A mammalian tryptophanyl-tRNA synthetase shows little homology to prokaryotic synthetases but near identity with mammalian peptide chain release factor

Proteomic analysis of the sheep caruncular and intercaruncular endometrium reveals changes in functional proteins crucial for the establishment of pregnancy

The expression and regulation of endometrial proteins are crucial for conceptus implantation and development. However, little is known about site-specific proteome profiles of the mammalian endometrium during the peri-implantation period. We utilised a two-dimensional gel electrophoresis/mass spectrometry-based proteomics approach to compare and identify differentially expressed proteins in sheep endometrium. Caruncular and intercaruncular endometrium were collected on days 12 (C12) and 16 (C16) of the oestrous cycle and at three stages of pregnancy corresponding to conceptus pre-attachment (P12), implantation (P16) and post-implantation (P20). Abundance and localisation changes in differentially expressed proteins were determined by western blot and immunohistochemistry. In caruncular endometrium, 45 protein spots (5% of total spots) altered between day 12 of pregnancy (P12) and P16 while 85 protein spots (10% of total spots) were differentially expressed between P16 and C16. In intercaruncular endometrium, 31 protein spots (2% of total spots) were different between P12 and P16 while 44 protein spots (4% of total spots) showed differential expression between C12 and C16. The pattern of protein changes between caruncle and intercaruncle sites was markedly different. Among the protein spots with implantation-related changes in volume, 11 proteins in the caruncular endometrium and six proteins in the intercaruncular endometrium, with different functions such as protein synthesis and degradation, antioxidant defence, cell structural integrity, adhesion and signal transduction, were identified. Our findings highlight the different but important roles of the caruncular and intercaruncular proteins during early pregnancy.

RNA-protein interactions at the initial and terminal stages of protein biosynthesis as investigated by Lev Kisselev (on the occasion of his 70th anniversary)

This review highlights studies by Lev L. Kisselev and his colleagues on the initial and terminal stages of protein biosynthesis, which cover the period of the last 45 years (1961-2006). They investigated spatial structure of tRNAs, structure and functions of aminoacyl-tRNA-synthetases of higher organisms, and the final step of protein synthesis, termination of translation. L. Kisselev and his team have made three major contributions to these fields of molecular biology; (i) they proposed the hypothesis on the role of anticodon triplet of tRNA in recognition by cognate aminoacyl-tRNA synthetase, which has been experimentally confirmed and is now included in textbooks; (ii) identified primary structures and functions of two eukaryotic protein factors (eRF1 and eRF3) playing a pivotal role in translation termination; (iii) characterized a structural basis for stop codon recognition by eRF1 within the ribosome and discovered the negative structural elements of eRF1, limiting its recognition of one or two stop-codons.

Mapping and molecular characterization of novel monoclonal antibodies to conformational epitopes on NH2 and COOH termini of mammalian tryptophanyl-tRNA synthetase reveal link of the epitopes to aggregation and Alzheimer's disease

Tryptophanyl-tRNA synthetase (TrpRS) is an interferon-induced phosphoprotein with autoantigenic and cytokine activities detected in addition to its canonical function in tRNA aminoacylation. The availability of monoclonal antibodies (mAbs) specific for TrpRS is important for development of tools for TrpRS monitoring. A molecular characterization of two mAbs raised in mice, using purified, enzymatically active bovine TrpRS as the inoculating antigen, is presented in this report. These IgG1 antibodies are specific for bovine, human and rabbit but not E. coli TrpRS. Immunoreactivity and specificity of mAbs were verified with purified recombinant hTrpRS expressed in E. coli and TrpRS-derived synthetic peptides. One of the mAbs, 9D7 is able to disaggregate fibrils formed by Ser32-Tyr50 TrpRS-peptide. Epitope mapping revealed that disaggregation ability correlates with binding of 9D7 to this peptide in ELISA and immunocytochemistry. This epitope covers a significant part of N-terminal extension that suggested to be proteolytically deleted in vivo from the full-length TrpRS whereas remaining COOH-fragment possesses a cytokine activity. For epitope mapping of mAb 6C10, the affinity selected phage-displayed peptides were used as a database for prediction of conformational discontinuous epitopes within hTrpRS crystal structure. Using computer algorithm, this epitope is attributed to COOH-terminal residues Asp409-Met425. In immunoblotting, the 6C10 mAb reacts preferably with (i) oligomer than monomer, and (ii) bound than free TrpRS forms. The hTrpRS expression was shown to correlate with growth rates of neuroblastoma and pancreatic cancer cells. Immunohistochemically both mAbs revealed extracellular plaque-like aggregates in hippocampus of Alzheimer's disease brain.

An interferon-induced protein with release factor activity is a tryptophanyl-tRNA synthetase

Interferon gamma induces expression of a protein termed IFP 53 according to its molecular weight of 53 kDa. IFP 53 shows significant sequence homology to rabbit peptide chain release factor as well as to bovine tryptophanyl-tRNA synthetase. IFP 53 has been shown to possess release factor activity for the UGA stop codon. We demonstrate here, by using a recombinant IFP 53 fusion protein, that IFP 53 tryptophanylates tRNA. These data indicate that IFP 53 is a protein with two activities: peptide chain termination and aminoacylation.

Tryptamine-mediated stabilization of tryptophanyl-tRNA synthetase in human cervical carcinoma cell line

Tryptamine is an endogenous neuroactive metabolite of tryptophan. Interpretation of the function of this bioamine, however, is restricted to manipulation with tryptamine synthetic pathways. Meanwhile, tryptamine is a potent inhibitor of protein biosynthesis, via the competitive inhibition of tryptophanyl-tRNA synthetase (TrpRS). The influence of the persistent tryptamine inhibition on the half-life and cellular content of TrpRS was examined by chase labeling of HeLa cells and the tryptamine-resistant subline with [35S]methionine. The results indicate that long-term tryptamine treatment of HeLa cells led to a significant increase in the half-life of TrpRS while the content, in vivo phosphorylation and gene dose of TrpRS were unchanged. These findings suggest that survival of drug-resistant cells may not be due to TrpRS gene amplification, but to stabilization of TrpRS. It was shown that tryptamine is an effective inhibitor of HeLa cell growth. In contrast to the well-characterized antineoplastic compounds, conferring a many hundred-fold elevated drug resistance to tumor cells, resistance to tryptamine at very low levels was difficult to achieve, i.e. the 2-fold resistant subline was selected after 19 months of treatment of HeLa cells with gradually increasing concentrations of tryptamine. The tryptamine-resistant HeLa subline exhibited a slower growth rate than the original HeLa line when similar concentrations of both cell populations were seeded on the plates. A low tryptamine resistance and a lack of TrpRS gene amplification were observed in two tryptamine-resistant HeLa sublines and three Chinese hamster sublines. The role of TrpRS in oncogenesis and the perspective for tryptamine as a potential anti-cancer drug are discussed.

A multifunctional repeated motif is present in human bifunctional tRNA synthetase

Tandem repeats located in the human bifunctional glutamyl-prolyl-tRNA synthetase (EPRS) have been found in many different eukaryotic tRNA synthetases and were previously shown to interact with another distinct repeated motifs in human isoleucyl-tRNA synthetase. Nuclear magnetic resonance and differential scanning calorimetry analyses of an isolated EPRS repeat showed that it consists of a helix-turn-helix with a melting temperature of 59 degrees C. Specific interaction of the EPRS repeats with those of isoleucyl-tRNA synthetase was confirmed by in vitro binding assays and shown to have a dissociation constant of approximately 2.9 microM. The EPRS repeats also showed the binding activity to the N-terminal motif of arginyl-tRNA synthetase as well as to various nucleic acids, including tRNA. Results of the present work suggest that the region comprising the repeated motifs of EPRS provides potential sites for interactions with various biological molecules and thus plays diverse roles in the cell.

Genetic code in evolution: switching species-specific aminoacylation with a peptide transplant

The genetic code is established in aminoacylation reactions whereby amino acids are joined to tRNAs bearing the anticodons of the genetic code. Paradoxically, while the code is universal there are many examples of species-specific aminoacylations, where a tRNA from one taxonomic domain cannot be acylated by a synthetase from another. Here we consider an example where a human, but not a bacterial, tRNA synthetase charges its cognate eukaryotic tRNA and where the bacterial, but not the human, enzyme charges the cognate bacterial tRNA. While the bacterial enzyme has less than 10% sequence identity with the human enzyme, transplantation of a 39 amino acid peptide from the human into the bacterial enzyme enabled the latter to charge its eukaryotic tRNA counterpart in vitro and in vivo. Conversely, substitution of the corresponding peptide of the bacterial enzyme for that of the human enabled the human enzyme to charge bacterial tRNA. This peptide element discriminates a base pair difference in the respective tRNA acceptor stems. Thus, functionally important co-adaptations of a synthetase to its tRNA act as small modular units that can be moved across taxonomic domains and thereby preserve the universality of the code.

A mammalian tryptophanyl-tRNA synthetase is associated with protein kinase activity

Bovine Trp-tRNA synthetase is a dimer with subunit molecular mass of 60 kDa (p60) which catalyzes ATP-dependent formation of tryptophanyl-tRNA. Evidence is presented that Trp-tRNA synthetase whose homogeneity had been proven by SDS/PAGE and silver staining of the gel is autophosphorylated in vitro. Anti-(Trp-tRNA synthetase) antibodies, whose specificity was verified by using a combination of different approaches, were able to effectively inhibit and immunoprecipitate the Trp-tRNA-synthetase-associated kinase activity. The two-dimensional tryptic phosphopeptide map of autophosphorylated p60 Trp-tRNA synthetase was found to be similar to that of its major 40-kDa degradation fragment bearing resemblance to previously demonstrated unlabeled peptide patterns of the Trp-tRNA synthetase forms. Trp-tRNA synthetase which had undergone denaturation during SDS/PAGE, regained serine/threonine specific protein kinase activity (PK 60) after guanidine treatment. Trp-tRNA synthetase induced phosphorylation of specific substrate such as 100-kDa protein in non-immune but not in anti-(Trp-tRNA synthetase) sera which distinguishes Trp-tRNA-synthetase-associated kinase from other protein kinases. Sequence analysis permitted the identification of regions of bovine Trp-tRNA synthetase sharing similarity with the catalytic domains of known protein kinases. These findings suggest that PK 60 and Trp-tRNA synthetase (p60) are either closely related or identical.

A root-specific iron-regulated gene of tomato encodes a lysyl-tRNA-synthetase-like protein

The tomato mutant chloronerva exhibits a defect in iron-uptake regulation. Despite high apoplastic and symplastic iron concentrations, the mutant shows characteristic symptoms of iron deficiency. Using a subtractive-hybridisation approach, we have screened for cDNA clones specific for genes with altered expression in wild-type versus mutant root tissue. Based on this clone collection, we have isolated and characterised a 2075-bp full-length cDNA encoding a lysyl-tRNA-synthetase-like protein. The corresponding gene is localised as a single copy on chromosome 10. Its expression is strongly induced by changes in the iron status of the plant. This iron-dependent regulation is superimposed upon a strict root specificity of gene expression. Possible functions of the gene product other than in protein biosynthesis will be discussed.

Identification and expression of the Saccharomyces cerevisiae cytoplasmic tryptophanyl-tRNA synthetase gene

The enzymes that aminoacylate tRNAs have been studied extensively and can be organized into two distinct classes based on signature sequences and the position of aminoacylation. The class I enzymes have canonical HIGH and KMSKS sequences as part of a Rossman fold nucleotide-binding site. The tryptophan-specific enzymes have been placed in class I based on analysis of the cognate genes from Escherichia coli, B. stearothermophilus, B. taurus, and Homo sapiens. An unidentified open reading frame (ORF) on Saccharomyces cerevisiae chromosome XV, HRE342, has 46% identity with the bovine tryptophanyl-tRNA synthetase and possesses the appropriate signature sequences. The predicted molecular weight of the putative HRE342 protein also closely matched the expected monomer size of the S. cerevisiae enzyme. The HRE342 ORF plus about 250 bp of 5' and 3' flanking sequence was amplified by polymerase chain reaction, cloned into a 2 mu based vector, and transformed into a host strain, S. cerevisiae JG369.3B. Nucleotide sequence analysis of the clone confirmed the presence of HRE342. Extracts from transformed yeast have a 30- to 100-fold increase in specific activity of the tryptophanyl-tRNA synthetase. An HRE342 locus in a diploid strain, PTY33XPTY44, was disrupted with a LEU2 insert. Sporulation and tetrad analysis of the HRE342::LEU2 strain demonstrated that HRE342 is an essential gene. We conclude that HRE342 is the S. cerevisiae gene encoding the cytoplasmic tryptophanyl-tRNA synthetase, WRS1. A search of the Saccharomyces Genome Database using amino acid sequences from other eukaryotic aminoacyl-tRNA synthetase suggests there is sufficient similarity to identify both class I and class II genes.

Interaction between human tRNA synthetases involves repeated sequence elements

Aminoacyl-tRNA synthetases (tRNA synthetases) of higher eukaryotes form a multiprotein complex. Sequence elements that are responsible for the protein assembly were searched by using a yeast two-hybrid system. Human cytoplasmic isoleucyl-tRNA synthetase is a component of the multi-tRNA synthetase complex and it contains a unique C-terminal appendix. This part of the protein was used as bait to identify an interacting protein from a HeLa cDNA library. The selected sequence represented the internal 317 amino acids of human bifunctional (glutamyl- and prolyl-) tRNA synthetase, which is also known to be a component of the complex. Both the C-terminal appendix of the isoleucyl-tRNA synthetase and the internal region of bifunctional tRNA synthetase comprise repeating sequence units, two repeats of about 90 amino acids, and three repeats of 57 amino acids, respectively. Each repeated motif of the two proteins was responsible for the interaction, but the stronger interaction was shown by the native structures containing multiple motifs. Interestingly, the N-terminal extension of human glycyl-tRNA synthetase containing a single motif homologous to those in the bifunctional tRNA synthetase also interacted with the C-terminal motif of the isoleucyl-tRNA synthetase although the enzyme is not a component of the complex. The data indicate that the multiplicity of the binding motif in the tRNA synthetases is necessary for enhancing the interaction strength and may be one of the determining factors for the tRNA synthetases to be involved in the formation of the multi-tRNA synthetase complex.

Tryptophanyl-tRNA synthetase as a human autoantigen

Autoantibodies to highly purified tryptophanyl-tRNA synthetase, consisting of two approximately 60-kDa subunits (6.1.1.2, TrpRS), were detected in some sera of donors and patients with various diagnosis using the newly developed 125I-TrpRS-radiodot, 125I-TrpRS-radioblot, ELISA and Western immunoblotting. The percentage of positive sera appears to be dependent upon the method of sera testing. The autoimmune sera recognized both the native and denatured TrpRS forms. The binding of the human serum to the 60-kDa band of tissue extract was demonstrable by the 125I-TrpRS-blot as well as Western blot techniques. The possible role of infections in the induction of anti-TrpRS antibodies and maintenance of the autoimmune response is discussed.

Termination of translation in eukaryotes

Termination of translation is governed in ribosomes by polypeptide chain release factors (pRF and eRF in prokaryotes and eukaryotes, respectively). In prokaryotes, three pRF have been indentified and sequenced, while in eukaryotes, only a single eRF has been identified to date. Recently, we have characterized a highly conserved protein family called eRF1. At least, human and Xenopus laevis proteins from this family are active as eRFs in the in vitro assay with any of the three stop codons. No structural similarity has been revealed between any of the three pRFs and eRF1 family. Furthermore, GTP-binding motifs have not been revealed, although translation termination in eukaryotes is a GTP-dependent process. We have demonstrated that in eukaryotes a second eRF exists in addition to eRF1, called eRF3. The eRF3 family has two features in common: presence of GTP-binding motifs and high conservation of the C-terminal domain structure. The C-terminal domain of the X. laevis eRF3 has no RF activity although it stimulates the eRF1 activity considerably at low concentration of the stop codons, conferring GTP dependence to the termination reaction. Without eRF3, the eRF1 activity is entirely GTP independent. Some features of X. laevis eRF3 (C-terminal domain) resemble those of pRF3. The newly identified eRF1 and eRF3 are structurally conserved and distinct from the respective pRF1/2 and pRF3 proteins, pointing to the possibility of different evolution of translation termination machinery in prokaryotes and eukaryotes. Bipartition of the translation termination apparatus probably provides high rate and accuracy of translation termination.

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.

Tryptophanyl-tRNA synthetase crystal structure reveals an unexpected homology to tyrosyl-tRNA synthetase

BACKGROUND

Tryptophanyl-tRNA synthetase (TrpRS) catalyzes activation of tryptophan by ATP and transfer to tRNA(Trp), ensuring translation of the genetic code for tryptophan. Interest focuses on mechanisms for specific recognition of both amino acid and tRNA substrates.

RESULTS

Maximum-entropy methods enabled us to solve the TrpRS structure. Its three parts, a canonical dinucleotide-binding fold, a dimer interface, and a helical domain, have enough structural homology to tyrosyl-tRNA synthetase (TyrRS) that the two enzymes can be described as conformational isomers. Structure-based sequence alignment shows statistically significant genetic homology. Structural elements interacting with the activated amino acid, tryptophanyl-5'AMP, are almost exactly as seen in the TyrRS:tyrosyl-5'AMP complex. Unexpectedly, side chains that recognize indole are also highly conserved, and require reorientation of a 'specificity-determining' helix containing a conserved aspartate to assure selection of tryptophan versus tyrosine. The carboxy terminus, which is disordered and therefore not seen in TyrRS, forms part of the dimer interface in TrpRS.

CONCLUSIONS

For the first time, the Bayesian statistical paradigm of entropy maximization and likelihood scoring has played a critical role in an X-ray structure solution. Sequence relatedness of structurally superimposable residues throughout TrpRS and TyrRS implies that they diverged more recently than most aminoacyl-tRNA synthetases. Subtle, tertiary structure changes are crucial for specific recognition of the two different amino acids. The conformational isomerism suggests that movement of the KMSKS loop, known to occur in the TyrRS transition state for amino acid activation, may provide a basis for conformational coupling during catalysis.

A highly conserved eukaryotic protein family possessing properties of polypeptide chain release factor

The termination of protein synthesis in ribosomes is governed by termination (stop) codons in messenger RNAs and by polypeptide chain release factors (RFs). Although the primary structure of prokaryotic RFs and yeast mitochrondrial RF is established, that of the only known eukaryotic RF (eRF) remains obscure. Here we report the assignment of a family of tightly related proteins (designated eRF1) from lower and higher eukaryotes which are structurally and functionally similar to rabbit eRF. Two of these proteins, one from human and the other from Xenopus laevis, have been expressed in yeast and Escherichia coli, respectively, purified and shown to be active in the in vitro RF assay. The other protein of this family, sup45 (sup1) of Saccharomyces cerevisiae, is involved in omnipotent suppression during translation. The amino-acid sequence of the eRF1 family is highly conserved. We conclude that the eRF1 proteins are directly implicated in the termination of translation in eukaryotes.

Role of the TIGN sequence in E. coli tryptophanyl-tRNA synthetase

Tryptophanyl-tRNA synthetase in E. coli does not have the HIGH sequence that is normally characteristic of class I aminoacyl-tRNA synthetases (EC 6.1.1.2), but instead contains a TIGN sequence at residues 17-20, which has been suggested to be equivalent to the HIGH sequence (Jones, M.D. et al. (1986) Biochemistry 25, 1887-1891). We have overexpressed E. coli Trp-tRNA synthetase and have used site-directed mutagenesis to mutate Thr-17 in the TIGN sequence to alanine. The mutant enzyme has the same Km values as the wild-type for tryptophan or tRNA(Trp), and a slightly increased Km for ATP, from 0.37 to 0.64 mM. On the other hand, the kcat for either the first step or the overall reaction is decreased by a factor of 30. In comparing the Thr-17 and Ala-17 enzymes, the delta delta G for the conversion of substrate to transition state is +9.6 kJ/mol (2.3 kcal/mol). Thr-17 is therefore important in binding the substrate in the transition state, thus supporting the suggestion that TIGN may fulfill the role of a HIGH sequence.

The "eRF" clone corresponds to tryptophanyl-tRNA synthetase, not mammalian release factor

To study the similarity between a putative cloned mammalian release factor (RF) and tryptophanyl-tRNA synthetase (TRS), a recombinant rabbit RF fusion protein was expressed from prokaryotic expression vectors. Purified fractions of the fusion proteins were tested for TRS and RF activities. Addition of the fusion protein to a TRS assay increased the binding of tryptophan to tRNA(Trp). However, in an assay for RF activity, the addition of the fusion protein resulted in release of only 1-3% of formylmethionine from an fMet-tRNA-AUG-ribosome intermediate that had been provided with UAAA as message. To confirm this result, the coding region of the putative eukaryotic RF clone "eRF" was used for in vitro transcription and translation in a rabbit reticulocyte lysate system, resulting in the synthesis of a single 56-kDa protein. The influence of this 56-kDa protein on the termination of translation directed by tobacco mosaic virus was studied. Tobacco mosaic virus RNA produced a major 126-kDa protein and a minor 184-kDa readthrough protein in an in vitro translation system. The protein generated from the "eRF" coding region did not inhibit biosynthesis of the 184-kDa readthrough virus protein. Instead, it increased the yield of both viral proteins. This increase was presumably due to its TRS activity. Chromatography of proteins derived from human lymphoblasts separated RF from TRS activity. Thus, our results indicate that the previously cloned "eRF" clone encodes TRS and that rabbit reticulocyte RF activity lies in a different protein.

Nucleoside triphosphatase activity associated with the N-terminal domain of mammalian tryptophanyl-tRNA synthetase

Bovine tryptophanyl-tRNA synthetase (EC 6.1.1.2) deprived of Zn2+ by chelation with the phosphonate analog of Ap4A hydrolyzed ATP(GTP) to ADP(GDP) although its ability to form tryptophanyl adenylate was impaired. This hydrolytic activity is stimulated by Mg2+ and Mn2+ ions and inhibited by Zn2+. Monoclonal antibody Am1 against the N-terminal domain of the enzyme completely abolished ATP(GTP)ase activity. The core peptide generated after proteolytic splitting of the N-domain lacks this activity. We suggest that the nucleotide binding site(s) different from ATP sites involved in aminoacylation reaction reside(s) at the N-terminal domain(s) of the enzyme.

Interferon inducibility of mammalian tryptophanyl-tRNA synthetase: new perspectives

Mammalian aminoacyl-tRNA synthetases are indispensible components of the cell's protein-synthesizing machinery. Surprisingly, recent experiments have demonstrated that synthesis of tryptophanyl-tRNA synthetase (WRS) is markedly enhanced after incubation of human cells with interferons. Why is this housekeeping enzyme interferon-inducible? Several hypotheses have been suggested. One hypothesis, that premature termination of protein synthesis was involved, was boosted by the discovery that the deduced amino acid sequence of the mammalian peptide chain release factor (RF) closely resembled that of WRS. Further investigation, however, suggests that the DNA encoding RF was wrongly identified and in fact encodes a rabbit WRS subunit. Other hypotheses on the interferon-inducibility of WRS, including the possibility that the protein performs other, regulatory functions in addition to its core enzymic activity, remain to be explored.

The human gene encoding tryptophanyl-tRNA synthetase: interferon-response elements and exon-intron organization

Recently, we cloned and sequenced the cDNA encoding human tryptophanyl-tRNA synthetase (hWRS) [Frolova et al., Gene 109 (1991) 291-296]. Independently, it has been shown that this protein is induced by interferons (IFN) gamma and alpha [Fleckner et al., Proc. Natl. Acad. Sci. USA 88 (1991) 11520-11524; Rubin et al., J. Biol. Chem. 266 (1991) 24245-24248]. This unusual feature of a housekeeping enzyme raises the problem of how the gene is regulated. Since at present the genomic structure of hWRS is unknown, this issue remains unsolved. Here, the exon-intron organization of hWRS has been deciphered. This gene consists of at least 12 exons that span more than 35 kb of DNA. At least two alternative noncoding exons precede ten coding exons. Upstream from the first exon, two GGAAAN(N/-)GAAA sequences, which are considered to be IFN-stimulating response elements (ISRE), have been revealed. The same consensus was also found in the intron region in close vicinity to the 5' end of the second exon. Thus, the IFN-stimulated synthesis of hWRS is presumably due to gene activation at the transcriptional level. Alignment of hWRS amino acid sequences has shown that exons V to XI of hWRS encode regions of structural similarity with bacterial WRS, whereas the N-terminal portion of the protein encoded by exons II to IV exhibits no homology with bacterial WRS.(ABSTRACT TRUNCATED AT 250 WORDS)

Gamma interferon potently induces tryptophanyl-tRNA synthetase expression in human keratinocytes

Incubation of human keratinocytes with gamma interferon (gamma-IFN) induces the synthesis of a 53-kDa protein of unknown nature and function. We report the identification of this protein through amino acid microsequencing. The NH2-terminal amino acid sequence of the 53-kDa antigen demonstrated that this protein was tryptophanyl-tRNA synthetase (Frolova et al, Gene 109:291-296, 1991, Genbank accession number 61715). This result was validated by the sequencing of tryptic peptides. Identification of the 53-kDa gamma-IFN-induced protein was confirmed by immunoblotting with an antiserum directed against beef pancreas tryptophanyl-tRNA synthetase. Northern blot analysis using a synthetic oligonucleotidic 32P-labeled probe evidenced a 3.1-kb transcript in gamma-IFN-treated cells indicating that the gene was regulated at the pre-translational level. These data show that gamma-IFN potently induces in keratinocytes the expression of an enzyme directly involved in protein biosynthesis. Elevated levels of tryptophanyl-tRNA synthetase in treated cultured keratinocytes might be involved in the cell-growth-inhibitory activity of gamma interferon.

Are the tryptophanyl-tRNA synthetase and the peptide-chain-release factor from higher eukaryotes one and the same protein?

Recently, cDNA clones encoding the bovine (b) [M. Garret, B. Pajot, V. Trézéguet, J. Labouesse, M. Merle, J.-C. Gandar, J.-P. Benedetto, M.-L. Sallafranque, J. Alterio, M. Gueguen, C. Sarger, B. Labouesse and J. Bonnet (1991) Biochemistry 30, 7809-7817] and human (h) [L. Yu. Frolova, M. A. Sudomoina, A. Yu. Grigorieva, O. L. Zinovieva and L. L. Kisselev (1991) Gene 109, 291-296] tryptophanyl-tRNA synthetases (TrpRS) were sequenced; the deduced amino acid sequences exhibit typical structural features of class I aminoacyl-tRNA synthetases [G. Eriani, M. Delarue, O. Poch, J. Gangloff and D. Moras (1990) Nature 237, 203-206] and limited, although significant, similarity with bacterial TrpRS. Independently, it was shown that a major protein whose synthesis is stimulated in human cell cultures by interferon gamma [J. Fleckner, H. H. Rasmussen and J. Justesen (1991) Proc. Natl Acad. Sci. USA 88, 11,520-11,524], and interferons gamma or alpha [B. Y. Rubins, S. L. Anderson, L. Xing, R. J. Powell and W. P. Tate (1991) J. Biol. Chem. 226, 24,245-24,248], exhibits TrpRS activity and an amino acid sequence identical to that of hTrpRS. The amino acid sequences of bTrpRS and hTrpRS are highly similar and are surprisingly very similar to the amino acid sequence deduced from a cloned and sequenced cDNA reported to encode rabbit (r) peptide-chain-release factor (RF) [C. C. Lee, W. J. Craigen, D. M. Muzny, E. Harlow and C. T. Caskey (1990) Proc. Natl Acad. Sci. USA 87, 3508-3512]. This close similarity between mammalian TrpRS and cloned RF is unexpected given the distinct functional properties of these proteins. Consequently, the question arises as to whether the mammalian TrpRS and RF activities reside on identical or very similar polypeptides. Alternatively, one may assume that the cloned rabbit cDNA encodes a protein other than rRF. Several properties (immunochemical, biochemical and physico-chemical) of mammalian TrpRS and RF have been compared. rTrpRS and rRF have distinct thermostability behaviours, and dissimilar chromatographic profiles on phosphocellulose. Both the anti-bTrpRS polyclonal antibodies and the monoclonal antibody Am2 strongly inhibit the bTrpRS and hTrpRS aminoacylation activities, but not the rRF activity. In addition, neither bTrpRS nor hTrpRS exhibit RF activity.(ABSTRACT TRUNCATED AT 400 WORDS)

Mammalian tryptophanyl-tRNA synthetases

Aminoacyl-tRNA synthetases of higher organisms are far less studied compared to their prokaryotic and unicellular eukaryotic counterparts. However, many aminoacyl-tRNA synthetases from multi-cellular organisms exhibit certain features not yet described for the same enzymes of bacteria or yeast. Tryptophanyl-tRNA synthetases (TrpRS) are among the most thoroughly studied mammalian enzymes of this group. TrpRS are Zn(2+)-dependent, dimeric, class I aminoacyl-tRNA synthetases with known amino acid sequence for four different mammalian orders. TrpRS is not associated in a stable multi-synthetase complex, although it exhibits a long N-terminal extension absent from bacterial TrpRS. The human gene encoding TrpRS belongs to the interferon-responsive gene family and TrpRS activity drastically increases after interferon gamma induction. For unknown reasons TrpRS is overproduced in pancreas of Ruminantia. Other data on TrpRS available so far are summarized and briefly discussed here.

The yeast nuclear gene MRF1 encodes a mitochondrial peptide chain release factor and cures several mitochondrial RNA splicing defects

We report the molecular cloning, sequencing and genetic characterization of the first gene encoding an organellar polypeptide chain release factor, the MRF1 gene of the yeast Saccharomyces cerevisiae. The MRF1 gene was cloned by genetic complementation of a respiratory deficient mutant disturbed in the expression of the mitochondrial genes encoding cytochrome c oxidase subunit 1 and 2, COX1 and COX2. For COX1 this defect has been attributed to an impaired processing of several introns. Sequence analysis of the MRF1 gene revealed that it encodes a protein highly similar to prokaryotic peptide chain release factors, especially RF-1. Disruption of the gene results in a high instability of the mitochondrial genome, a hallmark for a strict lesion in mitochondrial protein synthesis. The respiratory negative phenotype of mrf1 mutants lacking all known mitochondrial introns and the reduced synthesis of mitochondrial translation products encoded by unsplit genes confirm a primary defect in mitochondrial protein synthesis. Over-expression of the MRF1 gene in a mitochondrial nonsense suppressor strain reduces suppression in a dosage-dependent manner, shedding new light on the role of the '530 region' of 16S-like ribosomal RNA in translational fidelity.

Ribosomal association of the yeast SAL4 (SUP45) gene product: implications for its role in translation fidelity and termination

The SAL4 gene of the yeast Saccharomyces cerevisiae encodes a novel translation factor (Sal4p) involved in maintaining translational fidelity. Using a polyclonal antibody raised against a Sal4p-beta-galactosidase fusion protein, Sal4p was shown to be almost exclusively associated with the ribosomal fraction. Even when the ribosomes were treated with 0.8 M KCl, only low levels of Sal4p were detected in the post-ribosomal supernatant, suggesting a very strong affinity between Sal4p and the ribosome. Analysis of the distribution of Sal4p in the ribosomal population revealed that it was principally associated with 40S subunits, monosomes and polysomes. Incubation in high salt concentrations (0.8 M KCl) suggested that the affinity of Sal4p for the 40S subunit was lower than that for monosomes or polysomes. The Sal4p:ribosome association was only maintained when ribosomes were prepared in the presence of the translation elongation inhibitor cycloheximide; in uninhibited cells much lower levels of Sal4p were detectable in the 'run-off' polysomes. In view of these data, and given the stoichiometry of Sal4p to individual ribosomal proteins (estimated at less than 1:20), we suggest that Sal4p plays an ancillary role in translation termination.

Carbohydrates in mammalian tryptophanyl-tRNA synthetase

Homogeneous preparations of bovine tryptophanyl-tRNA synthetase (EC 6.1.1.2) contain monosaccharides (mannose, fucose, galactose, N-acetylglucosamine) as revealed by liquid chromatography. Their content comprises 2.5-3.0% (w/w) of the enzyme composed of two subunits (60 kDa x 2). The same set of sugars was detected in elastase and CNBr-generated fragments (with molecular masses of approx. 40 kDa and 30 kDa, respectively). It is concluded that bovine tryptophanyl-tRNA synthetase, in addition to being a metallo- and phosphoprotein, is also a glycoprotein.

Sequence comparison of new prokaryotic and mitochondrial members of the polypeptide chain release factor family predicts a five-domain model for release factor structure

We have recently reported the cloning and sequencing of the gene for the mitochondrial release factor mRF-1. mRF-1 displays high sequence similarity to the bacterial release factors RF-1 and RF-2. A database search for proteins resembling these three factors revealed high similarities to two amino acid sequences deduced from unassigned genomic reading frames in Escherichia coli and Bacillus subtilis. The amino acid sequence derived from the Bacillus reading frame is 47% identical to E.coli and Salmonella typhimurium RF-2, strongly suggesting that it represents B.subtilis RF-2. Our comparison suggests that the expression of the B.subtilis gene is, like that of the E.coli and S. typhimurium RF-2 genes, autoregulated by a stop codon dependent +1 frameshift. A comparison of prokaryotic and mitochondrial release factor sequences, including the putative B.subtilis RF-2, leads us to propose a five-domain model for release factor structure. Possible functions of the various domains are discussed.

Mechanism and regulation of eukaryotic protein synthesis

This review presents a description of the numerous eukaryotic protein synthesis factors and their apparent sequential utilization in the processes of initiation, elongation, and termination. Additionally, the rare use of reinitiation and internal initiation is discussed, although little is known biochemically about these processes. Subsequently, control of translation is addressed in two different settings. The first is the global control of translation, which is effected by protein phosphorylation. The second is a series of specific mRNAs for which there is a direct and unique regulation of the synthesis of the gene product under study. Other examples of translational control are cited but not discussed, because the general mechanism for the regulation is unknown. Finally, as is often seen in an active area of investigation, there are several observations that cannot be readily accommodated by the general model presented in the first part of the review. Alternate explanations and various lines of experimentation are proposed to resolve these apparent contradictions.

Human histidyl-tRNA synthetase: recognition of amino acid signature regions in class 2a aminoacyl-tRNA synthetases

We have determined the sequence of cDNA for the human histidyl-tRNA synthetase (HRS) in a hepatoma cell line and confirmed it in fetal myoblast and fibroblast cell lines. The newly determined sequence differs in 48 places, including insertions and deletions, from a previously published sequence. By sequence specific probing and by direct sequencing, we have established that only the newly determined sequence is present in genomic DNA and we have sequenced 500 hundred bases upstream of the translation start site. The predicted amino acid sequence now clearly demonstrates all three motifs recognized in class 2 aminoacyl-tRNA synthetases. Alignment of E. coli, yeast, and when available, mammalian predicted amino acid sequences for three of the four members of the class 2a subgroup (his, pro, ser, and thr) shows strong preservation of amino acid specific signature regions proximal to motif 2 and proximal to motif 3. These probably represent the active site binding regions for the proximal acceptor stem and for the amino acid. The first two exons of human HRS contain a 32 amino acid helical motif, first described in human QRS, a class 1 synthetase, which is found also in a yeast RNA polymerase, a rabbit termination factor, and both bovine and human WRS, suggesting that it may be an RNA binding motif.

Cloning and nucleotide sequence of the structural gene encoding for human tryptophanyl-tRNA synthetase

A structural gene encoding bovine (b) tryptophanyl-tRNA synthetase (WRS) has recently been cloned and sequenced [Garret et al., Biochemistry 30 (1991) 7809-7817]. Using part of this sequence as a hybridisation probe we have cloned and sequenced a structural gene encoding human polypeptide highly homologous with two mammalian proteins, bWRS [Garret et al., Biochemistry 30 (1991) 7809-7817; EMBL accession No. X52113] and rabbit peptide chain release factor [Lee et al., Proc. Natl. Acad. Sci. USA 87 (1990) 3508-3512]. Identification of the sequence encoding a human WRS is based on (i) the presence of 'HIGH' and 'KMSKS' structural motifs typical for class-I aminoacyl-tRNA synthetases [Eriani et al., Nature 347 (1990) 203-206]; (ii) coincidence of the number of SH groups per subunit estimated experimentally [Muench et al., Science 187 (1975) 1089-1091] and deduced from the cDNA sequence (six in both cases); (iii) close resemblance of two WRS polypeptides sequenced earlier [Muench et al., Science 187 (1975) 1089-1091] and the predicted structure in two different regions.

Identity determinants of E. coli tryptophan tRNA

The first base pair of the acceptor stem A1-U72 and the discriminator base G73, as well as the anticodon nucleotides, characterize the tryptophan tRNA in E. coli. To determine the contribution of these nucleotides to the tryptophan acceptor activity, various transcripts of E. coli tryptophan tRNA mutants were constructed. Substitutions of the discriminator base G73, which is conserved within prokaryotic tryptophan tRNAs, impaired aminoacylation with tryptophan. Substitutions of other purine-pyrimidine pairs for A1-U72 revealed that only U72 weakly contributed to recognition by tryptophanyl-tRNA synthetase. The E. coli aspartic acid tRNA transcript introducing the tryptophan anticodon CCA showed almost the same tryptophan charging activity as the tryptophan tRNA transcript possessing a G1-C72 base pair. Only a low activity was detected in the mutant tryptophan tRNA transcript possessing a set of G1-C72 and A73, which is observed in eukaryotic tryptophan tRNAs. These results indicate that the anticodon and G73 are major identity determinants of tryptophan tRNA in E. coli, whereas the A1-U72 base pair is only a weak recognition element.