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Transfer RNA Structure and Identity

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The structure of tRNA and its relationship with the biological necessity of specific tRNA aminoacylation reactions, in other words with identity, is reviewed. New structural data show the typical L-shaped tRNA architecture in great detail and highlight how adequate rigidity and plasticity of the molecule is essential for interaction with its biological partners, in particular with aminoacyl-tRNA synthetases. Identity is ensured by a small number of nucleosides predominantly located at the two distal extremities of the tRNA molecule. In several crystallographic complexes, these residues have been shown in contact with amino acids from the synthetases. In most cases, the interaction is accompanied by a conformational change of the tRNA. Assuming that the structural framework of tRNA displays identity elements to synthetases implies that altered and/or simplified RNA architectures can fulfill this role provided they contain correctly located identity elements. This paradigm holds true in nature where atypical and tRNA-like domains have been selected by evolution. Rationale-based engineering or selection by artificial evolution of novel RNA molecules recognized and aminoacylated by synthetases also verified it.

Introduction

Transfer RNAs (tRNAs) are ubiquitous molecules present in all forms of life. Unprecedented in biology, their necessity as the adapters translating the genetic code was predicted,1 before their biochemical characterization.2 Beside protein synthesis, specialized tRNAs and tRNA-like structures can participate in diverse metabolic pathways (reviewed in ref. 3). The universal occurrence of tRNA, its amino acid donor key role in protein synthesis, and its involvement in other cellular processes underline its ancient origin. Contemporary tRNAs participating in protein synthesis are structurally homogeneous but are versatile in function since during their functional cycle they interact with many enzymes (maturation and modification enzymes including RNase P, aminoacyl-tRNA synthetases), protein factors (for initiation, elongation, and termination) as well as with mRNA and the ribosome. Specialized tRNA functions such as initiation of protein synthesis,4,5 incorporation of selenocysteine into proteins,6 are in general correlated with atypical structural features. In what follows, emphasis is given to the tRNAs directly involved in protein synthesis and to the problem of tRNA identity that underlies their capacity to be specifically aminoacylated by synthetases and consequently to be responsible for the correct translation of the genetic message from the DNA into the protein language.

Structure of tRNAs

Sequences and Modified Nucleosides

Since 1965, when yeast tRNAAla was sequenced,7 sequences of more than 4000 tRNAs from more than 300 organisms have been included in the tRNA database (http://www.uni-bayreuth.de/departments/biochemie/trna/),8 and these numbers increase steadily due to the many genome projects. A vast majority of tRNA sequences adopt the cloverleaf folding which highlights the structural and functional domains of the molecule (Fig. 1A).

Figure 1A. Structure of cytoplasmic tRNA participating in protein synthesis.

Figure 1A

Structure of cytoplasmic tRNA participating in protein synthesis. (top) Cloverleaf folding emphasizing the different domains of the tRNA molecule as well as the position of conserved and semiconserved residues. Length of tRNA sequences ranges from 72 (more...)

Most information came from gene sequencing (3700 DNA versus 550 RNA sequences). The more difficult RNA sequencing revealed the presence of many modified nucleotides. To date, 81 such residues are in the tRNA modification database (http://medlib.med.utah.edu/RNAmods/).9 Some are common to almost all tRNA species, such as dihydrouridine (D) in D-loops and ribothymidine (T) in T-loops (for abbreviations of modified nucleosides, see ref. 8). Others are characteristic of individual tRNA species, of groups of organisms or of a given living kingdom (archaea, prokarya including the derived organelles or eukarya). For instance, wybutosine, a hypermodified G-residue formerly called the Y-base, and its derivatives, are exclusively found at position 37 of tRNAPhe and queuosine derivatives, other G-analogs, are found at the first anticodon position of certain tRNAAsn, tRNAAsp, and tRNATyr species. The triad Gm18, s2T54 and m1A58 in the D- and T-loop characterizes tRNAs from thermophilic organisms, as found in tRNAAsp from Thermus thermophilus,10 and likely contributes to their stability by increasing their melting temperature. 11 The methylated residue m1 at position 9 is typically mitochondrial. As demonstrated in the case of mitochondrial human tRNALys, it prevents misfolding of the molecule into an elongated hairpin by preventing formation of an alternative pairing with U64 from the T-stem,12 and therefore can be considered as an internal chaperone for correct folding. Likewise, archeosine, the G-like 7-deazaguanosine analog with ring substituted at position 7 by a formamidino group is exclusively archaeal and is found at position 15 in D-loops where it forms an atypical R15-Y48 Levitt tertiary pair.13

Sequence data soon revealed the presence of conserved (U8, A14, A21, U33, G53, T54, ψ55, C56, A58, C61, C74, C75 and A76) and semiconserved (Y11, R15, R24, Y32, R37, Y48, R57, and Y60) residues in tRNA. The steadily incoming sequences confirm their occurrence in almost all tRNAs, the main exceptions being organellar tRNAs (see e.g., website for mammalian mitochondrial tRNAs,14 [http://mamit-tRNA.u-strasbg.fr]) that often lack canonical D- and T-loop organizations. As demonstrated by crystallography, many of the conserved and semiconserved residues participate in the tertiary interactions that govern the three-dimensional structure of tRNA. In contrast, those in the anticodon loop play a role in mRNA decoding15 and sometimes in tRNA identity,16 the conserved 3'-terminal CCA triplet being crucial for tRNA recognition in the active site of synthetases. Helical regions of tRNAs are rich in G-U wobble base-pairs and to a lesser extent in other non-Watson-Crick pairs. The G-U pairs have unique structural characteristics that can be crucial to tRNA function.17,18

Organellar tRNAs, like human mitochondrial tRNASer or mitochondrial tRNAs from nematode worms, with part(s) of the canonical structure lacking, constitute remarkable exceptions to the conserved cloverleaf folding of cytoplasmic tRNAs.19,20 However, sequence compensations allow these molecules to adopt L-shaped conformations.21 Noticeable, the sequence features in canonical tRNAs deviating from consensus, like the −1 residue at the 5'-terminus of histidine-specific tRNAs, 22 or the uncommon G15-G48 Levitt pair (instead of R15-Y48) in Escherichia coli tRNACys were shown to be identity elements in these tRNAs.23,24

Three-Dimensional Structures of Free tRNAs

As first proposed for yeast tRNAPhe, the tRNA molecule has an L-shaped architecture that was established independently in three laboratories.25-28 It is based on the cloverleaf folding and shows a symmetrical organization with two helical branches of similar size oriented perpendicularly (Fig. 1B). One branch is formed by the amino acid acceptor stem stacked over the T-arm and the dumbbell-like other branch by a stack of the anticodon- and D-arms. The same overall structural organization is found in yeast tRNAAsp,29,30 in Escherichia coli initiator tRNAfMet,31 as well as in yeast initiator tRNAMet,32 and in the recently solved structure of human tRNALys3, the primer of HIV reverse-transcriptase.33 An NMR investigation of the anticodon stem-loop of this human tRNALys3 confirms the canonical U-turn structure of the anticodon loop,34 as found in the crystal structure of the whole tRNA. This conclusion arising from solution data excludes that packing effects in crystal lattices trigger U-turn conformations. Interestingly, the NMR study shows further that the modified nucleosides (mnm5s2U34, t6A37, and ψ39) stabilize this structure.

Figure 1B. Example of two crystallographic conformers of tRNA emphasizing its structural plasticity: at the left, free tRNAAsp mimicking a tRNA interacting with mRNA and at the right, the same tRNA complexed with cognate AspRS.

Figure 1B

Example of two crystallographic conformers of tRNA emphasizing its structural plasticity: at the left, free tRNAAsp mimicking a tRNA interacting with mRNA and at the right, the same tRNA complexed with cognate AspRS.

The above cited X-ray structures are of medium resolution (2.5Å at best) (Table 1) and except for tRNALys3, were refined with nonoptimized methods. For long, these structures constituted the only structural RNA database. They revealed the conserved tRNA conformation and gave an architectural significance to the conserved and semiconserved residues of tRNA that interconnect the D- and T-loops. They showed also novel structural features in RNA, like noncanonical pairings and metal binding sites, and suggested existence of faint conformational differences between tRNAs due to differences in semiconserved residues and in localization of the G18G19 dinucleotide in the D-loop and length variations in this loop and the variable region.35 Existence of such differences was clearly shown by structural mapping of tRNA by chemical probes.36

Table 1. Summary of tRNA structures in their free state or in complexes with proteins.

Table 1

Summary of tRNA structures in their free state or in complexes with proteins.

The structure of yeast tRNAAsp is of particular type (Fig. 1B). It deviates from that of tRNAPhe by a significant opening of the angle between the two branches of the molecule and by changes in the D-/T-loop interaction with a disruption of the G19-C56 tertiary base-pair. These features result from crystal packing effects, but have biological meaning. Indeed, tRNAAsp molecules interact via GUC/GUC anticodon/anticodon pairing in the crystal and this pairing mimics a tRNA/mRNA interaction. Thus, the crystal structure of tRNAAsp would mimic the structure of a tRNA interacting with mRNA.37 This interpretation was confirmed by solution data with tRNAs forming dimers, with in particular the demonstration of the opening of the G19-C56 pair by chemical probing.37,38

Recently, the structure of yeast tRNAPhe was revisited. New diffraction data were collected from monoclinic and orthorhombic crystals at synchrotron sources, and structural models were refined with advanced techniques. As a result, high-resolution electron density maps at ˜2Å resolution were obtained,39,40 even from 15-year-old crystals that yielded at best 2.5Å data in the past.40 The new versions of the tRNAPhe structure overall confirm the previous structural information but reveal novel details. The triple and other tertiary base-pairs are now seen with high accuracy together with their hydration patterns and associated Mg2+ ions well defined (Fig. 2). Other striking improvements concern identification of new divalent cation binding sites and of many ordered water molecules.39 Interestingly, in the case of the monoclinic crystals, four different cleavage sites, the major one in the D-loop, have been localized next to bound Mg2+ ions. The presence of such in situ Mg2+-induced cleavages was suggested in the orthorhombic tRNAPhe crystals,41 and clearly demonstrated in tRNAAsp crystals.37 It is likely that this intrinsic chemical fragility explains many crystallization failures with free tRNA.

Figure 2. Details in the high-resolution structure of yeast tRNAPhe as seen in the monoclinic crystal form.

Figure 2

Details in the high-resolution structure of yeast tRNAPhe as seen in the monoclinic crystal form. Typical examples of tertiary interactions are shown: the U8-A14-A21, A9-[A23-U12], and [C13-G22]-m7G46 triples and the G15-C48 Levitt pair. Notice the well-defined (more...)

Polyamines are obligatory additives for the crystallization of free tRNAs.42 Their role becomes clearly apparent in the high-resolution structure of tRNAPhe which shows a spermine molecule in the major groove of the T-arm that connects a symmetry-related tRNA molecule in the crystal lattice.40

Antibiotics from the aminoglycoside family are tRNA ligands, besides interacting with various other targets such as the ribosome (see Chapter 26 by D. Fourmy et al). The recently solved X-ray structure at 2.6Å resolution of a complex between yeast tRNAPhe and neomycin B shows that the elongated antibiotic molecule is anchored in the tRNA core between residues G20, A44, and G45.43 This binding site overlaps with known divalent metal ion binding sites and corresponds also to the location of major determinants for E. coli PheRS recognition. This suggests that binding of the antibiotic occurs by metal displacement and explains why neomycin and other structurally related aminoglycosides inhibit Pb2+ cleavage of tRNAPhe by hindering binding of the metal cation. It explains also that neomycin B inhibits aminoacylation of E. coli tRNAPhe.43

The modular structure of tRNA in two domains connected by a network of tertiary interactions explains that the molecule can be dissected in individual parts with intrinsic structure and functional properties.44 For instance, NMR45 and crystallographic46 investigations on a duplex RNA recapitulating the acceptor stem of E. coli tRNAAla informed about the structural environment of the G3-U70 base-pair that determines alanine identity. Other biochemical and biophysical studies confirmed the existence of anticodon- and T-loop structures and highlighted the importance of modified residues for their local conformation (see e.g., refs. 34,4750).

The Structure of tRNA in Macromolecular Complexes

As examples, Figure 3A shows how E. coli tRNAGln and yeast tRNAAsp bind to class I and class II synthetases.51,52 In both tRNAs, binding to the synthetase triggers significant conformational changes in the anticodon loop. Bases become unstacked and point towards the recognition amino acids from the synthetases, and in the aspartate system the overall structure of complexed tRNAAsp becomes more closed than in the free molecule (Fig. 1B). In tRNAGln, the terminal base-pair is disrupted to facilitate bending of the 3'-terminal CCA into the active site of GlnRS. Such bending is not needed in tRNAAsp where the CCA-strand is in helical continuity with the acceptor stem to reach the catalytic site of AspRS. These structural differences in the acceptor stem of the two tRNAs rely to different binding modes in the catalytic site of class I and class II synthetases: in the minor groove in tRNAGln (class I) and the major groove in tRNAAsp (class II). This differential binding has been verified by chemical probing of an unmodified tRNAAsp transcript chargeable by both class I ArgRS and class II AspRS (Fig. 3B).53

Figure 3. Comparison of tRNA binding to class I and class II synthetases.

Figure 3

Comparison of tRNA binding to class I and class II synthetases. (A) Structure of tRNAAsp (left) and tRNAGln (right) with residues in contact with AspRS and GlnRS shown in blue and yellow, respectively. (B) Mirror image recognition of a tRNAAsp unmodified (more...)

In nature, tRNAs are modified and the obvious question is to know whether modifications affect binding to synthetases. A complex between unmodified tRNAGln and GlnRS shows no structural differences with a complex comprising modified tRNA, except the absence of bound water molecules crosslinking the N5 atom of ψ-residues to their 5'-phosphate. This finding suggests a possible role of pseudouridylation in tRNA stabilization through water-mediated binding of ψ-residues to the tRNA backbone.54 Interestingly, one of the three ψs in tRNAGln is located in the anticodon loop at identity position 38,55 and contacts GlnRS.56 These data on tRNAGln are in line with the general assumption that modified tRNAs have more rigid structures than unmodified transcripts.48,57

From a different viewpoint, two crystal structures of active tRNAGln mutants in complexes with GlnRS and an adenylate analog were solved.58 These mutants with G15-G48 atypical Levitt pairs, and for one of them with an additional change in sequence and length of the variable region, show structural perturbations confined to the core of the molecule near to the Levitt pair and the variable region. They consist among others in a syn conformation of the guanine ring of G48 with respect to the ribose moiety. This conformation differs from what observed in the native structure, where C48 is present as an anti conformer. Surprisingly, this anti conformation was also found in the crystal structure of a tRNA with a native G15-G48 Levitt pair, namely that of E. coli tRNACys complexed to EF-Tu.59

Further information on tRNA structure came from crystallographic work on four class I,6063 and nine class II,6471 tRNA/aaRS complexes, as well as from studies on complexes between tRNAs and other protein partners,59,72,73 and recently even from X-ray studies of the complete ribosome,74,75 (Table 1). As anticipated, the L-shaped structure of tRNA is confirmed, as well as the existence of conformational flexibility in the molecule (see below). Of particular interest are the structures of tRNASer and tRNACys, the two tRNAs with uncommon sequence characteristics. For tRNASer, the structure of the complex with SerRS identified novel tertiary interactions in the core of the molecule. Notably, it showed the role of conserved residue G20b in the D-loop that determines the orientation of the long variable arm at ˜45° to the plane of the L-shaped tRNA molecule.64 The case of E. coli tRNACys is noteworthy, since, to solve its structure, it was crystallized on purpose as a complex with elongation factor. Overall, the structure is canonical, but with a large interstem angle of ˜100° and a geometry of its noncanonical G15-G48 Levitt pair that exposes the N2-N3 side of G15 and the O6-N7 side of G48 to the solvent.59

RNA Plasticity versus RNA Rigidity for tRNA Function

Indirect evidence has soon suggested the necessity of structural plasticity of tRNA during its life cycle. Reversible inactive forms of tRNA were described (see e.g., ref. 76) and, in the case of E. coli tRNAGlu, it was shown recently that inactivation results from Mg2+-dependent alternate folding of the tRNA.77 Other changes were correlated with synthetase interaction.78 Crystallography brought direct evidence for tRNA plasticity and comparison of data in Table 1 highlights major conformational differences between the canonical structure of yeast tRNAPhe and that of other tRNAs in their free or complexed forms. In many systems, but not in all, anticodon loops undergo drastic conformational changes upon interaction with synthetases. Other functional constraints determine overall structural effects on tRNA, as the opening of its interstem angle (Fig. 1B) that likely occurs on the ribosome. This global tRNA flexibility in solution can be quantitatively approached by transient electric birefringence experiments. The method examines the bending motions of the L-shaped tRNA architecture and, with tRNAPhe, shows that the core of the molecule gains flexibility in the absence of Mg2+ ions.79

More subtle and local changes were seen by NMR spectroscopy. Studying microhelices recapitulating the acceptor stem of two E. coli tRNAs, it was shown that the nature of the discriminator base N73 influences in tRNAAla the structure of this stem,80 and determines in initiator tRNAMet the conformation of the 3'-terminal-N73CCA sequence which is stacked over the stem in the A73 wild-type molecule and folded back in the U73 variant.81 A structural deformability of the acceptor stem has been invoked in the mechanism of alanine identity expression,82 and a flexibility of the single-stranded acceptor end was shown to be a necessity for the editing function of class I IleRS,62 and ValRS.61

At opposite, conformational rigidity in tRNA domains can have a functional role. This is the case of base modifications in the anticodon loop of certain tRNA species. For instance, in a minor tRNALeu from E. coli, the conformational rigidity of Cm and cmnm5Um in the first position of the anticodon guarantees correct codon reading.83 From another viewpoint, conformational changes observed in the glutamine and aspartate class I and class II tRNA/synthetase complexes and thought to be class specific appear to be more system (or subclass) specific. So, in contrast with the opening of the first base-pair 1–72 in tRNAGln interacting with class I GlnRS, this pair does not disrupt in tRNAVal interacting with class I ValRS.84 Likewise, the anticodon loop in tRNAPheinteracting with class II PheRS keeps its native conformation,71 and does not deform as in other tRNAs interacting with class II synthetases.

Aminoacylation and Identity of tRNAs

The Aminoacylation Reaction and the Concept of Identity

Aminoacylation of tRNA occurs in two step reactions: first activation of the amino acids by ATP to form enzyme-bound aminoacyl-adenylates and second transfer of the activated amino acids to the 3'-terminal adenosine of tRNA. Amino acid attachment to tRNA occurs by ester bond formation with hydroxyl groups of the terminal ribose, either 2'-OH for the reactions catalyzed by class I synthetases or 3'-OH in the case of class II enzymes (reviewed in ref.85). The activation step is tRNA independent, except for ArgRS, GlnRS, and GluRS. Overall, aminoacylation reactions have to yield tRNAs correctly charged, otherwise wrong amino acids will be falsely incorporated into proteins.86 This implies correct recognition of both amino acids and tRNAs by the synthetases. However, synthetases can misactivate amino acids, are able to recognize noncognate tRNAs and can catalyze mischarging reactions (reviewed in ref.35). A first answer to the dilemma was brought when it was realized that fidelity in tRNA aminoacylation, and consequently in protein synthesis, mainly relies to highest kinetic efficiency of the synthetases for their cognate substrates and is mostly governed by the kcat of the tRNA charging reactions.87 This answer was refined when proofreading (or editing) mechanisms were discovered (reviewed in ref. 85). Altogether, the phenomenological view of tRNA aminoacylation fidelity implies a strict correspondence between the charged amino acid and the codon read by the carrier tRNA according to the rules of the genetic code. This correspondence is mediated by identity determinants within tRNAs and is defined by the tRNA identity rules, which constitute a ‘second’ genetic code.

Major elements defining identity of all E. coli tRNAs have been deciphered and much is known about identity determinants of most yeast tRNAs and of a few tRNAs from other organisms.16,8891 In short, identity of a tRNA is determined by a small number of nucleosides, and more precisely by chemical groups carried by these nucleosides that often have been seen interacting with amino acids on the synthetases. In each tRNA, these nucleosides constitute the so-called ‘identity set’ that can be completed by structural elements of the nucleic acid. Negative elements that prevent a tRNA to be mischarged by noncognate synthetases can participate in identity. Some of the positive identity determinants can be considered as ‘strong’ since their mutation strongly reduces the aminoacylation capacity of the mutant tRNA, others are ‘moderate’ or ‘weak’. As examples, Table 2 displays the strongest conserved identity determinants that have been characterized to date in prokaryotic tRNAs. At first glance, several features emerge: (i) Identity elements are mainly located at the two distal extremities of the tRNA. (ii) Except for glutamate and threonine identities, the discriminator base is a determinant, at least in E. coli tRNAs. (iii) Specific structural elements in tRNA often serve as identity determinants (i.e., the −1 residue in tRNAHis, the long extra-arm in tRNASer, the G3-U70 wobble pair in tRNAAla). (iv) For tRNAs specific for amino acids coded by more than four codons (leucine, serine, arginine), anticodon residues either do not participate in identity (leucine, serine) or, only for the middle C35 and semiconserved U/G36 positions (arginine).

Table 2. Major identity determinants found in E. coli tRNAs and correlations with class-ranking of synthetases.

Table 2

Major identity determinants found in E. coli tRNAs and correlations with class-ranking of synthetases.

In most systems, modified nucleosides do not participate in identity and thus are not recognized by the cognate synthetases. But they can play a major role in negative discrimination by preventing tRNAs to be recognized by noncognate synthetases, as was shown in the isoleucine and aspartate systems.92,93 At present, the universal nature of the identity rules is rather well established and only faint differences distinguish identity sets for a given amino acid specificity along evolution. However, much has to be learned about the structural and evolutionary relationships between identity sets, the precise molecular mechanisms by which they are expressed in different organisms, and the exact nature of identities of atypical tRNAs, in particular those of mitochondrial origin.

Establishment of tRNA Identities

Characterizing identity determinants constituted a challenge and was tackled by different methods. Determinants were searched both in vitro and in vivo by studying the aminoacylation capacity of tRNA variants or their effects on protein synthesis. Two breakthroughs were responsible for the wealth of results that accumulated in the last decade. First, use of mutant suppressor tRNAs in a genetic system based on expression of the reporter protein dihydrofolate reductase, with stop codon at position 10, and identification of the amino acid incorporated at the suppressed codon. This system was first employed in Abelson's laboratory to characterize leucine identity determinants in E. coli tRNALeu,94 and soon later in McClain's and Schimmel's laboratories to identify the G3-U70 base-pair as the major alanine determinant in E. coli tRNAAla.95,96 Second, the possibility to easily prepare tRNA variants by in vitro transcription of artificial genes by T7 RNA polymerase. This possibility was pioneered in Uhlenbeck's laboratory for deciphering the identity set of yeast tRNAPhe,97 and was largely employed for understanding the yeast aspartate identity,98,99 and many other identities (reviewed in ref.16). In its original and simplest version, the in vitro approach considered as potential determinants those nucleotides where mutation lead to a drastic loss of aminoacylation capacity. The assumption underlying this statement implies that mutating an identity determinant does not affect the three-dimensional structure of the tRNA, which is not always true. Completeness of an identity set is verified if transplantation of the putative determinants in another tRNA confers the new identity to this molecule. Aminoacylation efficiency of the transplanted tRNA, however, is often not optimal, indicating that sequence context and/or architectural features play a role in identity expression. The fact that engineering the structural framework of the receiving tRNA can improve activity supports this conclusion.16

Each of the two approaches has advantages and drawbacks. The in vivo method does not check anticodon residues and yields only rough estimates of the effects of mutations on tRNA aminoacylation efficiency. However, and this is most useful, conclusions arising from in vivo experiments take into account the cellular environment and the competition between tRNAs and synthetases of diverse specificities. On the other hand, the in vitro method does not probe modified nucleosides, but yields quantitative kinetic parameters and approaches mechanistic aspects of the aminoacylation reactions. Finally, one has to keep in mind that identity sets were seldom determined by both in vitro and in vivo approaches, that for a given identity mutational analyses were done on only one isoaccepting tRNA species, and that identity swap experiments concerned only one or a few foreign tRNAs and in most cases were conducted in a qualitative manner. Novel results along these lines are awaited and will refine the view on identity.

Selected Examples of Identities

Four representative identities (alanine, phenylalanine, aspartate, and glutamine) are discussed below. The aim is to present hard facts, to raise points of debate, and to highlight more subtle aspects underlying identity expression in general. Among others, a refined view of tRNA identity has to distinguish between direct and indirect effects triggered by identity determinants and to take into account the functional role of architectural features in tRNA.

Alanine Identity

It is at present well accepted that the G3-U70 wobble base-pair is the major alanine identity determinant.95,96 This pair is conserved in evolution,96,100 and its transplantation in other tRNA frameworks, and even in minihelices recapitulating amino acid accepting arms,44,101 confers to these molecules the capacity to be aminoacylated by AlaRSs, both in vitro and in vivo. The debate concerns the mechanisms by which this unique feature triggers specific charging. Does the recognition mechanism involve direct interaction of the synthetase with chemical groups on the G3-U70 identity pair or does it imply recognition of a shape created by this pair? In the absence of a crystallographic structure of a tRNAAla/AlaRS complex, only indirect evidence can be invoked. In support of the first possibility are the so-called ‘atomic mutagenesis’ experiments, which were used to decipher the functional role of chemical groups in the G3-U70 pair. To this end, minimalist substrates were chemically synthesized including variants with G3 or U70 replaced by base analogs. Experiments led to the conclusion that the exocyclic 2-NH2 group of G3 is essential for alanylation.102 Other studies, with tRNAs having their ribose substituted by deoxynucleotides, indicated dramatic activity decreases for the mutants substituted at identity position 70 and at neighboring position 71,103 suggesting disruption of contacts with AlaRS or perturbation of the solvation pattern around the G3-U70 pair. At the opposite, genetic investigations coupled with NMR analyses have shown that replacing the G3-U70 wobble pair with a C-C mispair preserves tRNAAla aminoacylation in vivo. Likely, the C-C pair, as does a G-U pair, provides deformability in the acceptor stem which does not occur in a structurally more rigid stem with a G-C pair.82 Altogether, these last data are better in line with an indirect recognition mechanism. What is then the real mechanism? Presumably, direct and indirect recognition mechanisms are not exclusive. In other words, alternate mechanisms can lead to the same level of specificity. We believe that structural adaptability may even confer functional advantages in maintaining a high degree of specificity when mutations or external circumstances (pH, salt, temperature changes...) perturb precise tuning of the tRNA/synthetase complex.

Related with these considerations are other data highlighting the importance of structural plasticity in tRNA alanylation systems and the existence of alternate mechanisms in identity expression. As to the first point, E. coli suppressor tRNAAla(CUA) can accommodate substantial structural flexibility in its core, since 15 out of 16 possible nucleotide pairs at positions 15 and 48 are functional in vivo and therefore are likely alanylated by AlaRS.104 Even the inactive variant in suppression, with the A15/A48 combination, is an efficient substrate of AlaRS in vitro, but in that case the mutation triggers a distal structural alteration in the anticodon loop that hampers its correct functioning in protein synthesis.104 By tuning the plasticity of tRNAAla at the level of the 15-48 nucleotide pair evolution established species discrimination in alanine identity. Indeed, although a majority of tRNAAla sequences have R15-Y48 pairs, one finds all the 12 other combinations in cytoplasmic and mitochondrial tRNAAla species. Concerning the second point, the presence of a shifted G2-U71 alanine identity pair in a mitochondrial insect tRNAAla is noteworthy105 and implies an alternate recognition mechanism by AlaRS. Other shifted determinants for expression of yeast arginine identity were discovered in anticodon loops within different tRNA frameworks.106,107

Phenylalanine Identity

The identity of yeast tRNAPhe was the first deciphered by the in vitro method. It is given by five elements, namely four determinants located at the extremities of the L-shaped tRNA (A73, the discriminator base and G34 A35 A36, the three anticodon residues) and a fifth determinant located in the central core of the molecule (G20, in the D-loop).97 Given the similarity of the phenylalanine identity sets in yeast and T. thermophilus and the crystal structure of the tRNAPhe/PheRS complex from T. thermophilus,71,108 it is likely that all five determinants in yeast tRNAPhe contact amino acids in yeast PheRS. Mutation of individual determinants, that would remove a contact, have rather moderate effects on specificity (kcat/KM reduced at most by a factor of ˜200 for an A35U mutation in the anticodon), but specificity is increased by the additive effects of the five determinants that act independently.109 The surprise arose when transplanted molecules with poor phenylalanine acceptance but bearing the five phenylalanine determinants were discovered.110 Indeed, specificity was found reduced by a factor of ˜2000 for variants with insertion of a G2-C71 pair in acceptor stems within different tRNA frameworks, notably that of E. coli tRNAAla and even of cognate yeast tRNAPhe. Surprisingly, the deleterious effect of the G2-C72 pair could be compensated by the insertion of a G3-U70 wobble pair, which by itself has no effect on phenylalanylation. From a mechanistic point of view, the G2-C72/G3-U70 combination is not a classical recognition element since its antideterminant effect can be compensated. Combinations that do not hinder aminoacylation are called “permissive”. Presence of permissive elements implies that no nucleotide within a tRNA is of random nature but has been selected by evolution so that tRNAs can fulfill their functions efficiently. In agreement with this view are recent studies on cysteine and glutamine identities, showing that structural effects due to alteration of the Levitt pair and its surrounding in the core of the tRNA can be interpreted in terms of permissive and non-permissive elements.58

Aspartate Identity

Like for phenylalanine, aspartate identity of yeast tRNAAsp is also triggered by determinants located at the distal extremities of the molecule and in its central core, namely G73, G34U35C36, C38, and G10-U25,98,111 with strongest determinants being the discriminator G73 base and the GUC anticodon. Expression of aspartate identity, however, differs from what was observed in the phenylalanine case, since strong anti-cooperative effects were found between discriminator and anticodon determinants.112 As a consequence, minihelices or microhelices with the single G73 aspartate determinant can be efficiently aspartylated.113 Aspartate determinants make direct contacts with AspRS, mainly via chemical groups of the bases.114 If some of these contacts are disrupted, structural adaptation of the tRNA on AspRS is not optimal and charging efficiency declines as concluded from footprinting and functional analyses.115 Most intriguing was the finding of a close functional relationship between the sequences of yeast tRNAAsp and yeast arginine accepting tRNAs, since the unmodified aspartate transcript can be efficiently charged by yeast ArgRS.93 However, biological specificity is prevented in native tRNAAsp by the m1 methylation of residue G37 next to the anticodon that acts as an antideterminant.116 Presence of antideterminants in tRNA (modified nucleosides or other structural elements) is not restricted to this particular system and is becoming better documented (see e.g., refs. 16, 92, 105, 117). In fact, negative discrimination appears to be a general mechanism in nature for improving specificity of enzymatic reactions involving tRNAs (see e.g., refs. 118, 119).

Glutamine Identity

Identity of E. coli tRNAGln has been studied in depth both from the structural and functional viewpoints. In contrast to other identities, glutamine identity is specified by a large set of nucleotides.120-122 It includes five residues in the anticodon region (the YUG anticodon itself and the two 3'-adjacent A37 and U38 residues) and five residues near the accepting end (the discriminator residue G73 and the second G2-C71 and third G3-C70 base-pair in the stem). As in the aspartate system,98 mutations at identity positions essentially affect kcat, but specificity constants (kcat/KM) in the glutamine system are decreased by greater factors (up to 105) than in the aspartate system (at most 530-fold). The tRNA determinants find their counterpart on the synthetase and it was shown that both nucleotides (e.g., U35) and amino acid (e.g., Arg341) determinants are coupled in establishing specificity during tRNAGln/GlnRS recognition.123 The tRNA acts as a cofactor in the recognition process and enables correct positioning of its acceptor arm in the catalytic site of the synthetase, thus optimizing amino acid activation.124 In this step, the 3'-terminal A of tRNAGln mediates the tRNA-dependent amino acid recognition by GlnRS.125 This gives structural support to the well known fact that amino acid activation by GlnRS requires tRNA. The next question was to verify whether identity nucleotides determine also the cognate amino acid affinity of the synthetase. To this end, glutaminylation kinetics of tRNAGln mutants were conducted under saturating amino acid conditions.126 Results indicate that the identity determinants can be subdivided in specificity determinants (exclusively in the acceptor stem of tRNAGln) and in elements responsible for binding (mainly the G10-C25 pair and the anticodon). All recognition events leading to tRNA charging imply conformational changes during the mutual adaptation of tRNAGln and GlnRS. Spectroscopic investigations suggest that only the cognate tRNA triggers the conformational changes that confer specific aminoacylation.127 Finally, correct charging of tRNAGln, or its mischarging, is dependent on the balance (in vivo or in vitro) of tRNAGln with GlnRS and noncognate synthetases.128

Peculiar Implications of Synthetases and Other Proteins in Identity Expression

Aminoacyl-tRNA synthetases are modular proteins comprising catalytic and anticodon recognizing domains, and often additional domains not indispensable for the aminoacylation function. This is in particular the case of eukaryotic synthetases that present appended domains to the N- or C-terminal end of their core structure.129 As examples we discuss the role in tRNA aminoacylation of two N-terminal appendices in yeast class I GlnRS130, and class II AspRS.131

The demonstration of a functional role of the appendix in yeast GlnRS came from genetic experiments aimed to rescue a GlnRS-deficient yeast strain by GlnRS from E. coli.130 In its first version, when the native E. coli enzyme was used, the experiment failed. Rescue occurred when the domain from yeast GlnRS was fused to E. coli GlnRS. In vitro experiments confirmed that the chimerical E. coli enzyme with the yeast appendix binds and glutaminylates better yeast tRNAGln than does native E. coli GlnRS.

The dimeric yeast AspRS is extremely sensitive to proteolytic cleavage leading to truncated species deprived of the first 20 to 70 residues but that retain enzymatic activity and dimeric structure. This N-terminal appendix is not seen in the crystallographic model of the tRNAAsp/AspRS complex and thus was considered as not essential for aminoacylation. However, it participates in tRNA binding, a finding that could be generalized to eukaryotic class IIb synthetases.131 Biochemical and mutagenesis experiments indeed showed that the extension connected to the anticodon binding module of AspRS contacts RNAAsp on the minor groove side of its anticodon stem and, as a consequence, lead to a stronger binding to AspRS. Sequence comparison of eukaryotic class IIb synthetases identified a lysine-rich sequence with the consensus xSKxxLKKxxK that is important for this binding.

Taken together, these two examples illustrate a more general phenomenon, namely the involvement of protein domains (as found also in the alanine system132) or even of specialized proteins like Arc1p,133 and Trbp111,134 that bind to tRNA and increase the global aminoacylation efficiency by chaperone-like effects. Along these lines, elongation factor EF-Tu that binds certain misacylated tRNAs more strongly (or weakly) than cognate aminoacyl-tRNAs may contribute to better identity expression and consequently to translational accuracy.135

Finally, mechanistic aspects of the tRNA aminoacylation reactions are certainly of crucial importance in expression of identities and need to be explored more thoroughly. For instance, the competitions between synthetases for interacting with a given tRNA, as studied for glutamine identity expression,128 are likely of more general relevance. This is also true for effects mediated by pyrophosphate, a reaction product of amino acid activation, on the activity of variants with mutation at identity positions, as seen in tRNAPhe,136 and in tRNAAsp (Khvorova, Wolfson and Giegé, unpublished results).

Structure and Identity of Atypical tRNAs and of tRNA-Like Domains

Figure 4 gives examples of the folding of natural RNAs with structural and/or functional characteristics different from those of canonical tRNAs. Structural deviations in these molecules likely reflect their specialized functions (protein synthesis in mitochondria, donor of selenocysteine in protein synthesis, tagging of abnormal proteins on the ribosome for proteolysis in the case of tmRNA, replication of viral RNA genomes for plant virus tRNA-like structures). All these RNAs are recognized by aminoacyl-tRNA synthetases and thus should contain identity determinants mimicking the determinants present in canonical tRNAs.

Figure 4. Schematized folding of atypical tRNAs emphasizing deviations from the canonical fold (dashed lines), domains mimicking tRNA features (in heavy lines), and location of identity determinants (full triangles) (adapted from ref.

Figure 4

Schematized folding of atypical tRNAs emphasizing deviations from the canonical fold (dashed lines), domains mimicking tRNA features (in heavy lines), and location of identity determinants (full triangles) (adapted from ref. ). (A) Mitochondrial tRNAs, (more...)

Several bovine mitochondrial tRNAs have been studied by chemical probing, modeling and NMR methods. For tRNASer(UCN), the structure is close to that of classical tRNA, but the connector between acceptor stem and D-stem has only one nucleotide and the anticodon stem contains six base-pairs.137 In tRNASer(AGY), the D-domain is missing and a novel pattern of tertiary interactions accounts for the three-dimensional structure of the molecule.138 Interestingly, and in contrast with cytoplasmic tRNASer species which have a large variable region, in the mitochondrial species, this region is always of small size. Further, because of the peculiar D- and T-loop sequences, interaction between these two loops is missing or strongly altered in most mitochondrial tRNAs. From the functional viewpoint, little is known about the identity determinants in these tRNAs, although it can be predicted from phylogenetic considerations and sequence comparisons that mitochondrial tRNAs contain identity elements found in E. coli tRNAs,14 but their importance awaits to be verified experimentally. This was already done for aspartate identity in a mitochondrial tRNAAsp from a marsupial, which like in prokaryotic tRNAAsp, relies on anticodon, notably on the central U35 residue.139 Of different outcome, however, were studies on serine identity of mitochondrial bovine tRNASer(AGY). Here, the importance of the T-loop and in particular of A58 is highlighted.140-142 This differs from what found for serine identity of E. coli tRNASer that is given by determinants in the acceptor stem and variable region.143 For more details, see chapter 8 by C. Florentz and M. Sissler, on mitochondrial synthetases.144

Selenocysteine inserting tRNAs differ from canonical tRNAs by an extended amino acid branch made of 13 base-pairs and novel tertiary interactions. They are recognized by SerRS, likely as are canonical tRNASer species. The specific properties of these atypical molecules rely on their potential to interact with specialized elongation factors and more generally to participate in the pathway of selenocysteine synthesis and incorporation into proteins (reviewed in ref. 145; see also chapter 4 by S. Blanquet et al, and chapter 22 by I.P. Ivanov et al). Another family of atypical tRNAs is constituted by the tmRNAs that have both mRNA and tRNA properties (see e.g., ref. 146 for recent structural aspects about the tRNA-like domain within E. coli tmRNA, and chapter 21 by R.H. Buckingham and M. Ehrenberg). These molecules are aminoacylated by AlaRS,147 and, as anticipated have a G3-U70 identity pair.

Viral tRNA-like structures were discovered at the 3'-end of genomic RNAs of several genera of plant viral RNAs (for early literature see e.g., refs. 148-151). Three groups of mimics have been characterized to date on the basis of their aminoacylation identity (valine, histidine, and tyrosine). Folding of these domains deviates markedly from the canonical tRNA cloverleaf. Closest sequence similarities with tRNA are found in the valine accepting structures in tymoviruses (e.g., TYMV). All the viral tRNA-like domains present a pseudoknotted acceptor stem. Recent advances in the field brought better understanding of the architectural features that actually mimic tRNA as well as of the rules that confer aminoacylation capacity to these molecules (reviewed in ref. 152). Because of the architectural properties of pseudoknotted stems,153 all three families of tRNA-like domains (from TYMV, TMV, BMV) present in their acceptor arm a mimic of the −1 major histidine identity nucleotide and consequently were found histidylatable.24 Interestingly, studies on tRNA showed that the phosphate group of residue −1 is in fact the actual histidine identity determinant.154 Strength of this determinant is strongest in the TMV tRNA-like structure and is much weaker in the context of TYMV and BMV RNAs, especially when compared to the dominant identity in these tRNA-like molecules (valine and tyrosine, respectively). It seems therefore unlikely that this property has in vivo implications in contemporary systems,155 and we believe it is more likely that histidine identity in TYMV and BMV RNAs is a functional remnant of the evolutionary history of these molecules. As to valine identity of TYMV RNA, mutagenesis experiments pointed to the importance of discriminator and anticodon residues,156,157 like in canonical tRNAVal. A recent investigation based on in vitro selection of molecules derived from the TYMV tRNA-like structure randomized in the anticodon loop and in the pseudoknot confirmed the importance of the anticodon residues in valine identity.158 It showed further that architectural rather than sequence features in the pseudoknot are important for efficient valylation. Finally, viruses belonging to the bromo-, cucumo- and hordeivirus genera possess tyrosine accepting tRNA-like structures at their 3'-extremity. All share a particularly intricate structure, as highlighted in the case of the BMV tRNA-like structure (Fig. 4F). In this structure, residues in the pseudoknotted acceptor arm,159 functionally mimic the major tyrosine identity determinants found in yeast tRNATyr, namely A73 and the first base-pair C1-G72 of the accepting stem.160 Tyrosine identity in yeast, however, relies also on anticodon, but, strikingly, the BMV tRNA-like structure possesses neither a canonical anticodon loop nor a tyrosine anticodon triplet GUA.160 In fact, recent experiments showed that yeast TyrRS interacts with a hairpin, oriented perpendicularly to the acceptor branch. This hairpin anchors the tRNA-like structure on the synthetase and contributes to the efficiency of the tyrosylation reaction, which otherwise relies only on identity elements in the acceptor branch.159

Altogether, the conclusions arising from investigations on atypical tRNAs and tRNA-like domains favor the view of a strict conservation of the identity nucleotides for recognition of different types of RNA substrates by synthetases, whatever the structural scaffold in which these nucleotides are embedded.16,161

Engineering Structure and Identity of tRNA

The concept of a structural scaffold carrying identity elements at its extremities, as visualized in Figure 5, provides a rational basis for engineering structure and identity of tRNA. It accounts for understanding the output of identity transplantation experiments. If presentation is sub-optimal, aminoacylation efficiency is poor, but can be improved by engineering the scaffold of the receiving tRNA. The concept is illustrated by identity switch experiments between tRNAs aminoacylated by class I GlnRS and class II AspRS,111 and by the design of a tRNA derived from yeast tRNAAsp having optimal phenylalanine identity,162 after remodeling the frameworks of the tRNAs. A further example is a E. coli tRNAGln variant that remained efficiently recognized by GlnRS upon transplantation of the large extra-arm of tRNASer (characteristic of class II tRNAs) in its architectural core.163 Generalizing such engineering, it was possible to construct four distinct designs of the core of class II tRNAs that present stable folding and are efficiently aminoacylated by GlnRS.164

Figure 5. L-shaped RNA scaffold of tRNA and distribution of major identity residues at its distal extremities (adapted from ref.

Figure 5

L-shaped RNA scaffold of tRNA and distribution of major identity residues at its distal extremities (adapted from ref. ). Size of spheres is proportional to the occurrence of identity elements - note the predominant occurrence at discriminator N73 position (more...)

Along the same lines, a molecule with multiple identity having lost its original identity (aspartate) and acquired three new identities (alanine, phenylalanine, and valine) was designed.165 Two of these identities have well-separated determinants (phenylalanine and alanine) and are therefore expressed as efficiently as in their original framework, while the third one (valine) has determinants overlapping with those of phenylalanine and consequently is expressed less efficiently. Similarly, a full-length and bimolecular (obtained by annealing of two fragments) versions of a tRNA with dual phenylalanine and alanine identity were obtained upon introduction of the G3-U70 alanine identity determinant in the framework of yeast tRNAPhe.103 Going one step further, the framework of atypical tRNAs was shown to be recognized by AspRS when it was realized that mutations in the D- and T-loops of yeast tRNAAsp, compatible with aminoacylation activity,166 created a core sharing structural resemblance with that of tRNASec. Direct identity swap experiments confirmed that the tRNA framework of tRNASec is indeed fully recognized by AspRS.167

In a more general perspective, the central core of the tRNA can be completely reorganized and again it can be anticipated that functional molecules can be obtained, provided that identity elements are properly located in the new scaffold. This engineering can be done either by combinatorial methods or by rationale based approaches (reviewed in ref. 168). Figure 6 shows examples of such engineered molecules that were derived from E. coli tRNAPhe,169 and yeast tRNAAsp.113,170 From a highly degenerate library of 63 nucleotides, several RNAs that tightly bind to E. coli PheRS were selected by a filter binding assay. Interestingly, all binders are missing canonical core features and contain an anticodon stem-loop of atypical sequence with a phenylalanine GAA anticodon.169 But the presence of this triplet, part of the E. coli phenylalanine identity set (Table 2), is not sufficient to confer phenylalanylation capacity to these molecules. Presumably, their flexibility is restricted so that proper accommodation of the accepting 3'-end in the catalytic site of PheRS is prevented. This accommodation is possible for three types of tRNAAsp-mimics having deep alteration in their central cores. A first architecture, well aspartylatable, resembles metazoan mitochondrial tRNASer lacking the D-arm. The second one lacks both D- and T-arms and has its acceptor and anticodon helices joined by two connectors. This construct is a substrate of AspRS that behaves like a minihelix, since mutating the anticodon identity determinants does not affect aminoacylation. Removing the connector at the 5'-side provides more flexibility, and allows aminoacylation that is dependent on both G73 and anticodon identity elements.170 Thus, neither a helical structure in the acceptor stem nor the presence of a D- or T-arm is mandatory for specific aspartylation. This conclusion is not restricted to the yeast aspartate system, since yeast PheRS is able to charge a tRNAPhe fragment encompassing a single-stranded acceptor domain.171

Figure 6. Engineered tRNA structures that interact with a synthetase or are aminoacylatable.

Figure 6

Engineered tRNA structures that interact with a synthetase or are aminoacylatable. (A) PheRS-binders selected from a library based on the acceptor stem of E. coli tRNAPhe with the other parts of the tRNA molecule degenerated (adapted from ref. ). (B) (more...)

A Few Remarks on Evolution

The structure of contemporary tRNA is the result of a long evolutionary history and it is most likely that the two domains of its modular L-shaped architecture have arisen independently with the acceptor branch appearing first. Likewise, modular structures, with well-defined catalytic cores, are found in synthetases. Here also the primitive versions of these enzymes would have been restricted to catalytic domains recognizing minimalist acceptor RNAs.172,173 The implication is that the primordial signals defining aminoacylation of tRNA should be present in the minimal structural elements needed for function. As seen in Table 2, identity elements are indeed present in the acceptor arm of all tRNA species. On the other hand, the similar structure of all tRNAs and the structural similarities in the catalytic core of each of the two classes of synthetases, imply evolutionary relationships between the different tRNA aminoacylation systems. Again, this assumption finds support in the distribution and nature of tRNA identity elements (Table 2). Although a complete picture on determinants is presently only available for E. coli tRNAs and that information on tRNAs from other organisms except yeast,16 is scarcer, it appears clearly that many determinants are conserved in evolution. This is true in many systems for the discriminator base and adjacent base-pairs in the acceptor stem. Exceptions to this trend are the nonconservations of the discriminator base in tRNAGly and tRNAHis and even its noninvolvement in the case of tRNAThr identity. Interestingly, these idiosyncrasies seem to be compensated by conservation in evolution of determinants in the acceptor stem of these tRNAs recognized by class IIa synthetases.

In the context of evolution, the structural and functional relationships that were discovered in the glutamate/glutamine and aspartate/asparagine tRNA aminoacylation systems deserve special attention. In both pairs the synthetases are structurally related, belonging to subclass Ic for GluRS and GlnRS and subclass IIb for AspRS and AsnRS. Likewise the identity sets in the corresponding tRNAs, specific for either glutamate and glutamine or aspartate and asparagine, overlap and share strong homologies. Altogether this suggests common evolutionary origins of the glutamate/glutamine and aspartate/asparagine pairs. The fact that in some organisms GlnRS or AsnRS is absent and that aminoacylation of tRNAGln or tRNAAsn occurs via a two-step process comprising tRNA mischarging by heterologous GluRS or AspRS followed by amidation of the mischarged amino acids by tRNA-dependent amidases (reviewed in ref. 174) supports this view. It suggests further that glutamine and asparagine identities originate from the glutamate and aspartate identities.

To conclude, we notice the idiosyncratic architectures of the anticodon-binding modules in synthetases that likely were appended to their catalytic cores late in the course of the primordial evolution of life. In most systems, these modules recognize identity determinants within the anticodon of the homologous tRNAs. Because of the universal nature of the genetic code, determinants in anticodons are obviously conserved in evolution. From that and other considerations, it can be suggested that the origin of tRNA aminoacylation systems is connected with the development of the genetic code (ref. 173 and references therein).

Acknowledgements

We thank C. Florentz for suggestions and critical reading of the manuscript. This work was supported by grants from the Centre National de la Recherche Scientifique (CNRS), Ministère de la Recherche (Programme PRFMMIP), Université Louis Pasteur, Strasbourg, and the European Community (BIO4-CT98-0189).

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