 changing a base involved in a tertiary interaction, significantly impair the processing of the tRNA precursor in vitro. In correlation with other studies, our results suggest that inefficient processing of certain mutant variants of mitochondrial tRNA(Leu)(UUR) is a primary molecular impairment leading to mitochondrial dysfunction and consequently to disease.

Solution structure of a purine.purine.pyrimidine DNA triplex containing G.GC and T.AT triples

BACKGROUND

Oligonucleotide-directed triple helix formation allows sequence specific recognition of double helical DNA. This powerful approach has been used to inhibit gene transcription in vitro and to mediate single site specific cleavage of a human chromosome.

RESULTS

Using a combined NMR and molecular dynamics approach (including relaxation matrix refinement), we have determined the solution structure of an intramolecular purine.purine.pyrimidine (R.RY) DNA triplex containing guanines and thymines in the third strand to high resolution. Our studies define the G.GC and T.AT base triple pairing alignments in the R.RY triplex and identify the structural discontinuities in the third strand associated with the non-isomorphism of the base triples. The 5'-d(TpG)-3' base steps exhibit a pronounced increase in axial rise and reduction in helical twist, while the reverse is observed, to a lesser extent at 5'-d(GpT)-3' steps. A third groove is formed between the purine-rich third strand and the pyrimidine strand. It is wider and deeper than the other two grooves.

CONCLUSIONS

Our structure of the R.RY DNA triplex will be important in the design of oligonucleotide probes with enhanced specificity and affinity for targeting in the genome. The third groove presents a potential target for binding additional ligands.

Triple helical polynucleotidic structures: an FTIR study of the C+ .G. Ctriplet

Triple helixes containing one homopurine poly dG or poly rG strand and two homopyrimidine poly dC or poly rC strands have been prepared and studied by FTIR spectroscopy in H2O and D2O solutions. The spectra are discussed by comparison with those of the corresponding third strands (auto associated or not) and of double stranded poly dG.poly dC and poly rG.poly rC in the same concentration range and salt conditions. The triplex formation is characterized by the study of the base-base interactions reflected by changes in the spectral domain involving the in-plane double bond vibrations of the bases. Modifications of the initial duplex conformation (A family form for poly rG.poly rC, B family form for poly dG.poly dC) when the triplex is formed have been investigated. Two spectral domains (950-800 and 1450-1350 cm-1) containing absorption bands markers of the N and S type sugar geometries have been extensively studied. The spectra of the triplexes prepared starting with a double helix containing only riboses (poly rC+.poly rG.poly rC and poly dC+.poly rG.poly rC) as well as that of poly rC+.poly dG.poly dC present exclusively markers of the North type geometry of the sugars. On the contrary in the case of the poly dC+.poly dG.poly dC triplex both N and S type sugars are shown to coexist. The FTIR spectra allow us to propose that in this case the sugars of the purine (poly dG) strand adopt the S type geometry.

Correlations between fluorine-19 nuclear magnetic resonance chemical shift and the secondary and tertiary structure of 5-fluorouracil-substituted tRNA

To complete assignment of the 19F nuclear magnetic resonance (NMR) spectrum of 5-fluorouracil-substituted Escherichia coli tRNA(Val), resonances from 5-fluorouracil residues involved in tertiary interactions have been identified. Because these assignments could not be made directly by the base-replacement method used to assign 5-fluorouracil residues in loop and stem regions of the tRNA, alternative assignment strategies were employed. FU54 and FU55 were identified by 19F homonuclear Overhauser experiments and were then assigned by comparison of their 19F NMR spectra with those of 5-fluorouracil-labeled yeast tRNA(Phe) mutants having FU54 replaced by adenine and FU55 replaced by cytosine. FU8 and FU12, were assigned from the 19F NMR spectrum of the tRNA(Val) mutant in which the base triple G9-C23-G12 substituted for the wild-type A9-A23-FU12. Although replacement of the conserved U8 (FU8) with A or C disrupts the tertiary structure of tRNA(Val), it has only a small effect on the catalytic turnover number of valyl-tRNA synthetase, while reducing the affinity of the tRNA for enzyme. Analysis of the 19F chemical shift assignments of all 14 resonances in the spectrum of 5-fluorouracil-substituted tRNAVal indicated a strong correlation to tRNA secondary and tertiary structure. 5-Fluorouracil residues in loop regions gave rise to peaks in the central region of the spectrum, 4.4 to 4.9 parts per million (p.p.m.) downfield from free 5-fluorouracil. However, the signal from FU59, in the T-loop of tRNA(Val), was shifted more than 1 p.p.m. downfield, to 5.9 p.p.m., presumably because of the involvement of this fluorouracil in the tertiary interactions between the T and D-loops. The 19F chemical shift moved upfield, to the 2.0 to 2.8 p.p.m. range, when fluorouracil was base-paired with adenine in helical stems. This upfield shift was less pronounced for the fluorine of the FU7.A66 base-pair, located at the base of the acceptor stem, an indication that FU7 is only partially stacked on the adjacent G49 in the continuous acceptor stem/T-stem helix. An unanticipated finding was that the 19F resonances of 5-fluorouracil residues wobble base-paired with guanine were shifted 4 to 5 p.p.m. downfield of those from fluorouracil residues paired with A. In the 19F NMR spectra of all fluorinated tRNAs studied, the farthest downfield peak corresponded to FU55, which replaced the conserved pseudouridine normally found at this position.

Structural elements in RNA

This chapter describes the RNA structural characteristics that have emerged so far. Folded RNA molecules are stabilized by a variety of interactions, the most prevalent of which are stacking and hydrogen bonding between bases. Many interactions among backbone atoms also occur in the structure of tRNA, although they are often ignored when considering RNA structure because they are not as well-characterized as interactions among bases. Backbone interactions include hydrogen bonding and the stacking of sugar or phosphate groups with bases or with other sugar and phosphate groups. The interactions found in a three-dimensional RNA structure can be divided into two categories: secondary interactions and tertiary interactions. This division is useful for several reasons. Secondary structures are routinely determined by a combination of techniques discussed in chapter, whereas tertiary interactions are more difficult to determine. Computer algorithms that generate RNA structures can search completely through possible secondary structures, but the inclusion of tertiary interactions makes a complete search of possible structures impractical for RNA molecules even as small as tRNA. The division of RNA structure into building blocks consisting of secondary or tertiary interactions makes it easier to describe RNA structures. In those cases in which RNA studies are incomplete, the studies of DNA are described with the rationalization that RNA structures may be analogous to DNA structures, or that the techniques used to study DNA could be applied to the analogous RNA structures. The chapter focuses on the aspects of RNA structure that affect the three-dimensional shape of RNA and that affect its ability to interact with other molecules.

Search of essential parameters for the aminoacylation of viral tRNA-like molecules. Comparison with canonical transfer RNAs

Comparative structural and functional results on the valine and tyrosine accepting tRNA-like molecules from turnip yellow mosaic virus (TYMV) and brome mosaic virus (BMV), and the corresponding cognate yeast tRNAs are presented. Novel experiments on TYMV RNA include design of variant genes of the tRNA-like domain and their transcription in vitro by T7 RNA polymerase, analysis of their valylation catalyzed by yeast valyl-tRNA synthetase, and structural mapping with dimethyl sulfate and carbodiimide combined with graphical modelling. Particular emphasis is given to conformational effects affecting the valylation capacity of the TYMV tRNA-like molecule (e.g., the effect of the U43----C43 mutation). The contacts of the TYMV and BMV RNAs with valyl- and tyrosyl-tRNA synthetases are compared with the positions in the molecules affecting their aminoacylation capacities. Finally, the involvement of the putative valine and tyrosine anticodons in the tRNA-like valylation and tyrosylation reactions is discussed. While an anticodon-like sequence participates in the valine identity of TYMV RNA, this seems not to be the case for the tyrosine identity of BMV RNA despite the fact that the tyrosine anticodon has been shown to be involved in the tyrosylation of canonical tRNA.

What does the homology between E. coli tRNAs and RNAs controlling ColE1 plasmid replication mean?

Nucleotide sequences of E. coli tRNAs and RNA I or RNA II (controlling replication of ColE1 plasmids) were compared using the computer. The homology between some of these molecules is over 60%. The distribution of homologous nucleotides among the functional elements (stems and loops) of either RNA I or RNA II and the tRNAs molecules was studied. It was found that the homologous domains are located mainly in the loop regions of RNA I or RNA II. A consensus sequence, the nonanucleotide AGUUGGUAG, was discovered in loop II of RNA I and in the dihydrouridylic loop of tRNAs showing homology with RNA I. Based on this observation, a hypothesis was drawn for a possible role of the tRNAs in the regulation of plasmid DNA replication.

3-D graphics modelling of the tRNA-like 3'-end of turnip yellow mosaic virus RNA: structural and functional implications

The tRNA-like structure of the aminoacylatable 3'-end of turnip yellow mosaic virus (TYMV) RNA was submitted to 3-D graphics modelling. A model of this structure has been inferred previously from both biochemical results and sequence comparisons which presents a new RNA folding feature, the "pseudoknot". It has been verified that this structure can be constructed without compromising accepted RNA stereochemical rules, namely base stacking and preferential 3'-endo sugar pucker. The model has aided interpretation of previous structural mapping experiments using chemical and enzymatic probes, and new accessibilities of residues could be predicted and tested. Pseudoknots have been considered as potential splice sites because they form antiparallel helical segments in a single RNA molecule. We have examined this possibility with the constructed 3-D model and could verify the hypothesis on a structural basis. The model presents a striking similarity with canonical tRNA and allows a valuable comparison between the protection patterns of yeast tRNA(Val) and tRNA-like viral RNA by cognate yeast valyl-tRNA synthetase against structural probes.

Restrained refinement of the monoclinic form of yeast phenylalanine transfer RNA. Temperature factors and dynamics, coordinated waters, and base-pair propeller twist angles

The structure of yeast phenylalanine transfer RNA in the monoclinic form has been further refined by using the restrained least-squares method of Hendrickson and Konnert. For the 4019 reflections between 10 and 3 A, with magnitudes at least 3 times their standard deviations, the R factor is 16.8%. The variation of the atomic temperature factors along the sequence indicates that the major flexibility regions are the amino acid and anticodon stems. The two strands of the amino acid helix exhibit large differential temperature factors, suggesting partial uncoiling or melting of the helix. In this work, the occupancy of all atoms was also varied. Residues D16 and D17 of the dihydrouridine loop as well as U33 and G37 of the anticodon loop have occupancies around 70%, indicating some local disorder or large-scale mobility at these positions. One hundred fifteen solvent molecules, including five magnesium ions, were found in difference maps. The role of several water molecules is clearly related to the stabilization of the secondary and tertiary interactions. The gold sites, which were not previously discussed, are described and show an energetically favored binding mode similar to that of cobalt and nickel complexes with nucleotides.

Crystallization of transfer ribonucleic acids

A compilation of crystallization experiments of tRNAs published in literature as well as original results are given and discussed in this paper. Up to now 17 different tRNA species originating from Escherichia coli and from the yeast Saccharomyces cerevisiae have been crystallized. All structural tRNA families are represented, namely the tRNAs with large or small extra-loops and among them the initiator tRNAs. The tRNAs with small variable loops (4 to 5 nucleotides), e.g. tRNAAsp and tRNAPhe, yield the best diffracting crystals. Crystalline polymorphism is a common feature; about 100 different crystal forms have been observed, but only 6 among them enabled structure determination studies by X-ray diffraction. Crystallization strongly depends upon experimental parameters such as the presence of polyamines and magnesium as well as upon the purity and the molecular integrity of the tRNAs. Crystals are usually obtained by vapour diffusion methods using salts (e.g. ammonium sulfate), organic solvents (e.g. isopropanol, dioxane or 2-methyl-2,4-pentane diol) or polyethylene glycol as precipitants. A methodological strategy for crystallyzing new tRNA species is described.

Construction of a UGA suppressor tRNA by modification in vitro of yeast tRNACys

In this paper we describe the construction of a yeast tRNACys UGA suppressor. After specific hydrolysis of the parent molecule, the first base of the anticodon GCA was replaced by a uracil. The resulting molecule, harboring a UCA anticodon, was injected into Xenopus laevis oocytes in order to test its biological activities. The level of aminoacylation was similar to that of the parent molecule. Readthrough of the UGA termination codon in beta-globin mRNA, coinjected with the tRNA, indicated suppressor activity; however, tRNACys (anticodon UCA) was a much less efficient suppressor than others tested under the same conditions. We see no post-transcriptional modification of the uracil in the anticodon wobble position after injection into oocytes. This may be related to the low suppressor activity; however, it is also possible that other features of tRNACys structure may be unadapted to efficient UCA anticodon function.

Reconstruction of tRNAPhe molecules from the fragments by linkage with T-4 RNA ligase in double-stranded regions

Phenylalanine-specific tRNA from yeast was hydrolysed with cobra venom ribonuclease in the double-stranded regions and the fragments isolated. The 'dissected' molecules with nicks in positions 28 and 41 were reconstructed from supplementary fragments and treated with T-4 RNA ligase. A phosphodiester bond between two fragments was formed when the fragment combination (1-28) + (29-76) was used. A strong discrimination in the ligation yield between different nick positions in the same helix is shown.

Interaction of tRNAPhe and tRNAVal with aminoacyl-tRNA synthetases. A chemical modification study

The alkylation by ethylnitrosourea of phosphodiester bonds in tRNAPhe from yeast and in tRNAVal from yeast and from rabbit liver and that by 4-(N-2-chloroethyl-N-methylamino)-benzylamine of N-7 atoms of guanosine residues in yeast tRNAVal have been used to study the interaction of these tRNAs with aminoacyl-tRNA synthetases. The modifications occurring at low yield were carried out on 3' and/or 5' end-labelled tRNAs either free or in the presence of cognate or non-cognate synthetases. After splitting of the tRNAs at the alkylated positions, the position of the modification sites in the tRNA sequences were detected by acrylamide gel electrophoresis. It was found that the synthetases protect against alkylation certain phosphate or guanosine residues in their cognate tRNAs. Non-cognate synthetases failed to protect efficiently specific positions in tRNA against modification. In yeast tRNAPhe the cognate phenylalanyl-tRNA synthetase protects certain phosphates located in all four stems and in the anticodon and extra-loop of the tRNA. Particularly strong protections occur on phosphate 34 in the anticodon loop and on phosphates 23, 27, 28, 41 and 46 in the D and anticodon stems. In yeast tRNAVal complexed with yeast valyl-tRNA synthetase the protected phosphates are essentially located in the corner between the amino-acid-accepting and D stems, in the D loop, anticodon stem and in the variable region of the tRNA. Three guanosine residues, located in the D stem, and another one in the 3' part of the anticodon stem were also found protected by the synthetase. In mammalian tRNAVal, complexed with the cognate but heterologous yeast valyl-tRNA synthetase, the protected phosphates lie in the anticodon stem, in the extra-loop and in the T psi arm. The location of the protected residues in the structure of three tRNAs suggests some common features in the binding of tRNAs to aminoacyl-tRNA synthetases. These results will be discussed in the light of informations on interaction sites obtained by nuclease digestion and ultraviolet cross-linking methods.

Structure in tRNA data

260 sequences of tRNA are compared, after their classification into six categories: prokaryotic (83 sequences) and eukaryotic (83 sequences) elongators, prokaryotic (10 sequences) and eukaryotic (11 sequences), initiators, lower eukaryotic mitochondrial tRNA (53 sequences) and archaebacterial tRNA (20 sequences). Beside the presence of invariable and semi-invariable positions in tRNA, non-random base distribution in almost all positions is also evident; most of them being characteristic of each class of tRNA. Therefore, during evolution it would seem that selectional pressures do act in so called variable positions as well as invariant positions of tRNA molecules. Results are discussed in relation to possible restrictions depending on functional and/or structural constraints of tRNA.

Tertiary structure of tRNAs in solution monitored by phosphodiester modification with ethylnitrosourea

The alkylation by ethylnitrosourea of phosphodiester bonds in yeast tRNAPhe, tRNAVal and in Escherichia coli tRNAGlu, tRNAfMet, tRNAmMet and tRNAPhe was investigated under various conditions. In unfolded tRNAs the reactivities of phosphates in various positions toward the reagent were similar. In the folded tRNAs remarkable differences in reactivities of phosphates located in various positions of the molecules were observed. In yeast and E. coli tRNAPhe, reactivities of phosphates in positions 9, 10, 11, 19, 49, 58, 59 and 60 were found to be strongly decreased. Some decrease in reactivity was observed for phosphates 23 and 24. Spermine and ethidium bromide did not influence the pattern of phosphate alkylation in the T psi C arm of yeast tRNAPhe. Our solution results fit with the crystal structure of tRNAPhe with respect to the potential availability of the phosphates in this tRNA to solvent as shown by others. Judging from the pattern of phosphate reactivities, the structure of E. coli tRNAPhe is very similar to that of yeast tRNAPhe. Upon thermal denaturation of the yeast tRNAPhe, the reactivity of the low-reactive phosphates increased, demonstrating a cooperative melting curve. A comparison of the patterns of phosphate alkylation in several tRNAs, essentially in their T psi C arms, revealed a striking similarity, suggesting that the folding of these tRNAs is essentially similar.

Study of the interaction between yeast tRNAphe and yeast phenylalanyl-tRNA synthetase by monochromatic ultraviolet irradiation at various wavelengths. Advantages and limits of the method

The interactions between yeast tRNAphe and phenylalanyl-tRNA synthetase were studied by analysis of the covalent adducts obtained upon monochromatic ultraviolet irradiation at different wavelengths (248, 282, 292, 302 and 313 nm). The high extent of inactivation of phenylalanyl-tRNA synthetase, together with the partial modification of tRNA, as well as the peculiar instability of most of the covalent bonds formed upon irradiation constitute severe limitations to the use of the technique and to the interpretation of the results. These disadvantages led us to select an irradiation wavelength of 248 nm and to use only mild isolation procedures allowing a good recovery of the covalent adducts formed. Seven major tryptic peptides of the enzyme were found to be cross-linked to tRNAPhe whereas six major T1-oligonucleotides were covalently linked to the protein, among these, the three cross-linked oligonucleotides previously described by Shoemaker and Schimmel (J. Biol. Chem. 250 (1975) 4440-4444) in the same system. The difference in the number of covalently linked oligonucleotides is discussed in the light of the instability of the covalent linkages. The localization of the six oligonucleotides at the inside of the two branches forming the L-shaped tRNA molecule is similar to that observed in the yeast valine system (Renaud et al., Eur. J. Biochem. 101 (1979) 475-483) and is consistent with the interaction model previously described (Rich and Schimmel, Nucl. Acids Res. 4 (1977) 1649-1665 and Ebel et al. in Transfer RNA: structure, properties and recognition, (1979) pp. 325-343 Cold Spring Harbor Laboratory, NY). The occurrence of covalent cross-linking upon irradiation in the tryptophan absorption band (302 nm) strongly suggests the participation of this residue in the stabilization of the tRNA enzyme complex.

The evolving tRNA molecule

The study of tRNA molecular evolution is crucial to understanding the origin and establishment of the genetic code as well as the differentiation and refinement of the machinery of protein synthesis in prokaryotes, eukaryotes, organelles, and phage systems. The small size of the molecule and its critical involvement in a multiplicity of roles distinguish its study from classical protein molecular evolution with respect to goals and methods. Here, the authors assess available and missing data, existing and needed methodology, and the impact of tRNA studies on current theories both of genetic code evolution and of the evolution of species. They analyze mutational "hot spots", the role of base modification, synthetase recognition, codon-anticodon interactions and the status of organelle tRNA.

A rapid method for mapping exposed cytosines in polyribonucleotides. Application to tRNATrp (yeast, beef liver)

A rapid method for mapping exposed cytosine residues in 5'-[32P]-labeled RNA molecules is suggested. The exposed cytosines (C's) are converted into uracyls (U's) by bisulphite treatment at pH 5.8 in the presence of Mg2+, followed by complete modification of the residual (non-exposed) C's by a methoxyamine and bisulphite mixture at pH 5.0. The control RNA is modified only by methoxyamine and bisulphite without the preliminary C leads to U conversion. The location of the exposed C's is determined by comparing the products of partial T1, T2, A and U2 ribonuclease digestions of the C leads to U converted and control RNAs after slab gel polyacrylamide electrophoresis and autoradiography. The method has been applied for mapping exposed cytosine bases in tRNATrp (yeast) which have been found in the anti-codon loop and at the 3'-end of the molecule. In tRNATrp (beef liver), in addition to the same exposed bases, C in the diHU-loop is exposed. The data obtained are in full agreement with what is known about exposed C's for other tRNAs.

Three-dimensional structure of Escherichia coli initiator tRNAfMet

The crystal structure of Escherichia coli tRNAfMet an initiator transfer RNA, has been determined. While grossly similar to that of the chain-elongating yeast tRNAPhe, there are three major differences. One involves the folding of the anticodon loop; in particular, the position of the constant uridine, U33. This difference was unexpected and may be of functional significance.

Prediction of pairing schemes in RNA molecules-loop contributions and energy of wobble and non-wobble pairs

Previously published models for predicting pairing schemes in RNA molecules, when applied to tRNA, give the clover leaf structure in only half the cases. We made a systematic investigation of the predictability of the clover leaf structure under various assumptions concerning the energetic contributions of single and double-stranded regions. We tested 21 different models and variants on a set of 100 tRNA sequences and many other variants on a smaller set of sequences. In our models we allowed not only G.C, A.U and G.U pairing, but also every other pair. Under conditions which are much less restrictive than those of previous attempts, we can nevertheless reach 90 per cent predictability for the clover leaf structure of tRNA. A most surprising and far-reaching result is that we can assign to C.G and C.C pairs binding energies quite close to the energies of G.U pairs, and still predict the clover leaf. The following ranking for non-complementary pairs was obtained : G.U, G.G and C.C, U.U, C.A, A.A and G.A, U.C. The main practical innovation which made possible the improvements in predictability are: i) not counting the stacking of base pairs separated by a bulge loop; ii) making the terminal C.C's in stems more stable than the terminal A.U's by merely -- 0.7 kcal; iii) replacing the distinction between G.C and A.U-closed loops by a distinction based on the presence of loop-favoring residues; iv) carefully adjusting the energetic balance between the various kinds of loops; v) narrowing the gap between the GC/GC and the GC/AU contributions; vi) using observations on nearest-neighbours in tRNA sequences to refine the contributions of G.U pairs.

Glutamyl transfer ribonucleic acid synthetase of Escherichia coli. Study of the interactions with its substrates

The binding of the various substrates to Escherichia coli glutamyl-tRNA synthetase has been investigated by using as experimental approaches the binding study under equilibrium conditions and the substrate-induced protection of the enzyme against its thermal inactivation. The results show that ATP and tRNAGlu bind to the free enzyme, whereas glutamate binds only to an enzyme form to which glutamate-accepting tRNAGlu is associated. By use of modified E. coli tRNAsGlu and heterologous tRNAsGlu, a correlation could be established between the ability of tRNAGlu to be aminoacylated by glutamyl-tRNA synthetase and its abilities to promote the [32P]PPi-ATP isotope exchange and the binding of glutamate to the synthetase. These results give a possible explanation for the inability of blutamyl-tRNA synthetase to catalyze the isotope exchange in the absence of amino acid accepting tRNAGlu and for the failure to detect an enzyme-adenylate complex for this synthetase by using the usual approaches. One binding site was detected for each substrate. The specificity of the interaction of the various substrates has been further investigated. Concerning ATP, inhibition studies of the aminoacylation reaction by various analogues showed the existence of a synergistic effect between the adenine and the ribose residues for the interaction of adenosine. The primary recognition of ATP involves the N-1 and the 6-amino group of adenine as well as the 2'-OH group of ribose. This first interaction is then strengthened by the phosphate groups- Inhibition studies by various analogues of glutamate showed a strong decrease in the affinity of this substrate for the synthetase after substitution of the alpha- or gamma-carboxyl groups. The enzyme exhibits a marked tendency to complex tRNAs of other specificities even in the presence of tRNAGlu. MgCl2 and spermidine favor the specific interactions. The influence of monovalent ions and of pH on the interaction between glutamyl-tRNA synthetase and tRNAGlu is similar to those reported for other synthetases not requiring their cognate tRNA to bind the amino acid. Finally, contrary to that reported for other monomeric synthetases, no dimerization of glutamyl-tRNA synthetase occurs during the catalytic process.

Evolution of methionine initiator and phenylalanine transfer RNAs

Sequence data from methionine initiator and phenylalanine transfer RNAs were used to construct phylogenetic trees by the maximum parsimony method. Although eukaryotes, prokaryotes and chloroplasts appear related to a common ancestor, no firm conclusion can be drawn at this time about mitochondrial-coded transfer RNAs. tRNA evolution is not appropriately described by random hit models, since the various regions of the molecule differ sharply in their mutational fixation rates. "Hot" mutational spots are identified in the Tpsic, the amino acceptor and the upper anticodon stems; the D arm and the loop areas on the other hand are highly conserved. Crucial tertiary interactions are thus essentially preserved while most of the double helical domain undergoes base pair interchange. Transitions are about half as costly as transversions, suggesting that base pair interchanges proceed mostly through G-U and A-C intermediates. There is a preponderance of replacements starting from G and C but this bias appears to follow the high G + C content of the easily mutated base paired regions.

Lack of correlation between affinity of the tRNA for the aminoacyl-tRNA synthetase and aminoacylation capacity as studied with modified tRNAPhe

The interactions of several modified yeast tRNAPhe [tRNAPhe lacking 7-methylguanine; a fragment comprising about 3/4 of the whole molecule: tRNAPhe (18--76); tRNAPhe (18--76) lacking 7-methylguanine] with yeast phenylalanyl-tRNA synthetase were studied. Upon excision of the 5'-quarter of the tRNAPhe molecule, the residual fragment still tightly binds to the synthetase, but can no longer by aminoacylated. Surprisingly, upon removal of the 7-methylguanine base at position 46 in this fragment, althought the affinity drops by a factor 10, a significant aminoacylation is restored. These results are discussed in terms of molecular flexibility and a model is proposed for tRNA-enzyme interaction, involving multisite recognition.

Structure and organization of the two tRNATyr gene clusters on the E. coli chromosome

The structure and organization of the gene clusters coding for the two tyrosine-accepting tRNA species (tRNA1Tyr and tRNA2Tyr) on the E. coli chromosome have been determined. The mature structural sequences of the two tRNATyr genes, located on opposite sides of the E. coli chromosome, differ by only 2 bp, but sequences surrounding these portions of the genes are very different. The genes coding for tRNA1Tyr (tyrT) comprise two mature structural sequences separated by a 200 bp "intergenic spacer." It is known that in transducing phage, the region adjoining the CCA end of the second mature structural sequence comprises a 178 bp repeated sequence which contains an in vitro, rho-dependent transcriptional termination site. We find that these potentially genetically unstable repeated sequences are present in the E. coli chromosome with the same organization as that determined from transducing phage analyses. The gene that codes for tRNA2Tyr (tyrU) is present in a single copy and is tightly clustered with three other tRNA genes. One of these genes (to be called thrU) encodes a previously undescribed tRNA (to be called tRNA4Thr). The organization of this cluster on the E. coli chromosome is tRNA4Thr--8 bp--tRNA2Tyr--115 bp--tRNA2Gly--6 bp--tRNA3Thr. The importance of correlating structural analyses derived from specialized transducing phage with those determined for the chromosome itself is demonstrated by results which show that out of four independently isolated tRNATyr transducing phage, two carrying the tRNA1Tyr genes [phi80psu3+,- (Cambridge) and phi80sus2psu3+ (Kyoto)] and two carrying the tRNA2Tyr gene (lambdarifd 18 and lambdah80dglyTsu+36), only the first phage from each group has the same gene organization as that found in the E. coli chromosome.