Participation of tRNA in regulation of protein biosynthesis at the translational level in eukaryotes

Transfer ribonucleic acid populations in concanavalin-A-stimulated bovine lymphocytes

Transfer RNA isolated from lymphocytes stimulated by concanavalin A and that from resting cells were compared with respect to amino-acid acceptance, integrity of the CCA-terminus, extent of modification and isoacceptor distribution. Following growth stimulation the overall amino-acid acceptance of the tRNA is elevated, in particular the relative acceptor activities for threonine and arginine are increased. The reduced acceptor activity of the tRNA from the quiescent cells is not due to a preferential degradation of the CCA-end, since it persists even in the presence of ATP(CTP):tRNA nucleotidyltransferase. We therefore conclude that this reduced activity is caused by structural differences of the tRNAs. The content of modified nucleotides in newly synthesized tRNA from lymphocytes cultured in the presence and absence of concanavalin A was determined. tRNA from resting cells was found to be undermodified with respect to pseudouridine and dihydrouridine. Upon monitoring the tRNA isoacceptor distribution by affinity chromatography on immobilized elongation factor Tu and subsequent two-dimensional gel electrophoresis, a preferential synthesis of particular lysine- and threonine-accepting tRNAs was observed upon mitogenic stimulation. Evidently, a specific tRNA population is needed by the proliferating cells. These results are discussed in view of the hypothesis that the commitment of lymphocytes to proliferation is at least in part under translational control.

Higher eukaryotic aminoacyl-tRNA synthetases in physiologic and pathologic states

The aminoacyl-tRNA synthetases play a dual role in cell metabolism by synthesizing aminoacyl-tRNAs and an odd dinucleotide diadenosine-5', 5''-P1, P4-tetraphosphate which appears to be involved in DNA replication and the control of cell proliferation. This review is a synthesis of recent results on the structure, genetics, cell biology, physiology, role in neoplasia, and role in autoimmune myositis of the higher eukaryotic aminoacyl-tRNA synthetases.

Expression of a synthetic human interferon-alpha 1 gene with modified nucleotide sequence in mammalian cells

We have constructed a recombinant interferon (IFN) gene whose coding region is a chemically synthesized human (Hu)IFN-alpha 1 gene [Edge et al., Nature 292 (1981) 756-762] encoding the same protein as its natural counterpart while possessing important modifications. These modifications were introduced in order to: change codon usage, destroy integrity of repeated and complementary oligodeoxynucleotides in the coding region, introduce an intron, substitute other sequences for the IFN specific 3'- and 5'-flanking sequences and remove the leader sequence (which encodes for the signal peptide). We report here on the transfection and isolation of murine cells which contain low-copy-number insertions of our recombinant gene. These lines maintain a high steady-state level of biologically active HuIFN-alpha in the cytoplasm, produced from mRNAs of Mr expected for correctly processed transcripts. These results show directly that the leader sequence is essential for secretion of IFN proteins. They also argue against a crucial role of the particular features of the transcribed sequence of the natural HuIFN-alpha 1 gene in regulating its expression.

Soluble factors of protein synthesis in rat liver during the acute-phase reaction

Cell sap of liver cells from rats undergoing an acute-phase reaction has an increased capacity for binding leucine to tRNA. This increased capacity does not depend on concurrent changes in the leucine pool. The kinetics of activity of leucyl-tRNA synthetase from acute-phase cell sap do not show relevant differences from the normal. Acute-phase cell sap contains more tRNA than its normal counterpart. Experiments performed with increasing amounts of exogenous deacylated tRNA demonstrate that under our experimental conditions the observed higher concentration of tRNA in acute-phase cell sap could explain the increased activity in leucine incorporation into leucyl-tRNA.

Inhibition of the aminoacylation of selected tRNA molecules by an estrogen-regulated factor on uterine ribosomes. Regulation of aminoacylation of tRNA by estrogens

Administration of estradiol to ovariectomized mature rats for 1 h induces a transient increase in the peptide elongation rate on uterine ribosomes. An inhibitor of the peptide elongation rate, which appears to be regulated by estrogen treatment in vivo, can be extracted from ribosomes of estrogen-deprived rats. The extracted inhibitor or a native inhibitor-ribosome complex affects the rate of the peptide elongation reaction in a uterine cell-free protein synthesis system by inhibiting the ability of selected tRNAs in the assay to be charged with amino acids by their respective aminoacyl-tRNA synthetases. The degree of inhibition of charging of the affected tRNAs ranges from 22% to 78%, the order of inhibition being Pro greater than Val greater than Arg greater than Try greater than Leu greater than Glu greater than Ile greater than Gly greater than His greater than Ser greater than Lys. Inhibition results from a specific dose-dependent, and presumably reversible, effect of the inhibitor on tRNA, but not on the aminoacyl-tRNA synthetase. The effect does not result from removal of A-C-C terminal nucleotides from the 3' end of tRNA, but does inhibit the ability of selected tRNAs to bind to the aminoacyl-tRNA synthetases. We propose that regulation of the peptide elongation rate on uterine ribosomes by estradiol occurs through the estradiol-induced inactivation of a ribosome-associated inhibitor, which causes a reversible alteration to selected tRNAs. The modified tRNAs are unable to bind to their respective aminoacyl-tRNA synthetase to become charged with an amino acid thus causing the availability of selected aminoacyl-tRNAs to become rate-limiting in the sequential elongation of peptides.

Polyacrylamide gel mapping of chicken tRNA: comparison of polysome-bound and whole-cell tRNA from normal and avian sarcoma virus-infected chicken embryo fibroblasts

Analysis of the tRNA population from chicken cells was performed by means of polyacrylamide gel mapping. About 60 species were detected; most of these were positively identified by their acceptor specificity. The comparison of polysome-bound and overall cellular tRNA gel patterns from normal and Rous sarcoma virus-infected chicken embryo fibroblasts led us to the following observations: some tRNA species were present in the same relative proportions in all the preparations, and within isoaccepting groups the same species was preponderant; however, although about 8% of whole-cell tRNA was recovered in polysomal preparations, amounts ranging from 3 to 30% were found for individual tRNA species. This points to the absence of a direct correlation between the amount of each mature tRNA species produced and the frequency with which it is used in this case of embryonic cells. No significant difference was observed between the whole-cell tRNA patterns from normal and infected cells. Thus, tRNA transcription appears unaltered when cells are transformed and virus producing. No change was observed in the extent of a post-transcriptional modification of tRNAPhe (the base Y). However, viral infection led to some changes in the relative proportions of individual species from polysomal preparations.

Effects of thyroidectomy on heart and liver rat tRNAs: study of chromatographic and electrophoretic behaviour

Modifications of tRNAs in various physiological or experimental conditions are well documented. We have compared isoacceptor tRNAs extracted from target organs (heart and liver) from thyroidectomized rats to those of control animals. Nine liver aminoacyl-tRNAs and eight heart aminoacyl-tRNAs from thyroidectomized and control rats were analysed by RPC-5 chromatography. Quantitative differences were demonstrated in the relative proportions of the various liver tRNA isoacceptors for glycine, lysine, methionine, phenylalanine and serine and of the heart isoacceptor tRNAs for glycine, lysine, methionine, phenylalanine and valine. A qualitative variation was noted only for tRNATyr from the heart and liver of thyroidectomized rats. Isoacceptor tRNAs were obtained at a high resolution using a two-dimensional polyacrylamide gel electrophoresis. Isoacceptor tRNAs corresponding to 14 amino acids for the liver and 12 amino acids for the heart were identified. Although for most of the tRNAs examined the number of isoacceptors remained unchanged, the number of spots corresponding to tRNAGlu and tRNAHis from the liver and tRNAAla from the heart was different after thyroidectomy. Furthermore the change in electrophoretic behaviour of tRNATyr from the liver of thyroidectomized rats suggests a structural modification of one of the isoacceptors in relation to the change in thyroid status. Thus, thyroid hormones appear to induce some modification of the isoacceptor tRNAs in their target organs.

The complement of cytoplasmic tRNAs, including queuosine-containing tRNAs, in adult and senescent Wistar rat liver and their levels of aminoacylation

Our previous studies showed that both total cytoplasmic tRNAs and aminoacyl-tRNA synthetases isolated from senescent (24-30 month) female Wistar rat liver were less capable of supporting cell-free protein synthesis than were the same fractions isolated from adult (10-13 month) rat liver. The present study investigates the molecular basis for this age-related result. No significant age-related differences were found in the extent of aminoacylation of the liver cytoplasmic tRNA population, the total tRNA synthetase activity, the rate of aminoacylation of individual tRNAs, or in the overall complement of tRNA species as detected by two-dimensional gel electrophoresis. In homologous senescent aminoacylation assays, consisting of tRNAs and tRNA synthetases from senescent animals, alanine, arginine and aspartic acid were charged to a greater extent and methionine to a lesser extent compared to homologous adult assays. In heterologous assays, adult synthetases were significantly more active than senescent synthetases when charging isoleucine, methionine, phenylalanine, proline and glutamic acid, and less active when charging alanine, aspartic acid and serine. Also, senescent synthetases charged both adult and senescent tRNAs with methionine to a lesser extent than did adult synthetases. In homologous senescent assays with queuosine-containing tRNAs, asparagine, aspartic acid and histidine were charged to a greater extent and tyrosine to a lesser extent compared to homologous adult assays. Results with queuosine-tRNAs are discussed in terms of their potential ability to lower the efficiency of translation in senescent liver.

Polyacrylamide gel mapping of chicken tRNA: comparison of polysome-bound and whole-cell tRNA from normal and avian sarcoma virus-infected chicken embryo fibroblasts

Analysis of the tRNA population from chicken cells was performed by means of polyacrylamide gel mapping. About 60 species were detected; most of these were positively identified by their acceptor specificity. The comparison of polysome-bound and overall cellular tRNA gel patterns from normal and Rous sarcoma virus-infected chicken embryo fibroblasts led us to the following observations: some tRNA species were present in the same relative proportions in all the preparations, and within isoaccepting groups the same species was preponderant; however, although about 8% of whole-cell tRNA was recovered in polysomal preparations, amounts ranging from 3 to 30% were found for individual tRNA species. This points to the absence of a direct correlation between the amount of each mature tRNA species produced and the frequency with which it is used in this case of embryonic cells. No significant difference was observed between the whole-cell tRNA patterns from normal and infected cells. Thus, tRNA transcription appears unaltered when cells are transformed and virus producing. No change was observed in the extent of a post-transcriptional modification of tRNAPhe (the base Y). However, viral infection led to some changes in the relative proportions of individual species from polysomal preparations.

Does quantitative tRNA adaptation to codon content in mRNA optimize the ribosomal translation efficiency? Proposal for a translation system model

Neither a dynamic nor an energetic approach of the translation process has taken into account that intracellular levels of iso-tRNA species are adapted or adjusted to the codon frequency of mRNA being decoded (Bombyx mori silk gland, rabbit reticulocyte). A critical study of available experimental data suggests that the average elongation rate of a protein is maximized in the presence of an adapted tRNA population, usually an homologous tRNA. In addition, the amount of synthesized protein parallels that of corresponding mRNA. Other evidences--including in vitro and in vivo elongation assays with fibroin mRNA--show that individual elongation rates are not uniform. Pauses occur at certain sites of the mRNA chain. The relative lifetime of these pauses depends on the tRNA pool used. Finally, it appears that translation accuracy also depends on the balanced tRNA population. We propose to explain these different effects by using a codon-anticodon recognition model, called "trial and error system" based on a stochastic processing of the ribosome. Accordingly, various acylated tRNA species which surround a ribosome randomly encounter the receptor A site. Every trapped tRNA species is tested for a proper pairing with the codon to be recognized at the level of a comparator or discriminator function. If the pairing is correct, transpeptidation becomes irreversible. If not, the aminoacyl-tRNA is rejected and another randomly trapped tRNA is processed in turn. Mathematical analysis of this model shows that the mean number of trials used for translating the whole sequence of a mRNA is minimized when the proportion of different iso-tRNA species is correlated with the square root of codon frequency. Quantitations of reticulocyte tRNA support such a parabolic relation. Our translation system model brings some light into the role of tRNA adaptation for optimizing translation efficiency, i.e. maximizing both speed and accuracy. Some consequences of the model are discussed.

Speed-accuracy relationships during in vitro and in vivo protein biosynthesis

Poly U-directed incorporation of phenylalanine and leucine into polypeptide has been described in at least 50 papers since 1961. In general, high translation activities are associated with high accuracies, and vice-versa. Moreover, a vast body of independent experimental data (effect of ethanol, temperature, urea, aminoglycosides, etc... on protein synthesis) put together here suggests that, in many circumstances, speed and accuracy of elongation are correlated. This result is to be contrasted with the view that the speed and the fidelity of protein synthesis are two opposing parameters. In this report, recent experimental data on the nature and effect of ribosomal ambiguity (ram) and streptomycin resistance (Strr) mutations are reexamined. Models on the action of streptomycin and other misreading-inducing antibiotics, as well as long-standing ideas on the control of misreading in mammalian systems are critically evaluated. An explanation is provided for the long-befuddling data on the action of gentamicin.

Codon catalog usage and the genome hypothesis

Frequencies for each of the 61 amino acid codons have been determined in every published mRNA sequence of 50 or more codons. The frequencies are shown for each kind of genome and for each individual gene. A surprising consistency of choices exists among genes of the same or similar genomes. Thus each genome, or kind of genome, appears to possess a "system" for choosing between codons. Frameshift genes, however, have widely different choice strategies from normal genes. Our work indicates that the main factors distinguishing between mRNA sequences relate to choices among degenerate bases. These systematic third base choices can therefore be used to establish a new kind of genetic distance, which reflects differences in coding strategy. The choice patterns we find seem compatible with the idea that the genome and not the individual gene is the unit of selection. Each gene in a genome tends to conform to its species' usage of the codon catalog; this is our genome hypothesis.