Interaction of the tRNA(Phe) acceptor end with the synthetase involves a sequence common to yeast and Escherichia coli phenylalanyl-tRNA synthetases

Idiosyncrasies in decoding mitochondrial genomes

Mitochondria originate from the α-proteobacterial domain of life. Since this unique event occurred, mitochondrial genomes of protozoans, fungi, plants and metazoans have highly derived and diverged away from the common ancestral DNA. These resulting genomes highly differ from one another, but all present-day mitochondrial DNAs have a very reduced coding capacity. Strikingly however, ATP production coupled to electron transport and translation of mitochondrial proteins are the two common functions retained in all mitochondrial DNAs. Paradoxically, most components essential for these two functions are now expressed from nuclear genes. Understanding how mitochondrial translation evolved in various eukaryotic models is essential to acquire new knowledge of mitochondrial genome expression. In this review, we provide a thorough analysis of the idiosyncrasies of mitochondrial translation as they occur between organisms. We address this by looking at mitochondrial codon usage and tRNA content. Then, we look at the aminoacyl-tRNA-forming enzymes in terms of peculiarities, dual origin, and alternate function(s). Finally we give examples of the atypical structural properties of mitochondrial tRNAs found in some organisms and the resulting adaptive tRNA-protein partnership.

Domains of phenylalanyl-tRNA synthetase from Thermus thermophilus required for aminoacylation

The contribution of entire domains or particular amino acid residues of the phenylalanyl-tRNA synthetase (FRS) from Thermus thermophilus to the interaction with tRNA(Phe) was studied. Removal of domain 8 of the beta subunit resulted in drastic reduction of the dissociation constant of the FRS x tRNA(Phe) complex. Neither the removal of arginine 2 of the beta subunit, which makes the only major contact between domains beta1-5 and the tRNA, nor the replacement of the conserved proline 473 by glycine had an influence on the aminoacylation activity of the FRS. Thus, the body comprising domains 1-5 of the beta subunit may not be essential for efficient aminoacylation of tRNA(Phe) by the FRS and rather be involved in other functions.

Affinity labeling of Escherichia coli histidyl-tRNA synthetase with reactive ATP analogues. Identification of labeled amino acid residues by matrix assisted laser desorption-ionization mass spectrometry

Recent affinity labeling studies have revealed that dimeric histidyl-tRNA synthetase from Escherichia coli displayed half-of-the-sites reactivity toward labeling with pyridoxal 5'-phosphate [Kalogerakos, T., Hountondji, C., Berne, P. F., Dutka, S. & Blanquet, S. (1994) Biochimie (Paris) 76, 33-44]. In the present report, affinity labeling studies were conducted by using other ATP analogues such as pyridoxal 5'-diphospho-5'-adenosine (pyridoxal-ppAdo), pyridoxal 5'-triphospho-5'-adenosine (pyridoxal-pppAdo), pyridoxal 5'-diphosphate (pyridoxal-P2) and 5'-p-fluorosulfonylbenzoyladenosine (FSO2BzAdo). The histidine-dependent isotopic [32P]PP/ATP exchange activity of His-tRNA synthetase was rapidly and completely lost upon incubation with either pyridoxal-ppAdo, pyridoxal-pppAdo or pyridoxal-P2, followed by reduction with sodium borohydride. Complete inactivation of His-tRNA synthetase corresponded to the incorporation of 2.8 mol of either pyridoxal-ppAdo or pyridoxal-P2/mol dimeric synthetase. Incubation of His-tRNA synthetase with FSO2BzAdo also resulted in a complete inactivation of the synthetase. However, contrasting with the pyridoxal derivatives, the plot of the residual enzymatic activity against the amount of covalently bound FSO2BzAdo appeared biphasic. In the early stages of inactivation, the relationship between the amount of residual activity and FSO2BzAdo incorporation was linear and extrapolated to a stoichiometry of 1.1 mol reagent/mol His-tRNA synthetase, suggesting that the labeling of one subunit was sufficient to inactivate one dimeric His-tRNA synthetase molecule. At longer incubation periods, additional reagent incorporation occurred and culminated at 2.5 mol label/mol His-tRNA synthetase. Excess of MgATP protected the enzyme against inactivation by either studied reagent. The labeled amino acid residues were identified by matrix-assisted-laser-desorption-ionization mass spectrometry, by measuring the peptide mass increase caused by the reagents. An identical set of four lysyl residues (Lys2, Lys118, Lys369 and Lys370 of His-tRNA synthetase) was found attached to pyridoxal-ppAdo or pyridoxal-P2. In addition, pyridoxal-ppAdo labeled the alpha-amino group of the N-terminal alanine. In a His-tRNA synthetase sample having incorporated 2.5 mol FSO2BzAdo/mol), the labeled amino acid residues were Lys118, Lys196, Tyr262 (or Tyr263), Lys369 and Lys377. Whatever the used reagent, Lys118 appeared to be the predominantly labeled residue, Lys118 belongs to fragment 112-124 (RHERPQK-GRYRQF) corresponding to motif 2 of class 2 aminoacyl-tRNA synthetases. The other modified lysyl residues (lysines 369, 370 and 377) are close to the catalytic motif 3, in the C-terminal region of the synthetase. Tyr262 and Tyr263 belong to a fragment 256-263 (LVRGLDYY) highly conserved among all known His-tRNA synthetase primary structures. Examination of the recently solved structure of crystalline E. coli His-tRNA synthetase [Amez, J. G., Harris, D. C., Mitschler, A., Rees, B., Francklyn, C. S. & Moras, D. (1995) EMBO J. 14, 4143-4155] shows that, with the exception of lysines 369, 370 and 377, the location of which may account for peculiar accessibility and reactivity, all the amino acid residues identified in this study map near the enzyme nucleotide-binding site, at the N-terminal catalytic domain of the synthetase.

Footprinting of tRNA(Phe) transcripts from Thermus thermophilus HB8 with the homologous phenylalanyl-tRNA synthetase reveals a novel mode of interaction

The phosphates of the tRNA(Phe) transcript from Thermus thermophilus interacting with the cognate synthetase were determined by footprinting. Backbone bond protection against cleavage by iodine of the phosphorothioate-containing transcripts was found in the anticodon stem-loop, the D stem-loop and the acceptor stem and weak protection was also seen in the variable loop. Most of the protected phosphates correspond to regions around known identity elements of tRNA(Phe). Enhancement of cleavage at certain positions indicates bending of tRNAPhe upon binding to the enzyme. When applied to the three-dimensional model of tRNA(Phe) from yeast the majority of the protections occur on the D loop side of the molecule, revealing that phenylalanyl-tRNA synthetase has a rather complex and novel pattern of interaction with tRNAPhe, differing from that of other known class II aminoacyl-tRNA synthetases.

Role of lysine-195 in the KMSKS sequence of E. coli tryptophanyl-tRNA synthetase

Lysine 195 in the K195 MSKS sequence of E. coli tryptophanyl-tRNA synthetase (TrpRS) was replaced with alanine. The resulting K195A mutant TrpRS had essentially unchanged Km values for ATP and Trp, but a 1500-fold decreased kcat in a pyrophosphate-ATP exchange reaction. This large decrease in kcat reduces the rate of aminoacyladenylate formation (step 1) to a rate comparable to the rate of aminoacylation of tRNA(Trp) (step 2) by the K195A mutant enzyme. Both the TIGN and KMSKS sequences are important for step 1 of class I aminoacyl-tRNA synthetase reactions.

Modification of aminoacyl-tRNA synthetases with pyridoxal-5'-phosphate. Identification of the labeled amino acid residues

The isotopic [32P]PPi-ATP exchange activity of isoleucyl-, valyl-, histidyl-, tyrosyl- and methionyl-tRNA synthetases from Escherichia coli are lost upon incubation in the presence of pyridoxal-5'-phosphate (PLP). When the residual activity of either isoleucyl-, valyl- or methionyl-tRNA synthetase (monomeric truncated form) was plotted as a function of the number of PLP molecules incorporated per enzyme molecule, the plots obtained appeared biphasic. Below 50% inactivation of these enzymes, PLP incorporation varied linearly with the isotopic exchange measurements, and extrapolation of the first half of the plot indicated a stoichiometry of 1.10 +/- 0.05 mol of PLP incorporated per mol of 100% inactivated synthetase. Beyond 50% inactivation, the graph deviated from its initial slope, and up to 4-5 mol of PLP were incorporated per mol of synthetase at the highest used PLP concentrations. In the cases of homodimeric histidyl- and tyrosyl-tRNA synthetases, extrapolation of the graph at 100% inactivation indicated 2.8 +/- 0.1 and 2.4 +/- 0.1 mol of PLP incorporated per mol of enzyme, respectively. PLP-labeled peptides were obtained through trypsin digestion and RPLC purification, prior to Edman degradation analysis. PLP-labeled residues were identified as lysines 132, 332, 335 and 402 of monomeric methionyl-tRNA synthetase, lysines 332, 335, 402, 465, 596 and 640 of native dimeric methionyl-tRNA synthetase, lysines 22, 117, 601, 604 and 645 of isoleucyl-tRNA synthetase, lysines 554, 557, 559, 593 and 909 of valyl-tRNA synthetase, lysines 2, 118, 369 and 370 of histidyl-tRNA synthetase, and lysine 237 of tyrosyl-tRNA synthetase. In addition, the amino terminal residue of the polypeptide chain(s) of either isoleucyl-, valyl-, histidyl- or methionyl-tRNA synthetases was found labeled. Among these residues, lysines 332, 335 and 402 of monomeric methionyl-tRNA synthetase as well as lysines 332, 335, 402 and 596 of dimeric methionyl-tRNA synthetase, lysines 601, 604 and 645 of isoleucyl-tRNA synthetase, lysines 554, 557 and 559 of valyl-tRNA synthetase, lysines 2, 369 and 370 of histidyl-tRNA synthetase, and lysine 237 of tyrosyl-tRNA synthetase were labeled in the presence of PLP concentrations smaller than or equal to 1 mM, and are shown to be critical for the activity of the enzymes. It is concluded that these residues participate to the binding sites of the phosphates of ATP on the studied synthetases.

Structure of the phenylalanyl-tRNA synthetase genes from Thermus thermophilus HB8 and their expression in Escherichia coli

A 4459 bp long BamHI restriction fragment containing the two genes for the Thermus thermophilus HB8 phenylalanyl-tRNA synthetase was cloned in Escherichia coli and its nucleotide sequence was determined. The genes pheS and pheT encode the alpha- and beta-subunits with a molecular weight of 39 and 87 kD, respectively. Three conserved sequence motifs typical for class II tRNA synthetases occur in the alpha-subunit. Secondary structure predictions indicate that an arm composed of two anti-parallel alpha-helices similar to that reported for the E.coli seryl-tRNA synthetase may be present in its N-terminal portion. In the beta-subunit clusters of hydrophilic amino acids and a leucine zipper motif were identified, and several pronounced alpha-helical regions were predicted. The particular arginine and lysine residues in the N-terminal portion of the beta-subunit, which were found to participate in tRNA binding in the yeast and E.coli PheRSs, have their counterparts in the T.thermophilus protein. The 5'-portion of an open reading frame downstream of pheT was found and codes for a yet unidentified, extremely hydrophobic peptide. The pheST genes are presumably cotranscribed and translationally coupled. A novel type of a putative transcriptional terminator in Thermus species was identified immediately downstream of pheT and other Thermus genes. The genes pheS and pheST were expressed in E.coli.

Amino acid substrate specificity of Escherichia coli phenylalanyl-tRNA synthetase altered by distinct mutations

Neither the tertiary structure nor the location of active sites are known for phenylalanyl-tRNA synthetase (PheRS; alpha 2 beta 2 structure), a member of class II aminoacyl-tRNA synthetases. In an attempt to detect the phenylalanine (Phe) binding site, two Escherichia coli PheRS mutant strains (pheS), which were resistant to p-fluorophenylalanine (p-F-Phe) were analysed genetically. The pheS mutations were found to cause Ala294 to Ser294 exchanges in the alpha subunits from both independent strains. This alteration (S294) resided in the well-conserved C-terminal part of the alpha subunit, precisely within motif 3, a typical class II tRNA synthetase sequence. We thus propose that motif 3 participates in the formation of the Phe binding site of PheRS. Mutation S294 was also the key for proposing a mechanism by which the substrate analogue p-F-Phe is excluded from the enzymatic reaction; this may be achieved by steric interactions between the para-position of the aromatic ring and the amino acid residue at position 294. The Phe binding site model was then tested by replacing the alanine at position 294 as well as the two flanking phenylalanines (positions 293 and 295) by a number of selected other amino acids. In vivo and in vitro results demonstrated that Phe293 and Phe295 are not directly involved in substrate binding, but replacements of those residues affected PheRS stability. However, exchanges at position 294 altered the binding of Phe, and certain mutants showed pronounced changes in specificity towards Phe analogues. Of particular interest was the Gly294 PheRS in which presumably an enlarged cavity for the para position of the aromatic ring allowed an increased aminoacylation of tRNA with p-F-Phe. Moreover, the larger para-chloro and para-bromo derivatives of Phe could interact with this enzyme in vitro and became highly toxic in vivo. The possible exploitation of the Gly294 mutant PheRS for the incorporation of non-proteinogenic amino acids into proteins is discussed.