REACTIONS OF FREE AND tRNA BOUND GLUTAMATE AND GLUTAMINE

—[¹⁴C]-Glutamate and [¹⁴C]-glutamine were incorporated into calf brain tRNA in the presence of homologous aminoacyl-tRNA synthetases. When the tRNAs were then deaminoacylated and chromatographed, a number of radioactive products were found in addition to the original amino acids. One of the products of glutamate transformation was identified to be glutamine. Formation of the radioactive products of glutamate in the presence and absence of tRNA indicated that glutamine was produced from glutamate at the level of the free amino acid followed by the incorporation of both substances into tRNA. Examination of the products of deaminoacylation of glutaminyl-tRNA showed that glutamine underwent structural alterations at the level of the aminoacyl-tRNAs to give rise to a cyclic derivative of glutarimide. This reaction was specific for glutamine, and constituted approximately 15 per cent of the total radioactivity in the deaminoacylation products of glutaminyl-tRNA.     

A method for the analysis of tRNA patterns in Drosophila melanogaster using an amino acid analyser

Using tRNA and aminoacyl-tRNA synthetase preparations from Drosophila melanogaster, a method has been developed for simultaneously estimating levels of at least 15 different species of aminoacyl-tRNA. ¹⁴C-labeled aminoacyl-tRNA, which is formed during a single incubation of tRNA with a mixture of 15 ¹⁴C-labeled amino acids, is purified, hydrolysed, and the composition of the mixture of ¹⁴C-labeled amino acids so obtained is determined using an Amino Acid Analyser.The sensitivity of the method and the reproducibility of the results obtained are such that it is suitable for detecting changes in tRNA patterns in comparative studies.     

STRUCTURAL ALTERATIONS OF AMINO ACIDS AT THE LEVEL OF AMINOACYL-tRNAS: TRANSFORMATION OF DICARBOXYLIC AMINO ACIDS

Abstract— Radioactive glutamate, glutamine, aspartate and asparagine were incorporated into calf brain tRNA in the presence of homologous aminoacyl-tRNA synthetases. When the aminoacyl-tRNAs were deaminoacylated and the products chromatographed in the phenol solvent, the glutaminyl-and asparaginyl-tRNAs showed two products GnP₂ and AnP₂ respectively, in- addition to the original amino acids. These new substances moved close to the solvent front in contrast to glutamine and asparagine which had much lower R _F values. Attachment of the amino acids to tRNA appeared to be a prerequisite for the formation of these substances, since they were not found in the reaction mixture used for aminoacylation in the absence of incubation or on omission of tRNA or when tRNA was degraded by RNase. Application of the deaminoacylation procedure to pure amino acids also failed to lead to their formation. In an other series of experiments, the dicarboxylic aminoacyl-tRNAs were hydrolysed with pancreatic RNase and then analysed by high voltage paper electrophoresis. Again, the glutaminyl- and asparaginyl-tRNAs showed two new components, GnE₃ and AnE₃, in addition to the expected glutaminyl- and asparaginyladenosines. GnE₃ and AnE₃ exhibited much faster electrophoretic mobilities in the direction of the cathode than the adenosine derivatives of the original amino acids and thus appeared to be more positively charged. The presence of these new compounds in the products of deaminoacylation or in R Nase hydrolysates was specific to glutaminyl- and asparaginyl-tRNAs and did not occur in the case of either glutamyl or aspartyl-tRNAs, indicating that the amide group was probably involved in the transformation reaction.     

Specificity of the ribosomal A site for aminoacyl-tRNAs

Although some experiments suggest that the ribosome displays specificity for the identity of the esterified amino acid of its aminoacyl-tRNA substrate, a study measuring dissociation rates of several misacylated tRNAs containing the GAC anticodon from the A site showed little indication for such specificity. In this article, an expanded set of misacylated tRNAs and two 2′-deoxynucleotide-substituted mRNAs are used to demonstrate the presence of a lower threshold in k_off values for aa-tRNA binding to the A site. When a tRNA binds sufficiently well to reach this threshold, additional stabilizing effects due to the esterified amino acid or changes in tRNA sequence are not observed. However, specificity for different amino acid side chains and the tRNA body is observed when tRNA binding is sufficiently weaker than this threshold. We propose that uniform aa-tRNA binding to the A site may be a consequence of a conformational change in the ribosome, induced by the presence of the appropriate combination of contributions from the anticodon, amino acid and tRNA body.     

STRUCTURAL ALTERATIONS OF AMINO ACIDS AT THE LEVEL OF AMINOACYL-tRNAS: IDENTIFICATION OF THE TRANSFORMATION PRODUCTS OF DICARBOXYLIC AMINO ACIDS

Abstract— Glutamyl-, glutaminyl-, aspartyl- and asparaginyl-tRNAs were separated into different isoacceptor species by reverse phase column chromatography. RNase hydrolysates of any of the isoacceptor [¹⁴C]aminoacyl-tRNAs for a given amino acid gave radioactivity profiles, on paper electrophoresis, very similar to unfractionated tRNA. This suggested a lack of tRNA specificity for the transformation reaction involving the aminoacyl moieties of asparaginyl and glutaminyl-tRNAs. GnP₂ and AnP₂ detected in the products of deaminoacylation of glutaminyl and asparaginyl-tRNA showed a number of properties in common with GnE₃ and AnE₃ present in the RNase hydrolysates of the same tRNAs. Thus, GnP₂ and GnE₃ chromatographed in the same position in the phenol: water solvent and both yielded glutamate on acid hydrolysis and a mixture of glutamine and isoglutamine on alkaline hydrolysis. Similarly, AnP₂ and AnE₃ had the same R_F value in phenol :water chromatography and gave aspartate or a mixture of asparagine and isoasparagine when hydrolyzed with acid or alkali. On the basis of these results and other evidence, GnP₂ and GnE₃ were assigned the structure, α-aminoglutarimide; AnP₂ and AnE₃ were identified as α-aminosuccinimide. These cyclic compounds are presumed to be formed by nucleophilic attack of the amide nitrogen of asparagine or glutamine on the carbon of the aminoacyl ester carbonyl group. The cyclization-deesterification appeared to be facilitated by RNase hydrolysis of aminoacyl-tRNA indicating that the aminoacyl-tRNA is probably more resistant to this reaction than aminoacyladenosine. Neither the imides nor the amino acid isoamides were detected in the reaction mixture in which aminoacylation of tRNA was performed, suggesting that a mechanism may exist for inhibition of the cyclization reaction under conditions of active aminoacylation.     

An efficient protocol for incorporation of an unnatural amino acid in perdeuterated recombinant proteins using glucose-based media

The in vivo incorporation of unnatural amino acids into proteins is a well-established technique requiring an orthogonal tRNA/aminoacyl-tRNA synthetase pair specific for the unnatural amino acid that is incorporated at a position encoded by a TAG amber codon. Although this technology provides unique opportunities to engineer protein structures, poor protein yields are usually obtained in deuterated media, hampering its application in the protein NMR field. Here, we describe a novel protocol for incorporating unnatural amino acids into fully deuterated proteins using glucose-based media (which are relevant to the production, for example, of amino acid-specific methyl-labeled proteins used in the study of large molecular weight systems). The method consists of pre-induction of the pEVOL plasmid encoding the tRNA/aminoacyl-tRNA synthetase pair in a rich, H₂O-based medium prior to exchanging the culture into a D₂O-based medium. Our protocol results in high level of isotopic incorporation (~95%) and retains the high expression level of the target protein observed in Luria–Bertani medium.     

Isolation of isoaccepting tRNAs

The N-hydroxysuccinimide ester of succinated polyethylene oxide (polyethylene glycol 6000) has been prepared. The ester has been used to make the N-acyl derivatives of valyl-tRNA and phenylalanyl-tRNA from E. coli K-12. Because of the large molecular weight, high solubility in phenol, and the binding to Corning porous glass of polyethylene oxide, the acyl derivative, N-(succinated polyethylene oxide)-aminoacyl-tRNA, has been separated from unreacted tRNA. Since the reaction is reasonably specific for the amino group of the amino acid, large purifications have been obtained for tRNA_val and tRNA_phe. Evidence is presented to show that the ester can react with tRNA at a slow rate. The limitations on the purification due to this reaction are quantitatively evaluated. The highest ratios, pmoles aminoacyl-tRNA/ OD₂₆₀, obtained for valyl-tRNA and phenylalanyl-tRNA were 800 and 360.     

An archaebacteria-derived glutamyl-tRNA synthetase and tRNA pair for unnatural amino acid mutagenesis of proteins in Escherichia coli

The addition of novel amino acids to the genetic code of Escherichia coli involves the generation of an aminoacyl-tRNA synthetase and tRNA pair that is ‘orthogonal’, meaning that it functions independently of the synthetases and tRNAs endogenous to E.coli. The amino acid specificity of the orthogonal synthetase is then modified to charge the corresponding orthogonal tRNA with an unnatural amino acid that is subsequently incorporated into a polypeptide in response to a nonsense or missense codon. Here we report the development of an orthogonal glutamic acid synthetase and tRNA pair. The tRNA is derived from the consensus sequence obtained from a multiple sequence alignment of archaeal tRNA^Glu sequences. The glutamyl-tRNA synthetase is from the achaebacterium Pyrococcus horikoshii. The new orthogonal pair suppresses amber nonsense codons with an efficiency roughly comparable to that of the orthogonal tyrosine pair derived from Methanococcus jannaschii, which has been used to selectively incorporate a variety of unnatural amino acids into proteins in E.coli. Development of the glutamic acid orthogonal pair increases the potential diversity of unnatural amino acid structures that may be incorporated into proteins in E.coli.     

Variations in activity of aminoacyl-tRNA synthetases as a function of development in Bacillus subtilis

Extracts from Bacillus sublilis cells at various stages of growth and spores were assayed for aminoacyl-tRNA synthetase and methionyl-tRNA transformylase activity. There was no major change in any synthetase activity or in methionyl-tRNA transformylase activity during the sporulation cycle, which implies that these are not sporulation induced enzymes. However, extracts from B. subtilis cultures showed a burst of activity of aminoacyl-tRNA synthetases during exponential growth.Preparations from dormant spores possessed the same kinds of aminoacyl-tRNA synthetase activities as vegetative cells for all the amino acids which were studied. Spores also contained methionyl-tRNA transformylases. These findings suggest that spores ought to be able to aminoacylate tRNA and formylate the initiator. N-formylmethionyl-tRNA, immediately upon germination.     

Purification and characterization of an aminoacyl-tRNA hydrolase from the filamentous fungus Fusarium culmorum

This paper describes the partial purification and characterization of an enzyme present in the fungus Fusarium culmorum which hydrolyzes aminoacyl-tRNA by splitting the ester linkage between the amino acid and the tRNA molecule. The enzyme has a molecular weight of 46 000 as estimated by gel filtration in Sephadex G-100, is maximally active in the presence of a divalent cation (Mg²⁺ or Mn²⁺) and has a pH maximum around neutrality. The enzyme is quite unspecific, hydrolyzing with practically the same efficiency aminoacyl-tRNAs with the amino group either free or substituted. The K_m of the enzyme for phenylalanyl-tRNA^Phe, and N-acetylphenylalanyl-tRNA is around 1 μM. Binding to the 80 S ribosomes but not to the 40 S ribosomal subunit renders the substrate resistant to the action of the hydrolase. The characteristics of this hydrolase are similar to those found for the aminoacyl-tRNA hydrolase of Artemia, and different from the more widely distributed peptidyl-tRNA hydrolases and other more specific aminoacyl-tRNA hydrolases found in different organisms.     

Exit Strategies for Charged tRNA from GluRS

For several class I aminoacyl-tRNA synthetases (aaRSs), the rate-determining step in aminoacylation is the dissociation of charged tRNA from the enzyme. In this study, the following factors affecting the release of the charged tRNA from aaRSs are computationally explored: the protonation states of amino acids and substrates present in the active site, and the presence and the absence of AMP and elongation factor Tu.Through molecular modeling, internal pK_a calculations, and molecular dynamics simulations, distinct, mechanistically relevant post-transfer states with charged tRNA bound to glutamyl-tRNA synthetase from Thermus thermophilus (Glu-tRNA^Glu) are considered. The behavior of these nonequilibrium states is characterized as a function of time using dynamical network analysis, local energetics, and changes in free energies to estimate transitions that occur during the release of the tRNA. The hundreds of nanoseconds of simulation time reveal system characteristics that are consistent with recent experimental studies.Energetic and network results support the previously proposed mechanism in which the transfer of amino acid to tRNA is accompanied by the protonation of AMP to H-AMP. Subsequent migration of proton to water reduces the stability of the complex and loosens the interface both in the presence and in the absence of AMP. The subsequent undocking of AMP or tRNA then proceeds along thermodynamically competitive pathways. Release of the tRNA acceptor stem is further accelerated by the deprotonation of the α-ammonium group on the charging amino acid. The proposed general base is Glu41, a residue binding the α-ammonium group that is conserved in both structure and sequence across nearly all class I aaRSs. This universal handle is predicted through pK_a calculations to be part of a proton relay system for destabilizing the bound charging amino acid following aminoacylation. Addition of elongation factor Tu to the aaRS·tRNA complex stimulates the dissociation of the tRNA core and the tRNA acceptor stem.     

Essentiality Assessment of Cysteinyl and Lysyl-tRNA Synthetases of Mycobacterium smegmatis

Discovery of mupirocin, an antibiotic that targets isoleucyl-tRNA synthetase, established aminoacyl-tRNA synthetase as an attractive target for the discovery of novel antibacterial agents. Despite a high degree of similarity between the bacterial and human aminoacyl-tRNA synthetases, the selectivity observed with mupirocin triggered the possibility of targeting other aminoacyl-tRNA synthetases as potential drug targets. These enzymes catalyse the condensation of a specific amino acid to its cognate tRNA in an energy-dependent reaction. Therefore, each organism is expected to encode at least twenty aminoacyl-tRNA synthetases, one for each amino acid. However, a bioinformatics search for genes encoding aminoacyl-tRNA synthetases from Mycobacterium smegmatis returned multiple genes for glutamyl (GluRS), cysteinyl (CysRS), prolyl (ProRS) and lysyl (LysRS) tRNA synthetases. The pathogenic mycobacteria, namely, Mycobacterium tuberculosis and Mycobacterium leprae, were also found to possess two genes each for CysRS and LysRS. A similar search indicated the presence of additional genes for LysRS in gram negative bacteria as well. Herein, we describe sequence and structural analysis of the additional aminoacyl-tRNA synthetase genes found in M. smegmatis. Characterization of conditional expression strains of Cysteinyl and Lysyl-tRNA synthetases generated in M. smegmatis revealed that the canonical aminoacyl-tRNA synthetase are essential, while the additional ones are not essential for the growth of M. smegmatis.     

Structure of Escherichia coli Arginyl-tRNA Synthetase in Complex with tRNAArg: Pivotal Role of the D-loop

Aminoacyl-tRNA synthetases are essential components in protein biosynthesis. Arginyl-tRNA synthetase (ArgRS) belongs to the small group of aminoacyl-tRNA synthetases requiring cognate tRNA for amino acid activation. The crystal structure of Escherichia coli (Eco) ArgRS has been solved in complex with tRNA^Arg at 3.0-Å resolution. With this first bacterial tRNA complex, we are attempting to bridge the gap existing in structure–function understanding in prokaryotic tRNA^Arg recognition. The structure shows a tight binding of tRNA on the synthetase through the identity determinant A20 from the D-loop, a tRNA recognition snapshot never elucidated structurally. This interaction of A20 involves 5 amino acids from the synthetase. Additional contacts via U20a and U16 from the D-loop reinforce the interaction. The importance of D-loop recognition in EcoArgRS functioning is supported by a mutagenesis analysis of critical amino acids that anchor tRNA^Arg on the synthetase; in particular, mutations at amino acids interacting with A20 affect binding affinity to the tRNA and specificity of arginylation. Altogether the structural and functional data indicate that the unprecedented ArgRS crystal structure represents a snapshot during functioning and suggest that the recognition of the D-loop by ArgRS is an important trigger that anchors tRNA^Arg on the synthetase. In this process, A20 plays a major role, together with prominent conformational changes in several ArgRS domains that may eventually lead to the mature ArgRS:tRNA complex and the arginine activation. Functional implications that could be idiosyncratic to the arginine identity of bacterial ArgRSs are discussed.     

Engineering of an Orthogonal Aminoacyl-tRNA Synthetase for Efficient Incorporation of the Non-natural Amino Acid O-Methyl-L-tyrosine using Fluorescence-based Bacterial Cell Sorting

We describe a strategy for the rapid selection of mutant aminoacyl-tRNA synthetases (aaRS) with specificity for a novel amino acid based on fluorescence-activated cell sorting of transformed Escherichia coli using as reporter the enhanced green fluorescent protein (eGFP) whose gene carries an amber stop codon (TAG) at a permissive site upstream of the fluorophore. To this end, a one-plasmid expression system was developed encoding an inducible modified Methanocaldococcus jannaschii (Mj) tyrosyl-tRNA synthetase, the orthogonal cognate suppressor tRNA, and eGFP_UAG in an individually regulatable fashion. Using this system a previously described aaRS with specificity for O-methyl-L-tyrosine (MeTyr) was engineered for 10-fold improved incorporation of the foreign amino acid by selection from a mutant library, prepared by error-prone as well as focused random mutagenesis, for MeTyr-dependent eGFP fluorescence. Applying alternating cycles of positive and negative fluorescence-activated bacterial cell sorting in the presence or in the absence, respectively, of the foreign amino acid was crucial to select for high specificity of MeTyr incorporation. The optimized synthetase was used for the preparative expression of a modified uvGFP carrying MeTyr at position 66 as part of its fluorophore. This biosynthetic protein showed quantitative incorporation of the non-natural amino acid, as determined by mass spectrometry, and it revealed a unique emission spectrum due to the altered chemical structure of its fluorophore. Our combined genetic/selection system offers advantages over earlier approaches that relied wholly or in part on antibiotic selection schemes, and it should be generally useful for the engineering and optimization of orthogonal aaRS/tRNA pairs to incorporate non-natural amino acids into recombinant proteins.     

Separation of aminoacyl-transfer RNAs by polyacrylamide gel electrophoresis

A polyacrylamide gel electrophoresis system for separating $\text{E.}$$\text{coli}$ tRNAs and aminoacyl-tRNAs is described. The tRNA was separated into 6 discrete bands which contained varyin aamounts of tRNA and therefore varying numbers of tRNA species. In order to locate specific tRNAs, tRNA was charged with a ¹⁴C amino acid and the aminoacyl-tRNA was located by autoradiography. With several amino acids, 2 isoaccepting species were found. In total, 30 aminoacyl-tRNAs were located.     

Quality control in tRNA charging -- editing of homocysteine

All living organisms conduct protein synthesis with a high degree of accuracy maintained in the transmission and flow of information from a gene to protein product. One crucial 'quality control' point in maintaining a high level of accuracy is the selectivity by which aminoacyl-tRNA synthetases furnish correctly activated amino acids, attached to tRNA species, as the building blocks for growing protein chains. When differences in binding energies of amino acids to an aminoacyl-tRNA synthetase are inadequate, editing is used as a major determinant of enzyme selectivity. Some incorrect amino acids are edited at the active site before the transfer to tRNA (pre-transfer editing), while others are edited after transfer to tRNA at a separate editing site (post-transfer editing). Access of natural non-protein amino acids, such as homocysteine, homoserine, or ornithine to the genetic code is prevented by the editing function of aminoacyl-tRNA synthetases. Disabling editing function leads to tRNA mischarging errors and incorporation of incorrect amino acids into protein, which is detrimental to cell homeostasis and inhibits growth. Continuous homocysteine editing by methionyl-tRNA synthetase, resulting in the synthesis of homocysteine thiolactone, is part of the process of tRNA aminoacylation in living organisms, from bacteria to man. Excessive homocysteine thiolactone synthesis in hyperhomocysteinemia caused by genetic or nutritional deficiencies is linked to human vascular and neurological diseases.     

The human tRNA(m(2)(2)G(26))dimethyltransferase: functional expression and characterization of a cloned hTRM1 gene

This paper presents the first example of a complete gene sequence coding for and expressing a biologically functional human tRNA methyltransferase: the hTRM1 gene product tRNA(m²₂G)dimethyltransferase. We isolated a human cDNA (1980 bp) made from placental mRNA coding for the full-length (659 amino acids) human TRM1 polypeptide. The sequence was fairly similar to Saccharomyces cerevisiae Trm1p, to Caenorhabditis elegans TRM1p and to open reading frames (ORFs) found in mouse and a plant (Arabidopsis thaliana) DNA. The human TRM1 gene was expressed at low temperature in Escherichia coli as a functional recombinant protein, able to catalyze the formation of dimethylguanosine in E.coli tRNA in vivo. It targeted solely position G₂₆ in T7 transcribed spliced and unspliced human tRNA^Tyr in vitro and in yeast trm1 mutant tRNA. Thus, the human TRM1 protein is a tRNA(m²₂G₂₆)dimethyltransferase. Compared with yeast Trm1p, hTRM1p has a C-terminal protrusion of ~90 amino acids which shows similarities to a mouse protein related to RNA splicing. A deletion of these 90 C-terminal amino acids left the modification activity in vitro intact. Among point mutations in the hTRM1 gene, only those located in conserved regions of hTRM1p completely eliminated modification activity.     

The determination of tRNALeu recognition nucleotides for Escherichia coli L/F transferase

Escherichia coli leucyl/phenylalanyl-tRNA protein transferase catalyzes the tRNA-dependent post-translational addition of amino acids onto the N-terminus of a protein polypeptide substrate. Based on biochemical and structural studies, the current tRNA recognition model by L/F transferase involves the identity of the 3′ aminoacyl adenosine and the sequence-independent docking of the D-stem of an aminoacyl-tRNA to the positively charged cluster on L/F transferase. However, this model does not explain the isoacceptor preference observed 40 yr ago. Using in vitro-transcribed tRNA and quantitative MALDI-ToF MS enzyme activity assays, we have confirmed that, indeed, there is a strong preference for the most abundant leucyl-tRNA, tRNA^Leu (anticodon 5′-CAG-3′) isoacceptor for L/F transferase activity. We further investigate the molecular mechanism for this preference using hybrid tRNA constructs. We identified two independent sequence elements in the acceptor stem of tRNA^Leu (CAG)—a G₃:C₇₀ base pair and a set of 4 nt (C₇₂, A₄:U₆₉, C₆₈)—that are important for the optimal binding and catalysis by L/F transferase. This maps a more specific, sequence-dependent tRNA recognition model of L/F transferase than previously proposed.