Mechanism of codon recognition by transfer RNA and codon-induced tRNA association

Role of Wybutosine and Mg2+ Ions in Modulating the Structure and Function of tRNAPhe: A Molecular Dynamics Study

Transfer RNA remains to be a mysterious molecule of the cell repertoire. With its modified bases and selectivity of codon recognition, it remains to be flexible inside the ribosomal machinery for smooth and hassle-free protein biosynthesis. Structural changes occurring in tRNA due to the presence or absence of wybutosine, with and without Mg²⁺ ions, have remained a point of interest for structural biologists. Very few studies have come to a conclusion correlating the changes either with the structure and flexibility or with the codon recognition. Considering the above facts, we have implemented molecular modeling methods to address these problems using multiple molecular dynamics (MD) simulations of tRNA^Phe along with codons. Our results highlight some of the earlier findings and also shed light on some novel structural and functional aspects. Changes in the stability of tRNA^Phe in native or codon-bound states result from the conformations of constituent nucleotides with respect to each other. A smaller change in their conformations leads to structural distortions in the base-pairing geometry and eventually in the ribose-phosphate backbone. MD simulation studies highlight the preference of UUC codons over UUU by tRNA^Phe in the presence of wybutosine and Mg²⁺ ions. This study also suggests that magnesium ions are required by tRNA^Phe for proper recognition of UUC/UUU codons during ribosomal interactions with tRNA.

Aminoglycoside interactions with RNAs and nucleases

One of the major challenges in medicine today is the development of new antibiotics as well as effective antiviral agents. The well-known aminoglycosides interact and interfere with the function of several noncoding RNAs, among which ribosomal RNAs (rRNAs) are the best studied. Aminoglycosides are also known to interact with proteins such as ribonucleases. Here we review our current understanding of the interaction between aminoglycosides and RNA. Moreover, we discuss briefly mechanisms behind the inactivation of aminoglycosides, a major concern due to the increasing appearance of multiresistant bacterial strains. Taken together, the general knowledge about aminoglycoside and RNA interaction is of utmost importance in the process of identifying/developing the next generation or new classes of antibiotics. In this perspective, previously unrecognized as well as known noncoding RNAs, apart from rRNA, are promising targets to explore.

Specific correlations between relative synonymous codon usage and protein secondary structure

We found significant species-specific correlations between the use of two synonymous codons and protein secondary structure units by comparing the three-dimensional structures of human and Escherichia coli proteins with their mRNA sequences. The correlations are not explained by codon-context, expression level, GC/AU content, or positional effects. The E. coli correlation is between Asn AAC and the C-terminal regions of beta-sheet segments; it may result from selection for translational accuracy, suggesting the hypothesis that downstream Asn residues are important for beta-sheet formation. The correlation in human proteins is between Asp GAU and the N termini of alpha-helices; it may be important for eukaryote-specific sequential, cotranslational folding. The kingdom-specific correlations may reflect kingdom-specific differences in translational mechanisms. The correlations may help identify residues that are important for secondary structure formation, be useful in secondary structure prediction algorithms, and have implications for recombinant gene expression.

Guanosine binds to the Tetrahymena ribozyme in more than one step, and its 2'-OH and the nonbridging pro-Sp phosphoryl oxygen at the cleavage site are required for productive docking

The dynamics of binding of various guanosine, or G, substrates to the Tetrahymena thermophila L-21 ScaI ribozyme have been investigated by fluorescence-detected stopped-flow experiments. Upon rapid mixing of various G substrates with a preformed complex of the ribozyme and the fluorescent 5' splice site analogue CCUCUepsilonA, fluorescence transients that provide rates for binding of G substrates and the rate-limiting step for transesterification are observed. The measured apparent bimolecular rate constant for binding of pG is 10(3) M-1 s-1, much slower than expected for diffusion. pG appears to bind to the preformed complex of the ribozyme and CCUCUepsilonA in at least two steps, a bimolecular step followed by at least one conformational change. This two-step binding of pG, involving a rapid pre-equilibrium, leads to the slow apparent rate constant for binding of pG. Furthermore, the 2'-OH of pG and of the 3' terminal G of the G substrate GUCG and the nonbridging pro-Sp phosphoryl oxygen atom at the site of phosphoryl transfer on CCUCUepsilonA appear to mediate formation of a properly conformed docked ternary complex of the G substrate, 5' splice site, and ribozyme which may represent an intermediate required for initiation of transesterification. It is possible that the 2'-OH of pG and this nonbridging pro-Sp phosphoryl oxygen interact, directly or indirectly, with one another.

Nuclear magnetic resonance study of the codon-anticodon interaction in Bombyx mori tRNA(GCCGly)

NMR spectra of Bombyx mori tRNA(GCCGly) were recorded in the GCC absence and presence of the oligonucleotide, GGCUp, which contains the codon sequence, GGC. The difference between the spectra with and without the codon oligonucleotide indicates the appearance of five new imino proton peaks. For the assignment of these peaks, G*GCUp, in which the 5'-terminal G was enriched with 95% 15N, was prepared (G*, 15N-labeled guanosine). In the imino proton spectrum of B. mori tRNA(GCCGly) on the addition of G*GCUp, the peak at 12 ppm became a doublet due to coupling with 15N nuclei. In the two-dimensional 1H-15N heteronuclear multiple-quantum correlation (HMQC) spectrum, only the peak at 12 ppm was observed, and thus it was assigned to the imino proton of the 5'-terminal G of GGCUp interacting with tRNA(GCCGly). Judging from the temperature effect and chemical shifts, the five new imino proton peaks are presumed to be due to three G.C base pairs, induced by the codon-anticodon interaction, and one U.U base pair, induced by an interaction between the 3' terminal U of GGCUp and U33 neighboring the anticodon. The binding of three trinucleotides (GGCp, GGUp and GCUp) to B. mori tRNA(GCCGly) was also investigated. Ultracentrifugation analysis showed that tRNA(GCCGly) underwent dimerization through the anticodon-anticodon interaction, but the dimerization was broken on addition of GGCUp. On 1H-NMR and ultracentrifugation analysis, it was found that GCUp not complementary to the anticodon also binds to the anticodon loop.

Dynamics of ribozyme binding of substrate revealed by fluorescence-detected stopped-flow methods

Fluorescence-detected stopped-flow and equilibrium methods have been used to study the mechanism for binding of pyrene (pyr)-labeled RNA oligomer substrates to the ribozyme (catalytic RNA) from Tetrahymena thermophila. The fluorescence of these substrates increases up to 25-fold on binding to the ribozyme. Stopped-flow experiments provide evidence that pyr experiences at least three different microenvironments during the binding process. A minimal mechanism is presented in which substrate initially base pairs to ribozyme and subsequently forms tertiary contacts in an RNA folding step. All four microscopic rate constants are measured for ribozyme binding of pyrCCUCU.

Permanent dipole moment of tRNA's and variation of their structure in solution

The structure of six different tRNA molecules has been analyzed in solution by electrooptical measurements and by bead model simulations. The electric dichroism measured as a function of the field strength shows that tRNA's are associated with substantial permanent dipole moments, which are in the range of 1 x 10(-27) cm(identical to 300 D; before correction for the internal directing field). Rotational diffusion time constants of tRNA molecules in their native state at 2 degrees C show a considerable variation. A particularly large value found for tRNA(Tyr) (50 ns) can be explained by its nine additional nucleotide residues. However, remarkable variations remain for tRNA molecules with the standard number of 76 nucleotide residues (tRNA(Phe) [yeast] 41.6 ns, tRNA(Val) [Escherichia coli] 44.9 ns, tRNA(Glu) [E. coli] 46.8 ns; tRNA(Phe) [E. coli] 48.3 ns). These variations indicate modulations of the tertiary structure, which may be due to a change of the L-hinge angle. Bead models are used to simulate both electric and hydrodynamic parameters of tRNA molecules according to the crystal structure of tRNA(Phe) (yeast). The asymmetric distribution of phosphate charges with respect to the center of diffusion leads, under the assumption of a constant charge reduction to 15% by ion condensation, to a theoretical dipole moment of 7.2 x 10(-28) cm, which is in reasonable agreement with the measurements. The dichroism decay curve calculated for tRNA(Phe) (yeast) is also consistent with the measurements and thus the structure in solution and in the crystal must be very similar in this case. However, our measurements also indicate that the structure of some other tRNA's in solution is different, even in cases with the same number of nucleotide residues.

Analysis of magnesium, europium and lead binding sites in methionine initiator and elongator tRNAs by specific metal-ion-induced cleavages

The specificity of cleavages in yeast and lupin initiator and elongator methionine tRNAs induced by magnesium, europium and lead has been analysed and compared with known patterns of yeast tRNA(Phe) hydrolysis. The strong D-loop cleavages occur in methionine elongator tRNAs at similar positions and with comparable efficiency to those found in tRNA(Phe), while the sites of weak anticodon loop cuts, identical in methionine elongator tRNAs, differ from those found in tRNA(Phe). Methionine initiator tRNAs differ from their elongator counterparts: (a) they are cleaved in the D-loop with much lower efficiency; (b) they are cleaved in the variable loop which is completely resistant to hydrolysis in elongator tRNAs; (c) cleavages in the anticodon loop are stronger in initiator tRNAs and they are located mostly at the 5' side of the loop whereas in elongator tRNAs they occur mostly at the opposite, 3' side of the loop. The distinct pattern of the anticodon loop cleavages is considered to be related to different conformations of the anticodon loop in the two types of methionine tRNAs.

The three conformations of the anticodon loop of yeast tRNA(Phe)

The complex conformational states of the anticodon loop of yeast tRNA(Phe) which we had previously studied with relaxation experiments by monitoring fluorescence of the naturally occurring Wye base, are analyzed using time and polarization resolved fluorescence measurements at varying counterion concentrations. Synchrotron radiation served as excitation for these experiments, which were analyzed using modulating functions and global methods. Three conformations of the anticodon loop are detected, all three occurring in a wide range of counterion concentrations with and without Mg2+, each being identified by its typical lifetime. The fluorescence changes brought about by varying the ion concentrations, previously monitored by steady state fluorimetry and relaxation methods, are changes in the population of these three conformational states, in the sense of an allosteric model, where the effectors are the three ions Mg2+, Na+ and H+. The population of the highly fluorescent M conformer (8ns), most affine to magnesium, is thus enhanced by that ligand, while the total fluorescence decreases as lower pH favors the H+-affine H conformer (0.6ns). Na+-binding of the N conformer (4ns) is responsible for complex fluorescence changes. By iterative simulation of this allosteric model the equilibrium and binding constants are determined. In turn, using these constants to simulate equilibrium fluorescence titrations reproduces the published results.

Codon choice and gene expression: synonymous codons differ in translational accuracy

Ribosomes programmed by different synonymous codons also differ in discriminating among near-cognate aminoacylated tRNAs. In the initial step of the recognition reaction ribosomes programmed by UUC discriminate less well than ribosomes programmed by UUU against ternary complexes containing three types of Leu-tRNA, and ribosomes programmed by CUC discriminate less well than ribosomes programmed by CUU against ternary complexes containing Phe-tRNA. Furthermore, in the proofreading step ribosomes programmed by UUC discriminate less well than ribosomes programmed by UUU against two of three near-cognate Leu-tRNAs, and ribosomes programmed by CUC discriminate less well than ribosomes programmed by CUU against near-cognate Phe-tRNA. The codon-induced change in reaction rate with near-cognate ternary complexes is greater than that with cognate ternary complexes: the most efficient codon is, therefore, the least accurate. Because the efficient, but inaccurate, codon UUC is used preferentially in highly expressed mRNAs of Escherichia coli, maximization of translational accuracy apparently has not been significant in the evolution of this particular biased codon choice in E. coli.

Transfer RNA structure and coding specificity. II. A D-arm tertiary interaction that restricts coding range

We investigated the structural basis of the kinetic effect on coding specificity by the D-arm mutant (G24 to A) of Escherichia coli tRNATrp. A set of tRNA genes with structural alterations in the D-arm was constructed by site-directed mutagenesis in vitro, and we determined the in vivo translational activities of these tRNAs. Our results suggest that a hydrogen-bond donor in the major groove of the D-helix at position 24 is required for the expansion of tRNA wobble coding specificity. From inspection of tRNA crystal structure, we identified a potential new tertiary pairing of base 24 with the base at position 9 (this base links the acceptor and D-stems). We constructed tRNAs with mutations at position 9 and showed that the phenotypes of position 11-24 D-arm mutants are indeed dependent on the identity of base 9. Our analysis of the effects of these mutations on the interactions of tRNA with the ribosome and with aminoacyl-tRNA synthetase suggests that the conformation or conformational dynamics of the middle of the tRNA molecule alters the kinetics of the interaction with the ribosomal coding site. The 9-23 and putative 9-24 tertiaries, and perhaps other normal tertiary interactions in this region, modulate these kinetics to increase or decrease coding specificity.

Characterization of the lead(II)-induced cleavages in tRNAs in solution and effect of the Y-base removal in yeast tRNAPhe

The specificity of lead(II)-induced hydrolysis of yeast tRNA(Phe) was studied as a function of concentration of Pb2+ ions. The major cut was localized in the D-loop and minor cleavages were detected in the anticodon and T-loops at high metal ion concentration. The effects of pH, temperature, and urea were also analyzed, revealing a basically unchanged specificity of hydrolysis. In the isolated 5'-half-molecule of yeast tRNAPhe not cut was found in the D-loop, indicating its stringent dependence on T-D-loop interaction. Comparison of hydrolysis patterns and efficiencies observed in yeast tRNA(Phe) with those found in other tRNAs suggests that the presence of a U59-C60 sequence in the T-loop is responsible for the highly efficient and specific hydrolysis in the spatially close region of the D-loop. The efficiencies of D-loop cleavage in intact yeast tRNA(Phe) and in tRNA(Phe) deprived of the Y base next to the anticodon were also compared at various Pb2+ ion concentrations. Kinetics of the D-loop hydrolysis analyzed at 0, 25, and 37 degrees C showed a 6 times higher susceptibility of tRNA(Phe) minus Y base (tRNA(Phe)-Y) to lead(II)-induced hydrolysis than in tRNA(Phe). The observed effect is discussed in terms of a long-distance conformational transition in the region of the interacting D- and T-loops triggered by the Y-base excision.

Contributions to selective binding of aromatic amino acid residues to tRNA(Phe)

The binding of aromatic amino acid amides to two fragments of tRNA(Phe) has been measured, in order to explore contributions to selective interactions of amino acid residues with tRNA(Phe). Measurements of the Wye base fluorescence demonstrate that the isolated anticodon loop of tRNA(Phe) (15 nucleotide residues) has a binding constant K = 75 M-1 for Phe-amide, which is only slightly lower than that observed previously for the complete tRNA(Phe) (K = 100 M-1). The hexamer GmAAYA psi - possessing most residues of the loop, but without loop structure - shows a further reduced binding constant of 42 M-1. According to these data, part of the selective interaction results from the special loop structure and another part probably from the nature of the Wye base. The particular influence of the loop structure is also demonstrated by binding experiments performed in the presence of Mg2+. As expected, addition of Mg2+ decreases the binding affinity of the aromatic amino acids amides. Moreover, Mg2+ at concentrations greater than or equal to 0.3 mM induces cooperative binding of the amides to the anticodon loop similar to that found previously for the complete tRNA(Phe), whereas the hexamer does not show any indication for cooperativity. A special coupling of Mg2+ and amide binding to the anticodon loop is also indicated by inhibition of Mg2+ binding in the presence of amides, which is much stronger than expected for a simple salt effect. These results demonstrate a complex coupling of Mg2+ and amide binding to different conformational states of the anticodon loop, which resembles an allosteric type of reaction mechanism.

Codon choice and gene expression: synonymous codons differ in their ability to direct aminoacylated-transfer RNA binding to ribosomes in vitro

Phe-tRNA (anticodon GAA)--polypeptide-chain elongation factor Tu-GTP ternary complexes react faster with ribosomes programmed with UUC codons than with ribosomes programmed with UUU codons. A similar preference is shown by Leu-tRNA2 (anticodon GAG) complexes, which react faster with ribosomes programmed with CUC than with those programmed with CUU. The difference is seen in the rate of ternary-complex binding to the ribosome; no differences are seen in peptide-bond formation. Highly expressed mRNAs in Escherichia coli favor codons terminating in cytosine rather than uracil when both codons are read by a single tRNA with an anticodon beginning with guanine. The results suggest that intrinsic differences between the efficiencies of synonymous codons play an important role in modulating gene expression in E. coli.

19F nuclear magnetic resonance as a probe of anticodon structure in 5-fluorouracil-substituted Escherichia coli transfer RNA

The use of 19F nuclear magnetic resonance (n.m.r.) spectroscopy as a probe of anticodon structure has been extended by investigating the effects of tetranucleotide binding to 5-fluorouracil-substituted Escherichia coli tRNA(Val)1 (anticodon FAC). 19F n.m.r. spectra were obtained in the absence and presence of different concentrations of oligonucleotides having the sequence GpUpApX (X = A,G,C,U), which contain the valine codon GpUpA. Structural changes in the tRNA were monitored via the 5-fluorouracil residues located at positions 33 and 34 in the anticodon loop, as well as in all other loops and stems of the molecule. Binding of GpUpApA, which is complementary to the anticodon and the 5'-adjacent FUra 33, shifts two resonances in the 19F spectrum. One, peak H (3.90 p.p.m.), is also shifted by GpUpA and was previously assigned to FUra 34 at the wobble position of the anticodon. The effects of GpUpApA differ from those of GpUpA in that the tetranucleotide induces the downfield shift of a second resonance, peak F (4.5 p.p.m.), in the 19F spectrum of 19F-labeled tRNA(Val)1. Evidence that the codon-containing oligonucleotides bind to the anticodon was obtained from shifts in the methyl proton spectrum of the 6-methyladenosine residue adjacent to the anticodon and from cleavage of the tRNA at the anticodon by RNase H after binding dGpTpApA, a deoxy analog of the ribonucleotide codon. The association constant for the binding of GpUpApA to fluorinated tRNA(Val)1, obtained by Scatchard analysis of the n.m.r. results, is in good agreement with values obtained by other methods. On the basis of these results, we assign peak F in the 19F n.m.r. spectrum of 19F-labeled tRNA(Val)1 to FUra 33. This assignment and the previous assignment of peak H to FUra 34 are supported by the observation that the intensities of peaks F and H in the 19F spectrum of fluorinated tRNA(Val)1 are specifically decreased after partial hydrolysis with nucleass S1 under conditions leading to cleavage in the anticodon loop. The downfield shift of peak F occurs only with adenosine in the 3'-position of the tetranucleotide; binding of GpUpApG, GpUpApC, or GpUpApU results only in the upfield shift of peak H. The possibility is discussed that this base-specific interaction between the 3'-terminal adenosine and the 5-fluorouracil residue at position 33 involves a 5'-stacked conformation of the anticodon loop. Evidence also is presented for a temperature-dependent conformational change in the anticodon loop below the melting temperature of the tRNA.

A stereochemical model of the transpeptidation complex

Molecular models are proposed to describe the relative arrangement of aminoacyl and peptidyl tRNAs when bound to their respective A and P sites on the ribosome. The crystallographically determined structures of tRNAasp and tRNAphe have served as the models for these bound structures, while the imposed steric constraints for the model complexes were based on the results of published experimental data. The constructed models satisfy the stereochemical requirements needed for codon-anticodon interaction and for peptide bond formation. In this paper, the results of the complex containing tRNAphe as the A and P site bound transfer RNAs, is compared to a similarly constructed model which uses tRNAasp as the ribosome-bound transfer RNAs. The models have the following three major features: 1) the aminoacyl and peptidyl transfer RNAs assume an angle of approximately 45 degrees relative to each other; 2) in providing the proper stereochemistry for peptide bond condensation, a significant kink must be present in the messenger RNA between the A site and P site codons; and 3) a comparison of the two model complexes indicates that structural variations between the tRNAs or any allosteric transitions of the transfer RNAs associated with codon-anticodon recognition may be accommodated in the model by way of freedom of rotation about the phosphate backbone bonds in the mRNA between consecutive codons.

Codon-induced association of the isolated anticodon loop of tRNAPhe

The binding of the codon UUC to the isolated anticodon loop of tRNAPhe (yeast) has been studied as a model of codon recognition by a simple adaptor. Fluorescence titrations demonstrate that UUC binds to the isolated anticodon loop with an equilibrium constant of 1.4 X 10(3) M-1 (at 7.2 degrees C). Equilibrium sedimentation curves reveal that UUC binding induces association of anticodon loops beyond the dimer stage. A set of complete sedimentation curves obtained for various reactant concentrations was analyzed according to a model with an infinite number of subsequent association steps for UUC-anticodon loop complexes and with equal affinity for each step. The coupling of association and sedimentation was considered quantitatively, and the information resulting from conservation of mass was used by integration. According to this procedure, the experimental data can be described by an isodesmic association constant of 8 X 10(3) M-1 with satisfactory accuracy. Temperature-jump relaxation detected by fluorescence measurements provides independent evidence for codon-induced association of the anticodon loop. The data are consistent with the following mechanism: UUC preferentially binds to one of two loop conformations with a rate constant of 4.5 X 10(6) M-1 s-1; the UUC-anticodon loop complex undergoes association with a rate constant of 6.5 X 10(6) M-1 s-1. The reactions observed for the isolated anticodon loop are surprisingly similar to those observed previously for the complete tRNA, suggesting that simple hairpin loops are appropriate adaptors for a translation process at an early stage of evolution; the codon-induced association of the hairpin loop should be very useful to facilitate the transfer of cognate amino acids during translation.

GTPase center of elongation factor Tu is activated by occupation of the second tRNA binding site

Interaction of the elongation factor EF-Tu with the antibiotic kirromycin results in activation of the GTPase center of the factor and in induction of an additional tRNA binding site (tRNA binding site II to distinguish it from the classical tRNA binding site I). Activation of the GTPase center under these conditions is stimulated by addition of tRNA. Two-fold evidence is presented that this stimulation is due to tRNA binding to site II rather than to site I. First, a strong correlation is observed between stimulation of the GTPase activity and enhancement of the reactivity of Cys-81 of EF-Tu toward N-ethylmaleimide at various concentrations of aminoacyl-tRNA, deacylated tRNA, and N-acetylaminoacyl-tRNA. The latter effects signal tRNA binding to site II. Stimulation of the kirromycin-induced GTPase activity by tRNA binding to the factor also occurs when binding to site I is completely abolished. Such an abolishment was achieved by treating EF-Tu extensively with the thiol reagent L-1-tosylamido-2-phenylethyl chloromethyl ketone. EF-Tu X GTP thus treated has lost its ability to protect the ester bond of aminoacyl-tRNA. The relevance of these data for the sequence of events during protein synthesis and for control of translational fidelity is discussed.

Fluorine-19 nuclear magnetic resonance study of codon-anticodon interaction in 5-fluorouracil-substituted E. coli transfer RNAs

Codon-anticodon interaction was investigated in fully active 5-fluorouracil-substituted E. coli tRNAVal1 (anticodon FAC) by 19F NMR spectroscopy. Binding of the codon GpUpA results in the upfield shift of a 19F resonance at 3.9 ppm in the central region of the 19F NMR spectrum, whereas trinucleotides not complementary to the anticodon have no effect. The same 19F resonance shifts upfield upon formation of an anticodon-anticodon dimer between the 19F-labeled tRNA and E. coli tRNATyr2 (anticodon QUA). These results permit assignment of the peak at 3.9 ppm to the 5-fluorouracil at position 34 in the anticodon of fluorouracil-substituted tRNAVal1. The methionine codon ApUpG also causes a sequence-specific upfield shift of a peak in the central part of the 19F NMR spectrum of fluorinated E. coli tRNAMetm. However, ApUpG has no effect on the 19F spectrum of 19F-labeled E. coli tRNAMetf, indicating possible conformational differences between the anticodon loop of initiator and chain-elongating methionine tRNAs. 19F NMR experiments detect no binding of CpGpApA to the complementary FpFpCpG (replaces Tp psi pCpG) in the T-loop of 5-fluorouracil-substituted tRNAVal1, in the presence or absence of codon, suggesting that the tertiary interactions between the T- and D-loops are not disrupted by codon-anticodon interactions.

Temperature jump relaxation studies on the interactions between transfer RNAs with complementary anticodons. The effect of modified bases adjacent to the anticodon triplet

We have used the temperature-jump relaxation technique to determine the kinetic and thermodynamic parameters for the association between the following tRNAs pairs having complementary anticodons: tRNA(Ser) with tRNA(Gly), tRNA(Cys) with tRNA(Ala) and tRNA(Trp) with tRNA(Pro). The anticodon sequence of E. coli tRNA(Ser), GGA, is complementary to the U*CC anticodon of E. coli tRNA(Gly(2] (where U* is a still unknown modified uridine base) and A37 is not modified in none of these two tRNAs. E. coli tRNA(Ala) has a VGC anticodon (V is 5-oxyacetic acid uridine) while tRNA(Cys) has the complementary GCA anticodon with a modified adenine on the 3' side, namely 2-methylthio N6-isopentenyl adenine (mS2i6A37) in E. Coli tRNA(Cys) and N6-isopentenyl adenine (i6A37) in yeast tRNA(Cys). The brewer yeast tRNA(Trp) (anticodon CmCA) differs from the wild type E. coli tRNA(Trp) (anticodon CCA) in several positions of the nucleotide sequence. Nevertheless, in the anticodon loop, only two interesting differences are present: A37 is not modified while C34 at the first anticodon position is modified into a ribose 2'-O methyl derivative (Cm). The corresponding complementary tRNA is E.coli tRNA(Pro) with the VGG anticodon. Our results indicate a dominant effect of the nature and sequence of the anticodon bases and their nearest neighbor in the anticodon loop (particularly at position 37 on the 3' side); no detectable influence of modifications in the other tRNA stems has been detected. We found a strong stabilizing effect of the methylthio group on i6A37 as compared to isopentenyl modification of the same residue. We have not been able so far to assess the effect of isopentenyl modification alone in comparison to unmodified A37. The results obtained with the complex yeast tRNA(Trp)-E.coli tRNA(Pro) also suggest that a modification of C34 to Cm34 does not significantly increase the stability of tRNA(Trp) association with its complementary anticodon in tRNA(Pro). The observations are discussed in the light of inter- and intra-strand stacking interactions among the anticodon triplets and with the purine base adjacent to them, and of possible biological implications.

Mechanism of codon recognition by transfer RNA studied with oligonucleotides larger than triplets

The binding of yeast tRNAPhe to UUCA, UUCC, UUCCC, UUCUUCU, U4, U5, U6 and U7 was analysed by fluorescence temperature jump and equilibrium sedimentation measurements. In all cases the two observed relaxation processes can be assigned to alpha) an intramolecular conformation change of the anticodon loop and beta) preferential binding of the oligonucleotides to one of the anticodon conformations. The anticodon loop transition is associated with inner sphere complexation of Mg2+ and proceeds with rate constants of about 10(3) s-1. The rate constants of oligonucleotide binding are between 4 and 10 X 10(6) M-1s-1 and reflect an increase of the association rate with the number of binding sites compensated to some degree by electrostatic repulsion in the preequilibrium complex. Neither temperature jump nor equilibrium sedimentation experiments provided evidence for UUCA or UUCC induced tRNA dimerisation, although UUC binding leads to strong tRNA dimerisation under equivalent conditions. The results obtained for the longer oligonucleotides are similar. In the case of UUCUUCU with its two potential binding sites for tRNAPhe there was no evidence for the formation of 'ternary' complexes. Apparently tRNAPhe binds preferentially to the second UUC of this 'messenger' and forms additional contacts with residues on either side of the codon. Some evidence for the formation of ternary complexes is obtained for U6 and U7, although the extent of this reaction remains very small. Our results demonstrate that the mode of tRNA binding to a codon is strongly influenced by residues next to the codon. The formation of cooperative contacts between tRNA molecules at adjacent codons apparently requires support by a catalyst adjusting an appropriate conformation of messenger and tRNA molecules.