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Mitochondrial Aminoacyl-tRNA Synthetases

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Mitochondria and chloroplasts have their own genomes that encode a small number of proteins whose synthesis depends on translation machineries of multiple origin. Whereas tRNAs, rRNAs and some ribosomal proteins are often encoded by the organellar genome, all other factors and in particular aminoacyl-tRNA synthetases (aaRSs) are nuclear encoded, synthesized in the cytosol and imported. Thus, two to three sets of aaRSs coexist in eukaryotic cells, namely cytosolic, mitochondrial and chloroplastic versions. Here, the diversity in the structural and functional properties of organellar aaRSs is illustrated by mammalian mitochondrial aaRSs (size, oligomeric structure, efficiency of aminoacylation, cross reactions, identity sets). Additionally, means by which nuclear genes encode cytosolic, mitochondrial and chloroplastic aaRSs are reviewed on the basis of database exploration on fully sequenced (although not completely annotated) genomes of Homo sapiens, Saccharomyces cerevisiae, Caenorabditis elegans, Drosophila melanogaster and Arabidopsis thaliana.


Eukaryotic cells are characterized by a high degree of organization due to the presence of numerous sub-cellular compartments. In addition to the nucleus sequestering the major genetic information, these include a variety of vesicles (lysosomes, peroxisomes, endoplasmic reticulum, ) in which activity is rather specialized and based on enzymes imported from the cytosol. Mitochondria and chloroplasts, organelles which perform numerous important metabolic functions, contain a specific genome allowing the synthesis of a limited number of essential proteins but also import metabolites and proteins from the cytosol. As illustrated by a few examples (Table 1), the size of organellar genomes is variable and unrelated to the complexity of the organism.1 Most animals have small and compact mitochondrial (mt) genomes, as illustrated in human, whereas lower eukaryotes such as Saccharomyces cerevisiae or alternatively, flowering plants such as Arabidopsis thaliana, have larger and less compact mt genomes with a significant amount of intragenic sequences. The genome sizes of chloroplasts are less variable and appear to be organized along similar lines. The gene content of organellar DNA display a great variability, ranging from very few genes (12 for the green algae Chlamidomonas eugametos mt genome) to several dozen (173 for the chloroplast genome of A. thaliana). All mt genomes code for at least some of the protein components of the respiratory chain complexes and for ribosomal RNAs (rRNAs). The more gene-rich mt genomes also code for transfer RNAs (tRNAs), ribosomal proteins and proteins involved in transcription and/or translation. Most chloroplast genomes possess the same set of about 200 genes, including rRNA and tRNA genes, as well as genes for ribosomal proteins and for proteins involved in photosynthesis.

Table 1. Organellar genomes vary both in size and gene content and encode only a small proportion of the macromolecules required for their translation.

Table 1

Organellar genomes vary both in size and gene content and encode only a small proportion of the macromolecules required for their translation.

This brief overview shows that organellar genomes not only encode proteins important for specific metabolic pathways, but also for part of the mt protein synthesis machinery, namely most if not all of the required RNAs and in some cases a few ribosomal proteins. The translation apparatus additionally requires a large variety of partners including the tRNA maturation enzymes, aminoacyl-tRNA synthetases (aaRSs), initiation, elongation and termination factors. All these partners are necessarily encoded by the nuclear genome and imported into mitochondria.

An immediate question concerns the distinguishing characteristics between the sets of macromolecules required for translation within the organelle(s) and in the cytosol. Of particular interest are aaRSs, for which each eukaryotic cell contains at least two sets of 20 enzymes, and three sets in the case of plants. How different are the organellar aaRSs from their cytosolic (cyt) counterparts in regard to their structural and functional properties? Biochemical properties include size, sequence, oligomeric status, aminoacylation efficiency and tRNA recognition. Since mitochondria and chloroplasts are endosymbiotic remnants,26 relationship with the biochemical properties of prokaryotic aaRSs is also worth considering. Additional questions concern the differences between nuclear genes which encode for aaRSs with different subcellular locations, namely cytosol, mitochondria and chloroplast. The recent discoveries of aminoacylation7 and translation8 in the nucleus complicates the situation with a need of aaRSs of nuclear location.

In this review, biochemical properties of organellar aaRSs are illustrated by the situation in mammalian mitochondria. Although knowledge of these enzymes is still limited, the accumulated data reflect those observed for other organelle aaRSs and in particular highlight a number of unusual features. Mammalian mt aminoacylation systems have also gained interest since the discovery of an expanding number of human disorders linked to mt tRNA mutations.912 In a second part, nuclear aaRS genes are considered. The genomic distinction between mammalian cyt and mt aaRSs is first considered in the case of human. For comparison, genes for cyt and mt aaRSs have also been compiled for three other organisms for which both the mt and the nuclear genomes are presently fully sequenced, namely S. cerevisiae, Caenorhabditis elegans, and Drosophila melanogaster. The genomic diversity of aaRS genes in an organism containing chloroplasts as well as mitochondria, namely the plant A. thaliana, is also examined. These examples illustrate the diverse gene combinations used to encode cytosolic as well as organellar aaRSs.

Structural and Functional Features of Mammalian Mitochondrial Aminoacyl-tRNA Synthetases

Search for Aminoacyl-tRNA Synthetase Activities

Biochemical studies on mammalian mt aminoacylation systems have been initiated on crude enzymatic extracts obtained from accessible tissues such as rat liver, bovine liver, human placenta and from HeLa cell lines. At the start, it was important to demonstrate that a mt extract indeed contains tRNA synthetase activities, and to distinguish these activities from those of the cyt counterparts. Due to the bacterial origin of mitochondria, a major question concerned the similarities and differences with prokaryotic aaRSs, so cross aminoacylation assays were performed from the beginning.

Examples of mammalian mt aaRS activities date back to the 60s. In rat liver extracts, 9 different activities were initially found (those specific for Arg, Asp, Gly, Leu, Met, Phe, Ser, Tyr and Val);13 in human HeLa cell lines, all activities except that for Asn, Gln, His and Pro were detected,14 and in human placental mitochondria, we were able to detect the activities for Gly, Ile, Leu, Lys, Ser and Thr whereas that for Pro was not found.15 Bovine mitochondria yielded initially Phe, Thr, Arg, Lys and Ser activities.16,17 Several enzymes were further purified by conventional biochemical approaches, with most success being achieved for bovine liver PheRS,16 SerRS18,19 and recently LysRS.20

The first genes coding for mammalian mt aaRSs were reported in 1994, almost a decade after assignment of the first yeast mt aaRS.21 Nuclear genes of S.cerevisiae coding for mt aaRSs were cloned by complementation of pet mutants with a recombinant plasmid library of yeast genomic DNA. Complementation experiments are not possible for mammalian cells, so that the first human aaRS genes, namely those for GlyRS22 and IleRS23 were searched for on the basis of structural homologies with enzymes from other organisms, either by EST (Expressed Sequence Tags) analysis or by PCR (Polymerase Chain Reaction) with oligonucleotides designed on the basis of sequence comparisons. The cyt and mt versions of both enzymes were distinguished from each other by the absence or presence of a potential mt target signal. Based on a similar approach, a hypothetical gene for human mt HisRS was described.24 This gene has more than 70% identity with the gene for cyt HisRS and has a potential mt target sequence at its N-terminus. Only very recently, the genes for 5 additional human or bovine mt aaRSs have been defined and cloned, the enzymes overexpressed and their structural and functional properties analyzed. These are human mt PheRS,25 LeuRS,26 LysRS,27 TrpRS,28 and bovine mt SerRS.29

Structural Features

All nuclear-encoded proteins required for structure and function of mitochondria are necessarily targeted from the cytoplasm, as are the aaRSs. Mt protein targeting sequences display large differences in size and amino acid composition and their same function is fulfilled by the presence of numerous positively charged residues and the formation of an amphiphilic α-helix.30,31 After import, maturation of the target sequence undergoes a twostep cleavage by the mt processing protease (MPP) and the mt intermediate peptidase (MIP). In the case of mammalian mt aaRSs, target sequences are located at the N-terminus of the enzyme, varying in length from 18 to 54 amino acids (Table 2).

Table 2. Mammalian mitochondrial aminoacyl-tRNA synthetases at the protein level.

Table 2

Mammalian mitochondrial aminoacyl-tRNA synthetases at the protein level.

Structural features of the mature human mt enzymes are further summarized in Table 2 and can be compared to those of other known aaRSs.32,35 The size of mature mt aaRSs is variable, ranging from 360 to 993 amino acids. These sizes are however mostly in the same range as aaRSs of the same specificity but from different organisms. Thus for example, comparison with yeast mt aaRSs shows at most 5% length variations with the exception of LysRS, composed of 625 amino acids in human mt and only of 546 amino acids in yeast mt. The oligomeric state of mt aaRSs is generally the same as that of cyt eukaryotic or of prokaryotic aaRSs. However, two major exceptions exist. Thus, the human mt GlyRS is dimeric (α2) as is the case for other mt GlyRS, a situation also found for the eukaryotic cytosolic enzymes, while prokaryotic GlyRSs are heterotetrameric (α2β2). More striking is the divergence between prokaryotic and eukaryotic tetrameric cyt PheRSs (α2β2), and the monomeric (α) version of the human mt enzyme. The N-terminal 314 amino acids of the mt enzyme are analogous to the α subunit of prokaryotic PheRS, while the C-terminal 100 amino acids resemble a region of the β-subunit.25 This observation overlaps with the situation in yeast where the drastic change in mt and cyt PheRS quaternary structures was first revealed.36 Whereas the cyt enzyme exhibits an α2β2structure of about 200KDa with both subunits required for activity, a single mt polypeptide of 52KDa is able to aminoacylate yeast mt tRNAPhe. A possible scenario from an evolutionary point of view is that mt PheRS evolved from the a subunit by the addition of two domains, one inserted in the catalytic domain and the other added at the C-terminus.36The latter is involved in tRNA aminoacylation and shares structural homology with the C-terminal end of the cyt enzyme's β-subunit. Despite their distant relationship, the cyt and mt PheRSs bind the tRNA in the same way and use the same set of identity elements.37 The initial site of tRNA aminoacylation at the 2'OH, an unusual property for a class II enzyme (see below), is also conserved for the yeast mt PheRS. Whether this property is related to a primitive translation system is not presently clear.

Sequence analysis of the 8 mammalian mt aaRS genes so far detected allows further comparison with the corresponding cyt enzyme and with enzymes of prokaryotic origin (Table 2). For mammalian GlyRSs and LysRSs, the same gene encodes both the cyt and the mt enzymes, so that the sequences of both mature enzymes are highly similar. For the other aaRSs which are all synthesized from two distinct genes, similarity with the corresponding cyt aaRSs is generally limited. A major exception concerns the putative mt HisRS gene, distinct from the cyt HisRS gene, but with more than 70% identity.24 in contrast, most mt enzymes have strong similarities with prokaryotic aaRSs (Table 2). The sequence similarities or divergences of mt aaRS genes with cyt or prokaryotic aaRS genes are directly linked to the evolutionary history of aaRS genes in eukaryotic cells (see below).

AaRSs can be partitioned into two distinct classes according to their catalytic site organization.38,39 This classification is the same all along the evolutionary scale with the sole exception of LysRS, usually a class II enzyme, but with enzymes from archaea and pathogenic spirochetes belonging to class I.40 Interestingly, the 8 reported mammalian mt aaRS genes contain the typical signature motifs of either class I or class II aaRSs and fit within the general classification. Notably, mammalian mt LysRS is a class II enzyme, as is the cyt LysRS.

Aminoacylation Properties

Slower Enzymatic Activity of Mammalian mt aaRSs

Aminoacylation of tRNAs is a two step process involving first activation of the cognate amino acid in the form of an aminoacyl-adenylate iN-termediate, a step where the tRNA is generally dispensable, and second, transfer of the activated amino acid to the tRNA. Mammalian mt tRNAs and in particular human tRNAs are difficult to obtain, so kinetics of formation of the aminoacyl-adenylate have been determined to evaluate the enzyme's activities.25,26,28 For human mt LeuRS, TrpRS and PheRS, kcat/KM for the amino acid is about 100fold lower than for the corresponding E. coli enzymes and kcat/KM for ATP is about 250-fold lower. Aminoacylation capacities of these enzymes have further been estimated in the presence of E. coli total tRNA; the specific activity of LeuRS is about 250- to 400-fold lower than that observed for the corresponding aaRSs of cytoplasmic and bacterial origins,26 and the specific activity of PheRS is 20- to 30-fold lower than other class II aaRSs.25 Comparative experiments performed with crude enzymatic preparations from human placental mitochondria and from E. coli with their respective homologous total tRNAs, also revealed about 10-fold lower specific activities for the subset of mt enzymes tested, namely IleRS, LysRS, SerRS, and ThrRS (our unpublished observations). Although incomplete, these examples highlight a general trend for mt aaRSs as slower catalysts than their cytosolic or E. coli homologues.

Cross-Aminoacylation Capacities

The co-existence of a cyt and a mt translation apparatus results also in two sets of distinct isoacceptor tRNAs specific for each amino acid. Comparison of cyt and mt aaRS activities includes analysis of their capacity to aminoacylate reciprocal tRNA substrates. One of the first series of experiments on cross aminoacylation reactions of mammalian enzymes, performed with crude rat liver extracts,13 revealed that whereas the subset of tested mt aaRSs were able to aminoacylate the corresponding cyt tRNAs, the opposite is not true. Indeed, the cyt aaRSs are unable to efficiently charge mt tRNAs. In similar work comparing cross aminoacylation of crude mt and cyt preparations from human HeLa cell extracts,14 twelve mt enzymes were able to aminoacylate cyt tRNAs whereas several cyt aaRSs where unable to charge mt tRNAs (Arg, Asp, Cys, Met, Val). These examples illustrate the higher ability of mt aaRSs to recognize cyt tRNAs than that of cyt aaRSs to recognize mt tRNAs. The rare cases of cross reactivities between the two enzymes may be correlated to sequence homologies between the cyt and mt enzymes and/or similar structural features of mt and cyt tRNAs (see below).

Mammalian and yeast aaRSs cross aminoacylation properties are similar.41 This property has been exploited in vivo in the case of MetRS in demonstrating that mt MetRS can replace a knock-out allele of the cytoplasmic MES1 gene, provided that yeast initiator or elongator tRNAMet is overproduced.42

Due to the endosymbiotic theory on the origin of mitochondria, the possibility for the mt aaRSs to aminoacylate prokaryotic tRNAs, and vice versa the capacity of prokaryotic enzymes to aminoacylate mt tRNAs have been considered. A thorough investigation of the relationships between mammalian mt and several eubacterial aminoacylation systems was pioneered for Arg, Lys, Phe, Ser and Thr systems.16,17,43 Bovine mt extracts efficiently aminoacylate eubacterial tRNAs, whereas the prokaryotic enzymes are unable to aminoacylate bovine mt tRNAs. Thus, in these systems there is a unilateral aminoacylation specificity. Consistent with these results we found that LeuRS and LysRS activities of human mt placenta extracts were able to charge both E. coli and yeast cyt total tRNAs, but LysRSs from E. coli and from yeast cytoplasm are unable to charge the human mt tRNAs (our unpublished results). The general trend towards unilateral aminoacylation properties of mt aaRSs and tRNAs may be correlated to the structural divergence of mt tRNAs from “canonical” tRNAs hindering recognition by heterologous enzymes.

Recognition of Mammalian Mitochondrial tRNAs

Mt tRNAs Are Structurally Unusual and Diverse

Whereas the vast majority of eukaryotic cytosolic and prokaryotic tRNAs share a canonical structure,44 mt tRNAs can be very different.4547 As shown in Figure 1, mammalian mt tRNAs diverge from the canonical, while yeast mt tRNAs do not. A systematic comparison of the 22 mt tRNA genes from 31 mammals has allowed to identify particular structural features of these tRNAs.48 Whereas most of these tRNAs have cloverleaflike structures (tRNASer(AGY) is an exception in that its D-arm is completely missing), large variations in D-, and especially T-loop sizes are seen. Conserved nucleotides are usually absent (e.g., G18, G19, and T54Y55C56) suggesting that tertiary interactions between D- and T-loops either are absent or at least are unconventional. Also, none of the mammalian mt tRNAs has a large variable loop. Strongly conserved mismatches or G·U pairs are frequent and may represent structural or recognition signals for proteic partners.48 So far, experimental structures of only 4 mammalian mt tRNAs are available, namely bovine tRNASer(AGY) and tRNASer(UCN) (refs 4954), bovine tRNAPhe (ref 55), and human tRNALys (refs. 56,57). Much larger structural deviations from canonical tRNAs such as complete absence of the T-arm or extensions of the anticodon arm can be found for mt tRNAs from other organisms.4547,58,59

Figure 1. Mammalian mitochondrial tRNA structures deviate from the classical cloverleaf.

Figure 1

Mammalian mitochondrial tRNA structures deviate from the classical cloverleaf. Four mammalian mt tRNAs (A) are compared to the equivalent yeast mt tRNAs (B). Whereas the yeast tRNAs have canonical structural features including size of stems and loops (more...)

Search for Aminoacylation Identity Sets on a Theoretical Basis

Recognition of a tRNA by its cognate aaRS is dependent on specific identity elements. Sets of such elements are well defined for canonical tRNAs. (e.g., see refs. 6063) In contrast, not much is known about the identity elements of mt tRNAs. Because of the endosymbiotic origin of mitochondria, the evolutionary conservation of identity elements,62,63 and because mt aaRSs are able to charge E.coli tRNAs, mt identity sets may share some common elements with prokaryotic sets. Along these lines, we found numerous E. coli identity elements in mammalian mt tRNAs.48 Interestingly, in two systems (Asn and Tyr), all E. coli elements are present, and in 12 mt systems, the nucleotide next to the CCA-end of the tRNA (the discriminator base, most frequently found as identity element) is identical to that in the corresponding E. coli tRNAs.62 Identity elements are often present in the anticodon loop of tRNAs,6164 and, accordingly, potential elements have also been found there in mammalian tRNAs. However, variations in the mt genetic code65 with corresponding changes in the tRNA anticodon sequences, suggest that identity elements in the anticodon triplets will be different in E. coli and mammalian mt tRNAs. In yeast mitochondria the existence of two different tRNAThr has been reported.66 While tRNAThr2 with a 3'-UGU-5' anticodon recognizes the usual ACN codons for threonine, tRNAThr1 with a 3'-GAU-5' anticodon is responsible for reading the leucine family of CUN codons as threonine.67 Surprisingly, the mt aaRS encoded by the MST1 gene has been found to acylate only tRNAThr1 and not tRNAThr2, the anticodon of which determines the identity of threonine tRNA in the E. coli system.64 Search for a second mt ThrRS in the database of S. cerevisiae genome failed. Therefore the origin of the aminoacylation of tRNAThr2 remains to be determined.

Importance of Post-Transcriptional Modification

The experimental search for mammalian mt tRNA identity sets is technically difficult. In vivo analysis is limited to naturally existing mt tRNA mutations, since transformation of mitochondria, remains impractical. Thus, aminoacylation levels of mutated tRNAs have been reported for cybrid cell-lines.68,69 These are cells containing “cloned” mitochondria, i.e., mitochondria with only mt DNA of wild-type sequence or with only mt DNA with a single point mutation at the level of a tRNA gene.70 The technical challenge of purification of mammalian mt tRNAs in sufficient amounts for experimental investigations in vitro was thought to be easily overcome by cloning the corresponding synthetic genes followed by in vitro transcription. This approach allowed synthesis of many variants and is a routine application for “classical” tRNAs (e.g., see refs. 62, 7173) with no (or only few) functional limitation due to absence of post-transcriptional modifications. In the case of human mt tRNAs, use of in vitro transcripts lead however to unexpected discoveries and difficulties. In the specific case of human mt tRNALys, the “naked” transcript is unable to fold into a cloverleaf but does fold into an extended bulged hairpin.74 A methyl group is necessary and sufficient to hinder this hairpin fold and allows for the cloverleaf structure. Thus, a post-transcriptional modification plays the role of a molecular internal chaperone.57 This unexpected result suggested that post-transcriptional modifications are likely to be of greater importance in mt tRNAs and that difficulties can be anticipated in working with in vitro transcribed tRNAs. Indeed, several transcribed tRNAs turned out to be barely chargeable with an amino acid (our unpublished results, and refs. 25,27). Despite these difficulties, some transcripts could be used for the investigation of aminoacylation properties. Comparative isoleucylation capacities of native (purified from placental mitochondria) and in vitro transcribed human mt tRNAIle revealed a 48fold decrease in efficiency,75 suggesting that post-transcriptional modifications are involved in efficient recognition by the cognate aaRS to some extent. However, they are not of major importance. This is at opposite to the situation in E. coli tRNAIle, where a modified C residue at position 34 is required for specific isoleucylation and protects the tRNA against misacylation by MetRS.76,77 The difficulties reported in aminoacylation of transcripts probably reflect a cumulative dependence of mt tRNAs on post-transcriptional modifications both for structure and function. Mt tRNAs have a lower level of modifications (7–8%) compared to other tRNA families (12%–15%), suggesting that those modifications retained do have special roles.78

Transcripts for both bovine mt tRNASer isoacceptors have also been used successfully in aminoacylation reactions,29,79 with as little as a 5-fold increase in KM compared to native tRNASer, suggesting that in this case, post-transcriptional modifications contribute to a limited extent to efficient interaction with the aaRS.

Deciphering Identity Sets

The first experimental information on mt identity elements came from the interpretation of heterologous tRNA aminoacylation reactions catalyzed by mt aaRSs. Efficient cross aminoacylations were interpreted to indicate the presence of shared identity elements. Failure to aminoacylate heterologous tRNAs was interpreted to indicate the absence of major identity elements. However, since cyt tRNAs often have different structural properties than mt tRNAs, simple sequence comparisons may only be considered as suggestive.

Studies on those in vitro transcribed tRNAs which are active in aminoacylation despite the absence of post-transcriptional modifications are more straightforward. For example, the central anticodon nucleotide in aminoacylation of a marsupial mt tRNAAsp was demonstrated to be important.80 According to the edited or non edited status of this nucleotide, the tRNA becomes an efficient substrate either for GlyRS (anticodon GCC) or for AspRS (anticodon GUC). Aminoacylation properties of several variants for human mt tRNAIle allowed the deciphering of elements important for isoleucylation.75,81,82 Nucleotide positions investigated were those correlated to human neurodegenerative disorders rather than those rationally designed for investigation of the tRNA aminoacylation identity elements. Each of the 6 mutated positions resulted in decreased aminoacylation efficiencies. However, the negative impact of all those mutations present in stem regions (5 out of the 6), converting Watson-Crick pairs into G·U pairs or C·A mismatches, could be overcome by compensatory mutations, and have thus to be considered as structural determinants rather than identity elements per se. The mutation located in the T-loop was also proposed to induce structural changes.75 Thus, so far, no direct isoleucine identity element has been found.

Native wild-type tRNALys as well as variants with a mutation at position 55 in the T-loop have been purified from specific human cell lines in sufficient amounts to analyze the effect of the mutation on different steps of translation, including aminoacylation.20 This tour de force lead to the finding that the mutated tRNA has only a 3-fold negative effect on catalytic efficiency (kcat/KM), suggesting that the mutated nucleotide, related to the severe myopathy MERRF (mitochondrial myopathy with ragged red fibers), is not an important lysine identity element.

Mammalian mt serine specific aminoacylation identity elements have been searched for in a rational systematic way and represent the best characterized system.19,29,79 The situation for serine is unique because a single aaRS recognizes two tRNAs having no apparent consensus sequence and presenting two distinct structural architectures (Fig. 1). Indeed, tRNASer(AGY) has no D-arm and tRNASer(UCN) has a cloverleaf structure with an extended anticodon stem and a short connector between the acceptor stem and the D-stem. An additional interesting feature is a small variable loop; a large variable loop is typical of cytosolic, prokaryotic and other mt serine specific tRNAs.18,83,84 A thorough and complete analysis of the recognition and interaction process of both mt tRNASer with cloned bovine mt SerRS has been performed.29 Footprinting of the enzyme on both native tRNAs revealed contact points at the level of the T-loops. Analysis of large sets of in vitro transcribed variants of both tRNAs (including hybrid molecules with exchanged D-domains, and minihelices mimicking the acceptor branch of the tRNAs), lead to the conclusion that mt SerRS recognizes both substrates as well based on the presence of common features within the T-loop. However, recognition of both substrates occurs in a distinctive way, in requiring or not, a long distance tertiary interaction with the D-loop. Since bovine mt tRNAGlu shares the sequence of the T-loop with tRNASer(UGA), it was also suggested that mis-serylation of tRNAGlu is restricted by the presence of a strong negative determinant, a single basepair in the T-stem of tRNAGlu.29

Unusual Functions of Mammalian mt aaRSs

AaRSs catalyze aminoacylation of tRNAs and also perform a number of alternative functions.85,86 Studies on organelle-specific aaRSs revealed interesting roles in tRNA import into mitochondria87 and intron splicing.88 Whereas these functions were initially described in yeast, the capabilities of mammalian mt aaRSs to substitute for the yeast enzymes in these processes were recently demonstrated. Import of nuclear-encoded tRNALys into yeast mitochondria is mediated by mt LysRS.87,89,90 The charged tRNA is co-imported across the protein import pore using the mt precursor of LysRS and at least one other as-yet-unidentified factor as carriers. Binding of tRNALys to the precursor enzyme depends on specific regions in the tRNA as well as on its aminoacylation by the cytosolic LysRS. The biological relevance of the single imported tRNALys remains unsolved since a mitochondria-encoded tRNALys present in the organelle is sufficient for mt translation. Recently it has been shown by in vitro experiments that it is possible to import tRNAs into human mitochondria. This process, which does not take place in vivo, is dependent upon either yeast or human soluble proteins, suggesting that human cells possess all factors needed for such an artificial translocation.90 Nuclear-encoded tRNALys import in marsupial mitochondria has been recently demonstrated,91 but direct involvement of marsupial mt LysRS in this process has not been established.

The role of certain aaRSs in splicing of mt tRNA has been reported for Neurospora crassa92 and S. cerevisiae93. While no splicing events are required for expression of the human mt genome deprived of introns, human mt LeuRS can substitute in splicing for the yeast mt LeuRS,94,95 suggesting that the role of LeuRS in yeast mt RNA splicing results from features of the enzyme that are broadly conserved in evolution.

Gene Relationships Between Cytosolic and Organellar aaRSs

As underlined above, organellar aaRSs are necessarily nuclear encoded, synthesized within the cytosol and targeted towards either mitochondrion or chloroplast thanks to a specific leader sequence. This raises the question as to the distinction between genes encoding cytosolic and organellar synthetases, and their evolutionary relationship. In what follows, we first report the situation for human aaRSs and then extend the analysis to 4 organisms for which nuclear genome as well as organellar genomes have been fully sequenced. These are the yeast S. cerevisiae (fungi), the worm C. elegans (nematode), the fruitfly D. melanogaster (arthropod) and the flowering plant A. thaliana. Genomic and protein databases (NCBI, euGenes, MIPS, WormBase, FlyBase) containing indexed DNA sequences, expressed sequence tags (ESTs) and open reading frames (ORFs), have been screened. An overview of the present knowledge on aaRS genes and proteins is summarized in Table 3, by indicating gene names, gene accession references and protein accession references. Additional genomic references of predicted aaRS sequences (not yet indexed) have been searched by a more detailed exploitation of the corresponding databases. Reported aaRSs within literature together with sequence similarities with characterized proteins have facilitated this search.

Table 3. Aminoacyl-tRNA synthetases in databases.

Table 3

Aminoacyl-tRNA synthetases in databases.

Mitochondrial versus Cytosolic Aminoacyl-tRNA Synthetase Genes

The human genome has been completely sequenced,96,97 but however is still not completely annotated. To date, 19 genes for cytosolic aaRSs are indexed (only ValRS is missing) and information for 8 mt enzymes is available (GlyRS, HisRS, IleRS, LeuRS, LysRS, PheRS, SerRS and TrpRS). The different combinations of genes for human cyt and mt aaRSs are schematized in Figure 2. Interestingly, two major pathways have been developed throughout evolution. These are:

Figure 2. Diversity of nuclear genes for cytosolic and mitochondrial aminoacyl-tRNA synthetases.

Figure 2

Diversity of nuclear genes for cytosolic and mitochondrial aminoacyl-tRNA synthetases. The two main strategies reported so far for the synthesis of mt aaRSs are schematized on each side of the dashed line. Either both enzymes are encoded by separate genes, (more...)

i. the existence of two independent genes for the two enzymes of same specificity, or

ii. the occurrence of a single gene for both enzymes.

In six cases, mt and cyt aaRSs are encoded by two different genes (Leu, His, Ile, Phe, Trp, Ser) as reflected by low sequence similarities. In the two remaining systems (Gly and Lys), mt and cyt enzymes are encoded by a single nuclear gene. However, the situation for these two systems is different. In the case of GlysRS, 2 translation initiation sites lead to the production of 2 enzymes, distinguished by the presence or the absence of a mt targeting sequence.22,98 In the case of LysRS, an unusual splicing mechanism of the primary transcript is responsible for the insertion—or not—of the mt leading sequence (encoded by exon 2 which is excluded within the cytoplasmic LysRS). After cleavage of this additional sequence, only the N-terminal regions of mature LysRSs are different. Identical splicing mechanisms of LysRS mRNAs have been detected for C. elegans, D. melanogaster, M. musculus and Zebrafish.27

Further human genome annotation and especially annotation of missing mttargeted aaRS genes will either reveal similar relationships with cyt enzymes, or highlight new possibilities. For example, alternative splicing mechanisms involving several combinations of exons may lead to distinct synthetases starting from a single gene.

Among the yeast aminoacylation systems, genes for the 20 cyt enzymes and for 15 mt aaRSs have been clearly identified (Table 3). In 12 systems, cyt and mt targeted enzymes are encoded by separate genes (ArgRS, AsnRS, AspRS, GluRS, IleRS, LeuRS, LysRS, MetRS, PheRS, ThrRS, TrpRS and TyrRS). In contrast to the human mt systems, both cyt and mt HisRSs arise from single nuclear genes. This holds true also for ValRSs. As in human, the same GlyRS gene encodes both mt and cyt enzymes. It is noteworthy to underline the existence of 2 distinctive genes for GlyRSs (GRS1 and GRS2, 59 % of identity). However, GRS1 (duplicated from GRS2) has been shown to encode both the cytosolic and mt GlyRSs and GRS2 to be a pseudo-gene (dispensable).99 In the case of yeast mt HisRS100 and ValRS,101 the polypeptide portions of the cyt and mt forms are synthesized from two distinct mRNAs differing in length but having the same coding frame. The longer message contains two AUGs and codes for the mt enzyme; the shorter one contains only the second AUG and codes for the cyt enzyme. For 4 further yeast aminoacylation systems (those specific for Ala, Cys, Pro and Ser), information about mt enzymes (or genes of these enzymes) is missing. Finally, examination of the yeast genome database reveals the absence of a mt GlnRS. It is therefore likely that synthesis of mt Gln-tRNAGln occurs via an indirect pathway involving two steps, first misacylation by GluRS yielding Glu-tRNAGln followed by amidation by a Glu-amidotransferase to match the tRNA specificity.102 This indirect pathway which has been found in chloroplastic and archaea system is believed to reflect a primitive system of tRNA aminoacylation.103

The gene distribution for cyt and mt aaRSs within C. elegans remains mostly unsolved since only the gene for cyt HisRS has been specifically annotated so far (Table 3). However, for 7 aminoacylation systems (those specific for Ala, Asp, Glu, Ile, Leu, Trp and Val), genes encoding both enzymes are identifiable. In all these cases, the genes are different for the two enzymes. A second gene encoding an ArgRS is predicted, but its targeting towards mitochondria is not yet established. For D. melanogaster, while the genes for the 20 cytosolic aaRSs are annotated, only 3 genes for mt targeted enzymes are listed (AlaRS, IleRS and PheRS).

In summary, while analysis of the genomes of H. sapiens, S. cerevisiae, C. elegans and D. melanogaster does not provide insight to each of the 20 aaRSs couples, two main pathways relating or distinguishing cyt from mt aaRS of the same specificity exist:

  1. two different genes lead to cyt and mt enzymes, or
  2. the same gene leads to the two enzymes with or without a targeting sequence allowing final different subcellular localization.

Synthetases of the same specificity are generally produced in a similar way (Ile, Leu, Phe, Trp are synthesized from 2 different genes and GlyRS from the same gene) in both human and yeast. However, differences between yeast and human can be highlighted. For instance, while the yeast LysRSs are encoded by different genes, human counterparts are encoded by a single nuclear gene by virtue of alternative splicing of the primary transcript. In contrast, the human HisRSs are likely encoded by 2 different genes while those of yeast are encoded by the same gene.

It is generally believed that the DNA from mitochondria evolved directly from prokaryotes that were engulfed by primitive eukaryotic cells in evolutionary history and developed a symbiotic relationship with them.2,4 In the billion or so years since the first eukaryotic cell appeared,104 mitochondria have lost much of their genome and have become dependent on proteins that are encoded by the nuclear genome (perhaps by selective transfer to- and recombination with- the nuclear genome), synthesized in the cytosol and then imported into mitochondria. The genomic integration process occurred for the genes encoding mt aaRSs which were further duplicated, or not, to give a separate set of genes for the cyt and mt forms.105,106 In some cases, mt aaRS genes were transferred to the nucleus and coexist now with the nuclear gene for the corresponding cyt enzyme, or the gene transfer lead to the replacement of the nuclear gene. Alternatively, mt genes were lost and have been replaced by the nuclear equivalents. Because of the prokaryotic origin of mitochondria, some of the mt aaRS are expected to be of prokaryotic lineage. The finding that the present day cytosolic PheRS is an a2b2 structure of high molecular size, whereas it is a monomer of low size in the mitochondria of yeast and human is consistent with this prediction. Indeed, the evolutionary trend is likely to occur from a simple to a more complicated architecture.

Cytosolic, Mitochondrial and Chloroplastic Aminoacyl-tRNA Synthetase Genes: The Situation in A. thaliana

The complete genome sequence of A. thaliana (nuclear genome as well as mitochondrial and chloroplast genomes) allows the complex situation of organisms dealing with 3 separate protein synthesizing compartments to be analyzed. A taste of the numerous gene combinations giving rise to cyt and organellar aaRSs in the model plant, is summarized in a specific database “tRNAs & aminoacyl-tRNA synthetases from A. thaliana” ( . The site contains so far 32 nuclear-encoded, identified and annotated aaRS genes. The predicted sub-cellular localization of the polypeptides is based either on computer-assisted predictions (search for targeting sequences) or on experimental data using transient expression of green fluorescent protein fusions.107,108 Two major gene combinations could allow for the synthesis of the 3 families of aaRS namely cyt, mt and chloroplastic enzymes. In a first combination, there are only two genes for three enzymes. Thus, for example one gene for the cytosolic enzyme and a second gene for both organellar enzymes (Asn, Cys, Glu, His, Lys, Met, Trp, Tyr) or alternatively, one gene for both the cyt and mt enzyme and another for the chloroplastic enzyme (ThrRS, GlyRS, ValRS). Second, a very simple situation has been reported for AlaRS, where all three enzymes are produced from one common gene. A third combination in which three distinct genes would code for each of the three enzymes has not been found and is not expected (I. Small, personal communication). For some aaRSs, the situation is however more complex. Thus, for ArgRS, while one gene product (SYR1) is exclusively addressed to the cytoplasm, the SYR2 gene is predicted to be expressed as 3 size versions: a “longest” version targeted to the chloroplast, and a “long” and a “short” version both targeted to the cytosol. A second case that does not follow these simple schemes concerns GlyRSs in which two different nuclearencoded enzymes are imported to mitochondria. The first one, GlyRS-1, is similar to human or yeast synthetases, while the second, GlyRS-2, is similar to the E. coli enzyme. Both enzymes are targeted to two different locations, GlyRS-1 to mitochondria and to the cytosol and GlyRS-2 to mitochondria and chloroplasts. Unexpectedly, GlyRS-1 seems to be active in the cytosol but inactive in mitochondrial fractions, whereas GlyRS-2 is likely to glycylate both the organelle-encoded tRNAGly and the imported tRNAGly present in mitochondria.109


Organellar activities are in part linked to a proper translational machinery which allows proteic expression of the organellar genome. This translational machinery is of dual origin, partly encoded by the organellar genome itself and partly by the nuclear genome. AaRSs belong to the family of nuclear encoded translational partners, with import to the organelle being fulfilled by a specific target sequence cleaved subsequently. Knowledge on this family of enzymes, either from a biochemical or a genomic point of view, remains presently incomplete. Indeed, even in the case of S. cerevisiae, the first eukaryote for which the complete genome has been sequenced, information for 4 mt aaRSs is still missing. In the case of H. sapiens, only 8 mt synthetases have been analyzed to some extent and for other fully sequenced organisms, knowledge is only tentative. However, the present active phase of genome annotation is expected to detect new organellar aaRS genes in the near future. Evolutionary closeness between aaRSs may be used to search for genes of interest. For example, by analogy to the situation in yeast and human, D. melanogaster genes for mt GlyRS and mt LysRS may not be different from those encoding the cyt enzymes.

While still an emerging field, the present knowledge on human mt aaRSs highlights a diversity in biochemical properties (size, oligomeric state, aminoacylation properties, and especially cross-aminoacylation capacities) which either make them resemble the corresponding prokaryotic or cytosolic aaRSs. Sequence comparisons of the mt aaRS genes with those of the other aaRSs, further extend and confirm analogies. Similar conclusions hold true for the better studied yeast mt aaRSs. They all reflect the evolutionary history of mitochondria, namely their prokaryotic origin, and a progressive gene transfer to the host genome. This transfer can occur with or without replacement of the corresponding nuclear genes, thus leading to a variety of organellar aaRSs. As briefly illustrated in the case of A. thaliana, organellar aaRSs in plants show a similar diversity, which is made more complex by the presence of two types of organelles, mitochondria and chloroplasts, and combinations of gene transfer to the nucleus from both of them.

Knowledge on mt aaRSs, and especially on human mt aaRSs, is becoming more and more important not only from a fundamental and evolutionary point of view, but also with regard to human medicine. Indeed, insight to the molecular mechanisms underlying the variety of neurodegenerative and neuromuscular disorders correlated to mt tRNA point mutations, necessarily requests investigation of aminoacylation properties. As already shown, aminoacylation defects are the most likely, although not the sole, primary impacts of the mutations and need to be investigated in a systematic way. Furthermore, new lines of research in the development of new classes of antibiotics focus on aaRSs as possible targets.110 According to the large contribution of mitochondria to numerous metabolic pathways and especially to the major cellular energy synthesis process, analysis of the impact of potential new drugs on mt aaRSs activities should not be omitted.


We would like to thank Ian Small and Laurence Maréchal-Drouard for helpful discussion on plant organellar aaRSs and Magali Frugier, Joëlle Rudinger-Thirion and Anne Théobald-Dietrich for comments on the manuscript. Investigations on human and yeast mitochondrial aminoacylation systems are supported by the Centre National pour la Recherche scientifique (CNRS), Université Louis Pasteur Strasbourg, Association Fran¸aise contre les Myopathies (AFM), European Community grant QLG2-CT-1999–00660.

Web sites

• OGMP, the Organelle Genome Megasequencing Program (

• MIPS, Munich Information Center for Protein Sequences ( 10.html)

• NCBI, National Center for Biotechnology Information (

• EuGenes, Genomic Information for Eukaryotic Organisms (

• FlyBase, a database of the Drosophila Genome (

• WormBase (

• taaRSAt, tRNA and aminoacyl-tRNA synthetases from Arabidopsis thaliana (


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