III. The RNA component of aminoacyl-tRNA synthetase complexes isolated from mouse liver. Absence of amino acid accepting activity.

A method is described which permits the simultaneous isolation and separation of insoluble aminoacyl-tRNA synthetase protein - RNA complexes containing high specific synthetase activity, and soluble tRNA which retains 25% to 50% of its specific amino acid accepting activity. A possible amino acid accepting activity of the RNA part of the insoluble aminoacyl-tRNA synthetase protein - RNA complex was investigated by assaying the unchanged complex and the RNA obtained after dissociation from the protein part of the synthetase complex. No amino acid accepting activity was found.     

Metabolic regulation of aminoacyl-tRNA synthetase biosynthesis in bakers' yeast.

The specific activities of 15 aminoacyl-tRNA synthetases in Saccharomyces cerevisiae were measured after growth under a variety of conditions that produced a range of cell-doubling times. The specific activity of each synthetase increased as cell-doubling time decreased. Control experiments eliminate the possibility that these results are due to preferential recovery of synthetases, or to the presence of activators in the faster growing cultures or inhibitors in the slower growing ones. These observations run counter to the expectation that synthetases in bacteria and yeast are negatively regulated by free amino acids, or, more likely, by aminoacyl-tRNA. In fact, as the growth medium was enriched, generation times decreased, and synthetase and aminoacyl-tRNA levels increased. It is suggested that cytoplasmic aminoacyl-tRNA synthetases may be more or less coordinately controlled such that their response to growth follows the pattern observed for ribosome production and RNA synthesis. This suggests the possibility of coordinated response of genes for components of the protein synthetic apparatus.     

CHO cell mutants for arginyl-, asparagyl-, glutaminyl-, histidyl- and methionyl-transfer RNA synthetases: identification and initial characterization

A number of conditional lethal mutants of CHO cells that are defective in protein synthesis have been characterized with respect to their biochemical lesions. A defective aminoacyl-tRNA synthetase appears to be the basis of each mutant phenotype. In each strain, the specific activity in vitro of the synthetase cognate for one of the following amino acids was substantially reduced: arginine, asparagine, glutamine, histidine or methionine. One mutant, Arg-1, gave no detectable arginyl-tRNA synthetase activity, suggesting that it contains an altered enzyme that is unstable in vitro. Most of the mutants correspondingly exhibited impaired aminoacylation in vivo under nonpermissive conditions. However, two mutants, Arg-1 and His-1, appeared to have normal levels of acylated tRNA under the nonpermissive conditions which inhibited protein synthesis to approximately 50% and 10%, respectively. The expression of each mutant's phenotype, measured by rates of protein synthesis or growth, was a function of temperature and/or the concentration of amino acid cognate for the synthetase found to be deficient in vitro. The properties of these mutants make them applicable to diverse problems related to translation in mammalian cells.     

Selective synthesis of mitochondrial proteins by Chinese hamster ovary cells severely starved for various amino acids

Chinese hamster ovary (CHO) cells were subjected to severe amino acid starvation for histidine, leucine, methionine, asparagine, tyrosine, glutamine, valine, and lysine, using amino acid analogs or mutations in specific aminoacyl-tRNA synthetases. At protein synthetic rates of less than 5%, in all cases, the newly synthesized proteins were found on two- dimensional electrophoretic gels to consist of a few intensely labeled spots, with the exception of lysine. This pattern could also be produced by strong inhibition of cytoplasmic protein synthesis with cycloheximide, and was abolished by preincubation with the mitochondrial protein synthesis inhibitor chloramphenicol. It appears therefore that the spots represent mitochondrial protein synthesis and that animal cells must have separate aminoacyl-tRNA synthetases for mitochondrial tRNAs corresponding to all these amino acids except, possibly, for lysine.     

Identifying the targets of aminoacyl-tRNA synthetase inhibitors by primer extension inhibition

Aminoacyl-transfer RNA (tRNA) synthetases (RS) are essential components of the cellular translation machinery and can be exploited for antibiotic discovery. Because cells have many different RS, usually one for each amino acid, identification of the specific enzyme targeted by a new natural or synthetic inhibitor can be cumbersome. We describe the use of the primer extension technique in conjunction with specifically designed synthetic genes to identify the RS targeted by an inhibitor. Suppression of a synthetase activity reduces the amount of the cognate aminoacyl-tRNA in a cell-free translation system resulting in arrest of translation when the corresponding codon enters the decoding center of the ribosome. The utility of the technique is demonstrated by identifying a switch in target specificity of some synthetic inhibitors of threonyl-tRNA synthetase.     

Reassignment of sense codons in vivo

The genetic code maps one or more of the 61 sense codons onto a set of 20 canonical amino acids. Reassignment of sense codons to non-canonical amino acids in model organisms such as Escherichia coli has been achieved through manipulation of the cellular protein synthesis machinery. Specifically, control of amino acid pools, coupled with engineering of the aminoacyl-tRNA synthetase activity of the host, has enabled assignment of sense codons to a wide variety of non-canonical amino acids under conditions routinely used for expression of recombinant proteins. Codon reassignment is leading to important advances in protein engineering and bioorganic chemistry. Here we summarize some of those advances, and provide detailed protocols for codon reassignment.     

Chloroplast leucyl-tRNA synthetase from Euglena gracilis. Purification, kinetic analysis, and structural characterization

Euglena gracilis chloroplast leucyl-tRNA synthetase was purified to homogeneity by a series of steps including ammonium sulfate precipitation and chromatography on hydroxylapatite, DEAE-cellulose, Sepharose 6B, phosphocellulose, and Blue Dextran-Sepharose. The purified enzyme exhibits a specific activity of 1233 units/mg of protein, which is one of the highest specific activities obtained for an aminoacyl-tRNA synthetase prepared from plant cells. The enzyme has an apparent Km value of 8 x 10(-6) M for L-leucine, 1.3 x 10(-4) M for ATP, and 1.3 x 10(-6) M for tRNALeu. Chloroplast leucyl-tRNA synthetase appears to be a monomeric enzyme with a molecular weight of 100 000. The amino acid composition of chloroplast leucyl-tRNA synthetase has been determined. It is the first reported for a chloroplast aminoacyl-tRNA synthetase, and it reveals a relatively large proportion of apolar residues, as in the case of prokaryotic aminoacyl-tRNA synthetases.     

Reprogramming the amino-acid substrate specificity of orthogonal aminoacyl-tRNA synthetases to expand the genetic code of eukaryotic cells

The genetic code of living organisms has been expanded to allow the site-specific incorporation of unnatural amino acids into proteins in response to the amber stop codon UAG. Numerous amino acids have been incorporated including photo-crosslinkers, chemical handles, heavy atoms and post-translational modifications, and this has created new methods for studying biology and developing protein therapeutics and other biotechnological applications. Here we describe a protocol for reprogramming the amino-acid substrate specificity of aminoacyl-tRNA synthetase enzymes that are orthogonal in eukaryotic cells. The resulting aminoacyl-tRNA synthetases aminoacylate an amber suppressor tRNA with a desired unnatural amino acid, but no natural amino acids, in eukaryotic cells. To achieve this change of enzyme specificity, a library of orthogonal aminoacyl-tRNA synthetase is generated and genetic selections are performed on the library in Saccharomyces cerevisiae. The entire protocol, including characterization of the evolved aminoacyl-tRNA synthetase in S. cerevisiae, can be completed in approximately 1 month.     

Changes in the restriction of molecular rotational diffusion of water-soluble spin labels during fatty acid starvation of yeast.

Yeast mutants lacking fatty acid synthetase activity (fas-) die when deprived of saturated fatty acid under conditions which are otherwise growth-supporting. The spin label technique is used to show that restriction of molecular rotational diffusion of spin label molecules dissolved in aqueous zones increases several fold under conditions of fatty acid starvation while the apparent physical state of cellular hydrocarbon zones remains essentially unchanged. We focus attention on the cellular aqueous interior as the potential site of alteration under selective starvation conditions. Correspondences exist between restriction of molecular motion of water soluble spin labels dissolved in the cell and loss of cell viability. The correspondences to changes in the molecular motion of hydrocarbon soluble spin labels are much less or are not detectable.     

Modulation of N-ethylmaleimide-sensitive factor activity upon amino acid deprivation

Adaptation of eukaryotic cells to changing environmental conditions entails rapid regulation of protein targeting and transport to specific organelles. Such adaptation is well exemplified in mammalian cells exposed to nitrogen starvation that are triggered to form and transport autophagosomes to lysosomes, thus constituting an inducible intracellular trafficking pathway. Here we investigated the relationship between the general secretory machinery and the autophagic pathway in Chinese hamster ovary cells grown in the absence of amino acid. Utilizing VSVG-YFP (vesicular stomatitis virus G protein fused to yellow fluorescent protein) and norepinephrine as markers for constitutive and regulated exocytosis, respectively, we found that secretion is attenuated in cells grown in media lacking amino acid. Such decrease in exocytosis stems from partial inhibition of N-ethylmaleimide-sensitive factor ATPase activity, which in turn causes an accumulation of SNARE complexes at both the Golgi apparatus and the plasma membrane of the starved cells. These findings expose a novel cellular strategy to attenuate secretion of proteins under conditions of limited amino acid supply.     

Expression of the aminoacyl-tRNA synthetase complex in cultured Chinese hamster ovary cells. Specific depression of the methionyl-tRNA synthetase component upon methionine restriction

Cultured Chinese hamster ovary cells were subjected to amino acid restriction to examine its effects on the level of expression of the nine aminoacyl-tRNA synthetase components of the multienzyme complex which was previously characterized (Mirande, M., Le Corre, D., and Waller, J.-P. (1985) Eur. J. Biochem. 147, 281-289). Lowering the methionine concentration in the medium from 100 to 1 microM led to growth arrest, rapid deacylation of tRNAMet, and progressive 2-fold elevation of the methionyl-tRNA synthetase level, as assessed by specific activity measurements and immunotitration. The levels of the other eight aminoacyl-tRNA synthetases were not affected. Total methionine deprivation led to the additional derepression of the leucyl- and isoleucyl-tRNA synthetase components, whereas the corresponding tRNAs remained fully acylated. These pleiotropic responses to total methionine restriction were abolished in the presence of 2 mM methioninol, suggesting that amino acid transport systems may play a role in the regulation of aminoacyl-tRNA synthetase expression. The effect of total deprivation of arginine, glutamine, isoleucine, leucine, lysine, or proline from the culture medium on the level of expression of the corresponding aminoacyl-tRNA synthetases was also examined. In all cases, no elevation of the level of the corresponding synthetase was observed. The behavior of methionyl-tRNA synthetase from Chinese hamster ovary cells displaying a 2-fold increased level of the enzyme due to methionine restriction was examined in detail. Failure to detect a free form of the enzyme by gel filtration, as well as the finding that the isolated complex displayed twice the amount of methionyl-tRNA synthetase relative to the other components, indicates that this multienzyme structure can accommodate at least one additional copy of one of its components.     

Regulation of ex-translational activities is the primary function of the multi-tRNA synthetase complex

During mRNA translation, tRNAs are charged by aminoacyl-tRNA synthetases and subsequently used by ribosomes. A multi-enzyme aminoacyl-tRNA synthetase complex (MSC) has been proposed to increase protein synthesis efficiency by passing charged tRNAs to ribosomes. An alternative function is that the MSC repurposes specific synthetases that are released from the MSC upon cues for functions independent of translation. To explore this, we generated mammalian cells in which arginyl-tRNA synthetase and/or glutaminyl-tRNA synthetase were absent from the MSC. Protein synthesis, under a variety of stress conditions, was unchanged. Most strikingly, levels of charged tRNA^Arg and tRNA^Gln remained unchanged and no ribosome pausing was observed at codons for arginine and glutamine. Thus, increasing or regulating protein synthesis efficiency is not dependent on arginyl-tRNA synthetase and glutaminyl-tRNA synthetase in the MSC. Alternatively, and consistent with previously reported ex-translational roles requiring changes in synthetase cellular localizations, our manipulations of the MSC visibly changed localization.     

A component of the multisynthetase complex is a multifunctional aminoacyl-tRNA synthetase.

In higher eukaryotes, nine aminoacyl-tRNA synthetases are associated within a multienzyme complex which is composed of 11 polypeptides with molecular masses ranging from 18 to 150 kDa. We have cloned and sequenced a cDNA from Drosophila encoding the largest polypeptide of this complex. We demonstrate here that the corresponding protein is a multifunctional aminoacyl-tRNA synthetase. It is composed of three major domains, two of them specifying distinct synthetase activities. The amino and carboxy-terminal domains were expressed separately in Escherichia coli, and were found to catalyse the aminoacylation of glutamic acid and proline tRNA species, respectively. The central domain is made of six 46 amino acid repeats. In prokaryotes, these two aminoacyl-tRNA synthetases are encoded by distinct genes. The emergence of a multifunctional synthetase by a gene fusion event seems to be a specific, but general attribute of all higher eukaryotic cells. This type of structural organization, in relation to the occurrence of multisynthetase complexes, could be a mechanism to integrate several catalytic domains within the same particle. The involvement of the internal repeats in mediating complex assembly is discussed.     

Superspecificity of aminoacyl-tRNA-synthases

The correct aminoacylation of tRNA with the proper aminoacid by aminoacyl-tRNA synthetase is one of the key reactions which determines the overall high fidelity of protein biosynthesis. The initial selection of the amino acid is achieved in the active centre of the synthetase at the activation step due to differences in the side chains binding energies of specific substrate and the competing amino acids present in cell. If, nevertheless, the activation of amino acids structurally similar to the cognate one does proceed, additional mechanisms of correction which are based on the decomposition of unstable noncognate (intermediate or final) product of the tRNA aminoacylation reaction, by synthetase are switched on. In this review the literature on the specificity of aminoacyl-tRNA synthetases at amino acid activation step is analyzed along with the proofreading mechanisms which allow the elimination of the errors, leading to so called superspecifity of aminoacyl-tRNA synthetases.     

The effect of amino acid starvation on nucleoside uptake and RNA synthesis in Tetrahymena

The uptake of nucleosides and the synthesis of RNA in Tetrahymena thermophila were examined following amino acid starvation. Omission of leucine, phenylalanine, or arginine from the medium resulted in a rapid decrease in the incorporation of [3H]uridine into the acid-soluble pool and acid-insoluble material (RNA). Amino acid starvation inhibited the uptake of all ribo- and deoxyribonucleosides tested but did not affect the uptake of amino acids or glucose. In addition, under the conditions used, the omission of an amino acid did not result in a large decrease in amino acid incorporation into total protein. Treatment of cells with cycloheximide or emetine gave results similar to the effects of amino acid starvation, but in these experiments the inhibition of protein synthesis was essentially complete. Nucleotide pool sizes were also measured following amino acid starvation. ATP and UTP levels were essentially unchanged, but the dTTP pool size was decreased by 40%. The decrease in RNA synthesis in vivo in the absence of an essential amino acid was reflected in the endogenous RNA synthetic activity of isolated nuclei. However, when solubilized RNA polymerase activity was measured with calf thymus DNA as template, no significant difference was observed between control and amino acid-starved cells.     

Phage selection for site-specific incorporation of unnatural amino acids into proteins in vivo.

The development of a method for the site-specific incorporation of unnatural amino acids into proteins in vivo would significantly facilitate studies of the cellular function of proteins, as well as make possible the synthesis of proteins with novel structures and activities. Our approach to this problem consists of the generation of amber suppressor tRNA/aminoacyl-tRNA synthetase pairs that are not catalytically competent with all the endogenous Escherichia coli tRNAs and aminoacyl-tRNA synthetases, followed by directed evolution of such orthogonal aminoacyl-tRNA synthetases to alter their amino acid specificities. To evolve the desired amino acid specificity, a direct selection for site-specific incorporation of unnatural amino acids into a reporter epitope displayed on the surface of M13 phage has been developed and characterized. Under simulated selection conditions, phage particles displaying aspartate were enriched over 300-fold from a pool of phage displaying asparagine using monoclonal antibodies raised against the aspartate-containing epitope. The direct phage selection offers high specificity for the amino acid of interest, eliminating the potential for contamination with synthetases active towards wild-type amino acids in multiple rounds of selection.     

Myocardial aminoacyl-transfer-ribonucleic acid synthetase and aminoacyl-transferring enzyme activity

The properties of cytoplasmic aminoacyl-tRNA synthetase and aminoacyl-transferring enzymes in the myocardium were examined and methods for the assay of the activity of these enzyme systems were developed. Aminoacyl-tRNA synthetase activity was measured from the rate of incorporation of ¹⁴C-labelled amino acid into aminoacyl-tRNA. Transferase activity was measured from the rate of incorporation of amino[¹⁴C]acyl-tRNA into protein in the presence of a standard preparation of hepatic ribosomes. Aminoacyl-tRNA synthetase activity is labile once the heart has been homogenized, whereas transferase activity is stable. The source of energy for synthetase activity is ATP; that for transferase is GTP. Transferase activity was inhibited by puromycin and stimulated by dithiothreitol, whereas synthetase activity was unaffected.