Phenylalanyl-tRNA synthetases from sheep liver and yeast. Correlation between net charge and binding to ribosomes

Unlike phenylalanyl-tRNA synthetase from lower eukaryotes, the corresponding enzyme from higher eukaryotes displays a pronounced tendency to associate with ribosomes in vitro. To attempt to uncover the structural features responsible for this difference in behavior, a comparative study of the enzymes purified to homogeneity from sheep liver and yeast was undertaken. The two alpha 2 beta 2-type enzymes displayed remarkably similar subunit molecular masses (71 and 63 kDa for sheep, 74 and 63 kDa for yeast), yet differed markedly in their isoelectric points (8.0 and 5.6 pH units, respectively). Mild tryptic digestion of the enzyme from sheep led to preferential degradation of the 63-kDa beta subunit into two major fragments of 35 and 25 kDa, respectively, with concomitant loss of activity. The isoelectric points of the denatured fragments were found to be distinctly lower than that of the denatured beta subunit, implying that the residues responsible for the basic net charge of the original beta subunit are mainly clustered in a small portion of the polypeptide chain which was excised during proteolysis. Despite their different isoelectric points, the enzymes from yeast and sheep displayed identical requirements for aminoacylation of tRNA at optimal rates. Moreover, the incidence of variations in pH and ionic strength on the kinetic parameters of the two enzymes was indistinguishable. Interpreted in terms of the polyelectrolyte theory, these results support the view that the residues responsible for the basic net charge of the mammalian enzyme are located in a region distal from the active site. It is suggested that the cationic charge of the enzyme allows anchorage to a cellular component carrying negative charges, possibly the ribosome.

Does the complex of aminoacyl-tRNA synthetases and tRNA-modifying enzymes prevent miscoding?

Several aminoacyl-tRNA synthetases of higher eukaryotes have always been found as multienzyme complexes. There are indications that these complexes can be associated with some tRNA-modifying enzymes. The function of such complexes is unclear. I have noticed that 6 out of 7 aminoacyl-tRNA synthetases most commonly occurring in complexes correspond to a group of tRNAs which must always contain a modified U in the first position of their anticodons. A hypothesis is proposed according to which association of 6 aminoacyl-tRNA synthetases with U-modifying enzymes can protect a cell from miscoding.

Comparative analysis of translation accuracy in an Escherichia coli and a mammalian cell-free system

The effect of environmental stress on the accuracy of protein synthesis in an Escherichia coli and a rat brain cell-free system was investigated. Poly-U was translated in a rat brain and an E. coli cell-free extract under identical ionic conditions. The fidelity of translation, both in the E. coli and the rat brain extracts, was commensurate with what is known about the accuracy of translation in vivo. The incorporation of phenylalanine (code: UUU) and leucine (code: CUU, UUG or A) was measured at various Mg2+ concentrations (3 to 22 mM), various pH's (6.6 to 8.6), various temperatures (23 to 42 degrees C), and in the presence or absence of 2.4% (v/v) ethanol. It was observed that (i) the accuracy of translation was generally higher in extracts from E. coli than from rat brain, and (ii) relative to that in E. coli, the translation fidelity in rat brain extracts was about 2 times more sensitive to ethanol, at least 5 times more sensitive to temperature, and at least 50 times more sensitive to pH. It was found that this differential sensitivity was not due to a differential behavior of the bacterial and the mammalian aminoacyl-tRNA synthetases under stress, but rather to the process of chain elongation itself. It is concluded that the accuracy of protein synthesis is more resistant to environmental stress in E. coli extracts than in extracts from at least one mammalian tissue.

Recognition of tRNAs by aminoacyl-tRNA synthetases: Escherichia coli tRNAMet and E. coli methionyl-tRNA synthetase

In previous work we identified several specific sites in Escherichia coli tRNAfMet that are essential for recognition of this tRNA by E. coli methionyl-tRNA synthetase (MetRS) (EC 6.1.1.10). Particularly strong evidence indicated a role for the nucleotide base at the wobble position of the anticodon in the discrimination process. We have now investigated the aminoacylation activity of a series of tRNAfMet derivatives containing single base changes in each position of the anticodon. In addition, derivatives containing permuted sequences and larger and smaller anticodon loops have been prepared. The variant tRNAs have been enzymatically synthesized in vitro by using T4 RNA ligase (EC 6.5.1.3). Base substitutions in the wobble position have been found to reduce aminoacylation rates by at least five orders of magnitude. Derivatives having base substitutions in the other two positions of the anticodon are aminoacylated 55-18,500 times slower than normal. Nucleotides that have specific functional groups in common with the normal anticodon bases are better tolerated at each of these positions than those that do not. A tRNAfMet variant having a six-membered loop containing only the CA sequence of the anticodon is aminoacylated still more slowly, and a derivative containing a five-membered loop is not measurably active. The normal loop size can be increased by one nucleotide with a relatively small effect on the rate of aminoacylation, which indicates that the spatial arrangement of the nucleotides is less critical than their chemical nature. We conclude from these data that recognition of tRNAfMet requires highly specific interactions of MetRS with functional groups on the nucleotide bases of the anticodon sequence. Several other aminoacyl-tRNA synthetases are known to require one or more anticodon bases for efficient aminoacylation of their tRNA substrates, and data from other laboratories suggest that anticodon sequences may be important for accurate discrimination between cognate and noncoagnate tRNAs by these enzymes.

Misaminoacylation by glutaminyl-tRNA synthetase: relaxed specificity in wild-type and mutant enzymes

Escherichia coli glutaminyl-tRNA synthetase (GlnRS) (EC 6.1.1.18) is a monomeric polypeptide of 553 amino acids. Its amino acid sequence and its gene (glnS) sequence are known. A structural gene mutation, glnS7, codes for a mischarging GlnRS, which acylates some noncognate tRNA species (e.g., su+3 tRNATyr) with glutamine. The mutant enzyme was shown to catalyze in vitro the acylation of glutamine to su+3 tRNATyr, but not to wild-type tRNATyr. The mutation responsible produces an amino acid change in the amino-terminal half of the enzyme. Unexpectedly, overproduction of wild-type GlnRS also leads to in vivo mischarging of su+3 tRNATyr. In vitro and in vivo studies have not revealed evidence for an attenuation or autogenous regulation mechanism for GlnRS, but have implicated transcriptional and translational control in the expression of this enzyme.

Isoleucyl-tRNA synthetase from bakers' yeast: variable discrimination between tRNAIle and tRNAVal and different pathways of cognate and noncognate aminoacylation under standard conditions, in the presence of pyrophosphatase, elongation factor Tu-GTP complex, and spermine

Error rates in discrimination between cognate tRNAIle and noncognate tRNAVal in the aminoacylation reaction with isoleucine catalyzed by isoleucyl-tRNA synthetase from yeast have been investigated in three sets of experiments under different assay conditions. The overall discrimination factor was first determined by isoleucylation of tRNAVal/tRNAIle mixtures. In the second set of experiments, the number of AMP molecules formed per Ile-tRNA in the cognate and noncognate reactions was measured. The higher AMP formation in the noncognate aminoacylation is assigned to a proofreading reaction step. The calculated proofreading factors and an estimated initial discrimination factor yield overall discriminations that are consistent with those obtained from the first set of experiments. In the third series of studies, the orders of substrate addition and product release of cognate and noncognate isoleucylation reactions were investigated by initial rate kinetic methods. From kcat and Km values, the overall discrimination factors were calculated and showed again a good coincidence with those observed in the preceding sets of experiments. Besides under standard assay conditions, aminoacylation reactions were studied in the presence of pyrophosphatase or elongation factor Tu-GTP complex, under addition of both these proteins, in presence of these two additional proteins and spermine at high and low magnesium concentrations, and under special conditions that favor misacylations. Furthermore, isoleucylation of tRNAIle was tested at increased and decreased pH in the standard enzyme assay. Variation of the assay conditions results in changing discrimination factors, which differ by a factor of about 10. Substitution of tRNAIle by tRNAVal in the isoleucylation reaction causes changes in substrate addition and product release orders and thus of the whole catalytic cycle. For aminoacylation of tRNAIle, four different orders of substrate addition and product release appear: the sequential ordered ter-ter, the rapid equilibrium sequential random ter-ter, the random bi-uni uni-bi ping-pong, and a bi-bi uni-uni ping-pong mechanism with a rapid equilibrium segment. tRNAVal is aminoacylated in rapid equilibrium random ter-ter order, in a bi-bi uni-uni ping-pong mechanism with a rapid equilibrium segment, and in two bi-uni uni-bi ping-pong mechanisms. It is assumed that the different assay conditions can be regarded as a stepwise approximation to physiological conditions and that considerable changes in error rates may be also possible in vivo up to 1 order of magnitude.

Overproduction of tryptophanyl-tRNA synthetase relieves transcription termination at the Escherichia coli tryptophan operon attenuator

Overproduction of tryptophanyl-tRNA synthetase increased trp operon expression by reducing transcription termination at the trp attenuator. The total cellular level of charged tRNATrp was not affected by increased levels of the synthetase. We propose that excess synthetase binds charged tRNATrp and reduces the concentration available for translation.

Reactions of the aminoacyl-tRNA synthetase-aminoacyl adenylate complex and amino acid derivatives. A new approach to peptide synthesis

Several kinds of dipeptide derivative were shown to be formed by the reactions of the aminoacyl adenylate-aminoacyl-tRNA synthetase complex and amino acid ester or amide. It was shown that the peptide bond could be formed by aminoacyl-tRNA synthetases even in the absence of the ribosome.

Threonyl-tRNA synthetase from Chinese hamster ovary cells is phosphorylated on serine

A Chinese hamster ovary cell line, 2000A, in which threonyl-tRNA synthetase accounts for 1.5% of the total soluble protein, was used to demonstrate that this enzyme is a phosphoprotein. Threonyl-tRNA synthetase was isolated by immunoprecipitation from cells labeled with 32Pi for 18 h. Phosphoamino acid analysis of radiolabeled threonyl-tRNA synthetase showed that phosphorylation occurs on serine.

[Interaction of aminoacyl-tRNA-synthetases with amino acids]

The review deals with interactions of the key enzymes of the protein biosynthesis-aminoacyl-tRNA synthetases (EC 6.1.1.) with amino acids and their analogues, considering the contribution of different groups in the process of specific complex formation and catalysis. The important role of alpha-amino group of amino acid in the enzyme recognition has been revealed. Modification of the carboxylic group does not change significantly the analogues complex formation with aminoacyl-tRNA synthetases. However this group is essential for amino acid rearrangement in the specific complex with the enzyme. The structural organization of the enzyme binding sites specific for amino acids and the enzyme interaction with the analogues of aminoacyladenylates are discussed.

[Covalent derivatives of aminoacyl-tRNA-synthetases with substrates]

The possibility of participation of covalent enzyme substrate's derivatives in reactions catalyzed by aminoacyl-tRNA synthetases is discussed in connection with general principles of enzyme catalysis. Tryptophanylated and pyrophosphorylated forms of beef pancreas tryptophanyl-tRNA synthetase were identified, isolated and characterized and the expected role of these derivatives in the enzyme function is discussed.

[Affinity modification of Escherichia coli ribosomes near the acceptor tRNA-binding site]

It was shown that Phe-tRNA Phe derivatives bearing arylazidogroups scattered statistically on N7 guanosine residues retain the ability to EF-Tu-dependent binding to E. coli ribosomes. UV-irradiation of the corresponding complex with the derivative of Phe-tRNA Phe located at A-site results in a specific modification of both ribosomal subunits to an approximately equal extent. It was found that proteins S9, S15, S16, S17, S18, S19 and L8/L9, L13, L15, L27 are labelled at A-site.

[Aminoacyl-tRNA-synthetases and their high molecular weight complexes in the regenerating rat liver]

Glutamyl- and lysyl-tRNA synthetase activities in total preparations and high-molecular complexes from rat liver increase 21 h after partial hepatectomy. Glutamyl-tRNA synthetase has been highly purified from normal and regenerating liver. Km, Vmax values and molecular activity were practically the same for both enzyme preparations. Total methyltransferase activity and that as a part of high-molecular complexes increase 1.5 fold 21 h after the operation but the changes of individual methyltransferase activities differ. The level of tRNA methylation in vivo is also higher during regeneration. Proteinkinases of high-molecular complexes from regenerating liver are sensitive to cyclic AMP and GMP in contrast to control.

A comparative study of sulfhydryl groups required for the catalytic activity of gramicidin S synthetase and isoleucyl tRNA synthetase

The sulfhydryl groups required for the catalytic activity of gramicidin S synthetase of Bacillus brevis and Escherichia coli isoleucyl tRNA synthetase were compared. In gramicidin S synthetase 2(GS 2), about four sulfhydryl groups react rapidly with 5,5'-dithiobis(2-nitrobenzoic acid) (DTNB) or N-ethylmaleimide (NEM), and are essential for gramicidin S formation in the presence of gramicidin S synthetase 1 (GS 1). These sulfhydryl groups are protected against DTNB and NEM reactions by the preincubation of GS 2 with amino acid substrates in the presence of ATP and MgCl2, like the sulfhydryl groups that react rapidly with DTNB or NEM and are required for the catalytic activity of GS 1 and isoleucyl tRNA synthetase. In GS 2, GS 1, and isoleucyl tRNA synthetase, the sulfhydryl group that reacts rapidly with NEM and is required for the catalytic activity is involved in the amino acid binding as a thioester. In isoleucyl tRNA synthetase, it is suggested that isoleucine may be transferred from the isoleucine thioester enzyme complex to tRNA by a mechanism similar to that proposed for gramicidin S synthetase.

[Aminoacyl-tRNA-synthetases and their high molecular weight complexes in experimental myocardial ischemia]

A number of aminoacyl-tRNA synthetases from rabbit liver during experimental myocardial infarction and from pig myocardium upon 15-min of autolysis were found to increase their activity in aminoacylation. Direct correlations between the activities of high molecular weight complexes and of the total extracts were not observed. It was shown that the specific activity of endogenous inorganic pyrophosphatase increased markedly during the ischemia of myocardium both in total myocardium extracts and in high molecular weight complexes.

Interaction between dimeric methionyl-tRNA synthetase and methionine accepting tRNAs from E. coli.-- Studies by partial ribonuclease digestion

Using different ribonucleases we have studied the digestion pattern of the two methionine accepting tRNAs, the initiator tRNAfMet and the elongator tRNAmMet from E. coli. The positions and intensities of cleavages are compared to those obtained when the tRNAs are complexed to methionyl-tRNA synthetase. Our results, in comparison with other studies, suggest a general pattern of interaction between tRNAs and their cognate synthetases including the amino acid stem and the anticodon region. Furthermore a lack of involvement of the central region and especially the extra arm seems to be a unique feature of the initiator tRNAMetf.

[Mechanism of functioning of aminoacyl-tRNA-synthetases]

The article reviews the data available concerning the kinetics of reactions catalysed by eukaryotic and procaryotic aminoacyl-tRNA synthetases (E.C.6.1.1). It is shown that most of these enzymes operate in accordance with the flip-flop mechanism although individual variations do exist. It is stressed that a simplified kinetic approach of Cleland is inappropriate if applied to the aminoacyl-tRNA synthetases where subunit interactions are involved in the overall kinetics. The fidelity of aminoacylation reaction depends not only on the proofreading mechanisms at catalytic centres but also on the contribution of mutual conformational changes induced in interacting subunits of the synthetases.

[Interaction of tRNA with ribosomes]

Definition of the site of tRNA-binding to ribosomes is suggested on the basis of a free energy of tRNA-ribosome interaction. From this point of view disagreements that have arisen in recent years concerning the numbers of tRNA binding sites on the ribosome, their distribution between subunits, the properties of the third site E in ribosomes and the compatibility of new experimental data with different models of elongation cycle are discussed. The observation of the third site in the ribosome (messenger independent and with a presumably exit function) is not a refutation but an extension of Watson's model of translating ribosome.

Reactions of the sulfhydryl groups of alanyl-tRNA Synthetase

The six sulfhydryl groups in each subunit of the alanyl-tRNA synthetase of Escherichia coli react with sulfhydryl reagents with at least four different rates. One reacts very rapidly with 5,5'-dithiobis-(2-nitrobenzoic acid) (DTNB), and a second reacts somewhat less rapidly with this reagent. These two groups are required for transfer activity, which is lost in proportion to the extent of derivatization. Two other groups react more slowly, with a consequent loss of exchange activity. The remaining two sulfhydryl groups do not react with DTNB until the protein is denatured. The inactivations are reversed by dithiothreitol. Two sulfhydryl groups react with N-ethylmaleimide (NEM) and with a spin-label derivative of NEM. These reactions resemble the modification of two sulfhydryl groups with DTNB, in that they also inactivate the transfer reaction but not the ATP:PPi exchange. The two spin labels are incorporated at similar rates but are in very different environments, one highly exposed and one highly immobilized. These groups do not interact with Mn2+, which is bound to the enzyme in the absence of ATP.

Isolation of Chinese hamster ovary cells that overproduce asparaginyl-tRNA synthetase

Temperature-resistant revertants, derived from the temperature-sensitive CHO asparaginyl-tRNA synthetase mutant, Asn-5, were isolated and characterized. Several lines of evidence indicate that the temperature-resistant phenotype of the revertants is due to their overproducing the same altered enzyme present in the Asn-5 parent.

Fast kinetic study of yeast phenylalanyl-tRNA synthetase: role of tRNAPhe in the discrimination between tyrosine and phenylalanine

An extensive study of the discrimination between phenylalanine and tyrosine by yeast phenylalanyl-tRNA synthetase was carried out in the presence of native tRNAPhe. Our results clearly show that, besides the previously reported dissociation of tyrosyl adenylate from the enzyme template [Lin, S. X., Baltzinger, M., & Remy, P. (1983) Biochemistry 22, 681-689], two more correction processes are involved in the rejection of tyrosine in the presence of tRNAPhe. A minor part of the misactivated tyrosine is indeed transferred to tRNAPhe, but the resulting misaminoacylated tRNA is very rapidly hydrolyzed (kh approximately equal to 60 s-1), as it has already been shown for other systems. However, the major part of the misactivated tyrosine is rejected as the result of a pretransfer correction consisting of the fast hydrolysis (k'h approximately equal to 20 s-1) of the enzyme-bound noncognate adenylate induced by the binding of native tRNAPhe. The transfer step itself is found to be non-specific, as the rate constant is almost the same for phenylalanine and tyrosine. This result is supported by the observation that tyrosine and phenylalanine are also transferred at the same rate to tRNAPheox-red. It is shown that the integrity of the 3'-terminal adenosine of the tRNA is critical for triggering the pretransfer hydrolysis of enzyme-bound noncognate aminoacyl adenylate. A detailed kinetic analysis is presented that shows that the observed rate constant of tRNAPhe tyrosylation and the rate of disappearance of enzyme-tyrosyl adenylate complex are in fact apparent rate constants.(ABSTRACT TRUNCATED AT 250 WORDS)

Thermostable valyl-tRNA, isoleucyl-tRNA and methionyl-tRNA synthetases from an extreme thermophile Thermus thermophilus HB8: protein structure and Zn2+ binding

Thermostable valyl-tRNA, isoleucyl-tRNA and methionyl-tRNA synthetases have been purified from an extreme thermophile, Thermus thermophilus HB8. Valyl-tRNA and isoleucyl-tRNA synthetases are found to be monomer proteins (Mr 108000 and 129000, respectively), while methionyl-tRNA synthetase is a dimer protein (Mr 150000). These enzymes are very similar with respect to amino acid compositions and alpha-helix contents as estimated by circular dichroism analyses. Furthermore, two Zn2+ are tightly bound to each of these synthetases. These data suggest that valyl-tRNA and isoleucyl-tRNA synthetases consist of two domains, each corresponding to the subunit of methionyl-tRNA synthetase.

The eucaryotic aminoacyl-tRNA synthetase complex: suggestions for its structure and function

Aminoacyl-tRNA synthetases from eucaryotic cells generally are isolated as high molecular weight complexes comprised of multiple synthetase activities, and often containing other components as well. A model is proposed for the synthetase complex in which hydrophobic extensions on the proteins serve to maintain them in their high molecular weight form, but are not needed for catalytic activity. The structural similarity of these enzymes to certain membrane-bound proteins, and its implications for synthetase localization and function in vivo, are discussed.