A kinetic model of protein synthesis. Application to hemoglobin synthesis and translational control

A regulatory element within a gene of a ribosomal protein operon of Escherichia coli negatively controls expression by decreasing the translational efficiency

The trmD operon of Escherichia coli consists of the genes for the ribosomal protein (r-protein) S16, a 21 kDa protein (21K) of unknown function, the tRNA(m1G37)methyltransferase (TrmD), and r-protein L19, in this order. Previously we have shown that the steady-state amount of the two r-proteins exceeds that of the 21K and TrmD proteins 12- and 40-fold, respectively, and that this differential expression is solely explained by translational regulation. Here we have constructed translational gene fusions of the trmD operon and lacZ. The expression of a lacZ fusion containing the first 18 codons of the 21K protein gene is 15-fold higher than the expression of fusions containing 49 or 72 codons of the gene. This suggests that sequences between the 18th and the 49th codon may act as a negative element controlling the expression of the 21K protein gene. Evidence is presented which demonstrates that this regulation is achieved by reducing the efficiency of translation.

Codon contexts from weakly expressed genes reduce expression in vivo

Nucleotides that neighbor codons in Escherichia coli genes are highly non-random. Furthermore, these context biases are stronger and extend farther from the codon in weakly expressed than in highly expressed genes. We therefore suggested that codon contexts are selected to reduce gene expression levels. We now compare the expression levels of lacZ genes containing two specific coding sequences (context inserts). One context insert represents contexts seen in weakly expressed genes (low variant); the other represents contexts seen in highly expressed genes (high variant). The two variants have identical nucleotide and codon compositions, and encode the same protein. A permutation of four nucleotides, which changes eight codon:codon interfaces of 1043, comprises the only difference between the high and low context variant genes. In three different lacZ mRNAs, the low variant was expressed at a level significantly below that of the high variant. This context effect depends entirely on translation of the contexts in the correct frame; its magnitude depends in part on the placement of other features (e.g. transcriptional pauses and terminators, or perhaps other slow codons or contexts) in the mRNAs. Changing the ribosome density on the message by changing the ribosome binding site distinguishes between dropoff, interference and polarity, three fundamentally different types of models for the context effect. The expression difference between context variants is eliminated by both increases and decreases in the ribosome initiation frequency, as uniquely predicted by the polarity model. In fact, data from all constructions are accommodated by a model in which slow translation of the low context insert increases rho-dependent transcriptional termination within the test gene. The data suggest that the rates of translational initiation and elongation are poised with respect to the rate of transcriptional elongation so that all are influential in setting the expression level of wild-type lacZ. We conclude that context-induced polarity will exist in genes wherever low and reproducible gene product levels have been selected.

Kinetics of interleukin 2 mRNA and protein produced in the human T-cell line Jurkat and effect of cyclosporin A

The kinetics of interleukin 2 mRNA accumulation in the leukemic T-cell line Jurkat, which can be induced with phytohemagglutinin and phorbol 12-myristate 13-acetate to produce large amounts of interleukin 2, was analyzed by a modified DNA-excess solution hybridization assay using a 5'-32P-labeled oligodeoxyribonucleotide 30 bases long as probe. Cyclosporin A was used as a valuable tool to gain more insight into the quantitative aspects of interleukin 2 production, on the basis of the assumption that transcription of the interleukin 2 gene is completely inhibited shortly after administration of cyclosporin A. The half-life of interleukin 2 mRNA was estimated to be approximately 2 h. With the aid of simple mathematical models, we have been able to relate the concentration of interleukin 2 protein in the supernatant to the interleukin 2 mRNA kinetics. This novel quantitative kinetic analysis revealed that, independent of the absence or presence of cyclosporin A, interleukin 2 protein is synthesized at a rate of approximately 1.3 molecules per molecule of interleukin 2 mRNA per second and secreted within 2 h after it is synthesized and that its half-life in the supernatant is approximately 10 h.

In vitro localization of the protein synthesis defect associated with experimental phenylketonuria

We have used a cell-free system derived from hamster brain to investigate protein synthesis during experimental phenylketonuria. In such a system the elongation inhibitor emetine impeded translation in extracts derived from both treated and control animals. On the other hand the initiation inhibitor aurintricarboxylic acid showed no effects on protein synthesis activity of treated hamsters, although it was severely inhibiting in controls. This suggests that initiation is the altered step in brain protein synthesis failure consecutive to phenylketonuria.

Site dependent time optimization of protein synthesis with special regard to accuracy

The efficiency of protein synthesis is determined by its rate, accuracy, and energy consumption. With the energy consumption fixed, we optimize the system with respect to time and accuracy. Using an analytic model for a simple system and computer simulations for more complex systems, where also the possibility of errors is included, we demonstrate how different parts of the messenger RNA influence the protein production rate differently. The first part of the coding sequence is of major importance, since the availability of empty initiation sites is crucial, and queuing back to that region may interfere with initiation. The elongation rate at different positions depends on codon usage, on the concentrations of substrate and co-factors, and on the kinetic rate constants, including those of the proofreading branch(es). Ribosomal proofreading is a time consuming process and by allowing for more errors in the beginning of a protein, it is possible to increase the production rate of that protein. We calculate the mean translation time per functioning protein for various translation accuracies, and discuss the different strategies open to living cells.

Mathematical modeling of the effects of the signal recognition particle on translation and translocation of proteins across the endoplasmic reticulum membrane

The kinetics of the signal recognition particle(SRP)-mediated process of protein translocation across the endoplasmic reticulum membrane was studied by mathematical modeling and complementary experiments. The following results were obtained. (1) A model according to which SRP directs the ribosome, rather than the mRNA, to the membrane is supported by experiments designed to discriminate between the two alternatives. (2) This model describes both steady-state and synchronized translation experiments and makes a number of predictions. (3) The interaction between a nascent protein and SRP may be described by two parameters: (i) a binding constant which can be attributed to the structure of the signal peptide, and (ii) the size of the "SRP-window", i.e. the distance between the first and the last site on the polypeptide chain that can interact with SRP. For preprolactin a binding constant of 1 to 2.5 nmol-1l was estimated. Modeling of the synchronized synthesis of ovalbumin indicates that it has a much weaker binding constant than preprolactin (approximately 0.25 nmol-1l) although we cannot exclude the possibility that the SRP-window may be also smaller. (4) A better understanding of the molecular effects of SRP on translation and translocation through the rough endoplasmic reticulum membrane has been achieved. Inhibition of the steady-state rate of translation by SRP requires a stoichiometric interaction of SRP with ribosomes carrying nascent polypeptide chains and will occur only when ribosomes are piled up back to the initiation site. Translocation, on the other hand, requires only the catalytic action of SRP and is determined by the local concentration of protein-synthesizing ribosomes accumulated at the site(s) of SRP interaction. As a consequence, translational inhibition by SRP may sometimes fail to occur, depending either on the type of protein or on experimental conditions, such as a high mRNA concentration, even if translocation can be demonstrated. (5) A rough extrapolation to the conditions in vivo indicates that all synthesized polypeptide chains destined for translocation across or integration into the endoplasmic reticulum membrane are indeed quantitatively translocated and that no translational inhibition occurs.

Theoretical modelling of protein synthesis

This article provides an overview of the use of mathematical and computer modelling in furthering the understanding of protein synthesis. In particular, we discuss issues such as the nature of the rate limiting step(s), error rates, tRNA-codon adaptation, codon bias, attenuation control, and problems of selection and error corrections, focussing on their theoretical treatment.

Translation rate modification by preferential codon usage: intragenic position effects

We present a model for calculating the protein production rate as a function of the translation rate. The model takes into account that the elongation rate along an mRNA molecule is non-uniform as a result of different tRNA availabilities for different codons. Initiation of ribosomes on an mRNA is normally the rate-limiting step in the translation process, and blocking of the initiation site can be avoided if the codons closest to this site allow fast translation by the ribosome. Hence, different selective forces may act on the choice of synonymous codons in the initiation region than elsewhere on a given mRNA. We show that the elongation rate along the whole mRNA influences the production rate of abundant proteins, whereas only the elongation rate in the initiation region is of importance for the production rate of rare proteins. We also present an analysis of the codon distribution along known mRNAs coding for abundant and rare proteins.

Polysomes during early postnatal development of brain in the rat

We have attempted to show eventual modifications in the brain protein synthesis apparatus of rat during the first three weeks after birth. Through this time we noted a steady decrease (about 60%) in the free polysomes, when expressed relative to tissue weight. This decrease does not correlate with changes in the polysome profile, indicating that no loss in the efficiency of protein synthesis was involved. Translation in a reticulocyte lysate also failed to reveal differences.

Effects of post-transcriptional base modifications on the site-specific function of transfer RNA in eukaryote translation

The site-specific function in translation of several naturally occurring mammalian transfer RNAs has been studied in a series of investigations with some similarities to studies in other laboratories of tRNAs in suppression. Equal amounts of aminoacyl-tRNA isoacceptors with contrasting isotopes were added in pairs to reticulocyte lysates and allowed to incorporate their amino acids into rabbit globin. Rates of incorporation from unlimiting amounts of each isoacceptor into the corresponding amino-acid-containing sites were determined. The tRNAs of each isoacceptor pair differed as to post-transcriptional base modifications. The natural occurrence of these isoacceptors can be correlated with rates of cellular division, with more rapidly dividing and neoplastic cells containing hypomodified tRNA. The overall incorporation of lysine into globin from a fully modified tRNALys that decodes AAG is faster by 25 to 30% than from the corresponding hypomodified tRNALys. There is considerable scatter in values for incorporation ratios at different lysine-containing sites, with the hypomodified isoacceptor even being preferred at one site. The AAG decoding isoacceptors are capable of translating AAA although much more slowly than AAG. In translating AAA, in contrast to translating AAG, the hypomodified tRNALys isoacceptor is preferred. A Y base-deficient hypomodified tRNAPhe isoacceptor found only in some kinds of rapidly dividing tumor cells donates its phenylalanine preferentially to globin in competition with the fully modified Y-containing tRNAPhe of liver by 15 to 17%. There is a considerable range of incorporation ratios at the different phenylalanine-containing sites of the globin subunits. No correlation can be made between the isoacceptor preferred and the phenylalanine codon being translated. The incorporation of histidine from a fully modified tRNAHis-containing Q base in its anticodon, compared with that from the hypomodified counterpart isoacceptor that lacks Q base and that occurs in rapidly dividing cells, showed no difference in their ability to incorporate overall or into individual histidine-containing sites. There is little evidence that adjacent bases or codons in messenger RNA affect the tRNAs preferred in the translation of most sites. A striking pattern of tRNA preference was observed in three cases in which there are tandem codons, with the same codon appearing twice in succession.(ABSTRACT TRUNCATED AT 400 WORDS)

Effect of distribution of unfavourable codons on the maximum rate of gene expression by an heterologous organism

We have analysed theoretically the effect of the relative position of unfavourable codons on the maximum level of synthesis of foreign proteins in E. coli. We predict that the occurrence of such codons scattered in the corresponding genes has little effect. In contrast, clustering (in our terminology indicating directly adjacent codons) of unfavourable codons is predicted to dramatically reduce the maximum level of protein synthesis. The context effect would explain the reduction of expression level for a chloramphenicol acetyl transferase gene modified by Robinson et al. (1984), which contains 4 contiguous unfavourable codons. As an example, we predict that due to the different downstream contexts of unfavourable codons in the alpha 1 and beta interferon genes, the maximum level of synthesis in E. coli for these proteins will be different.

Effect of exercise on protein turnover in muscles of lean and obese mice

The effect of work-induced hypertrophy on skeletal muscle protein metabolism was studied in lean mice and in mice rendered obese with goldthioglucose. After tenotomy of the gastrocnemius muscle, the adaptative growth of soleus muscle was less pronounced in obese than in lean mice. Protein turnover was studied in the isolated soleus muscle 4 days after the operation. Tyrosine incorporation in total proteins and tyrosine release in the incubation medium (indices of protein synthesis and degradation) were increased by 3- and 2-fold in overloaded (i.e. work-induced hypertrophied) muscles of lean and obese mice, respectively, compared to the control muscles isolated from the non-operated leg. The qualitative modifications in the pattern of proteins synthetized from 35S-methionine were identical in both groups of mice. This increase in protein turnover in overloaded muscles results from an increased rate of polypeptide chain initiation (3-fold in lean mice, 2.2-fold in obese mice) without any modification of peptide chain elongation rates. Work-induced hypertrophy was also able to reverse the defect in amino acid uptake which is present in soleus muscles of GTG-obese mice. These results suggest that the work-induced increase of skeletal muscle protein turnover is diminished in obese mice.

Effect of medium hypertonicity on reovirus translation rates. An application of kinetic modeling in vivo

Translation rates were determined for host and virus mRNAs in reovirus-infected SC-1 cells in hypertonic medium. The effect of low doses of cycloheximide on these translation rates was also measured. The results show that hypertonicity selectively stimulates viral translation relative to host translation. Moreover, in hypertonic medium, host translation is slightly stimulated by low doses of cycloheximide, whereas viral translation is markedly inhibited. This effect of cycloheximide is precisely the opposite to what was previously observed in isotonic media [Walden, W. E., Godefroy-Colburn, T., & Thach, R. E. (1981) J. Biol. Chem. 256, 11739-11746]. It is shown that both these effects of hypertonicity are predicted by the message competition/discrimination model previously described and thus provide support for the applicability of certain aspects of the model to translation rates in vivo.

Translation kinetics in cultured mouse hepatoma cells. Regulation of albumin synthesis by amino acids

The synthesis of albumin in the liver has been shown to correlate with the availability of essential amino acids in the diet. We have investigated this phenomenon in the highly differentiated mouse hepatoma cell line, Hepa. Cells were grown for three days in complete medium with daily changes. The cells were then incubated for 22 h in media containing varying concentrations of individual essential amino acids. The deficient media were then changed; 1.5 h later the cells were labeled for 0.5 h with [3H]leucine. Albumin was immunoprecipitated and total protein was acid-precipitated from postribosomal supernatants of detergents-solubilized cells. With the exception of isoleucine, the relative rates of albumin synthesis decreased as a function of amino acid concentration from 4.3% in complete medium to 2.5% in totally deficient media. This specific reduction in albumin synthesis was confirmed by analysis of labeled Hepa proteins displayed on sodium dodecyl sulfate/polyacrylamide gels. Essential amino acid limitation reduced total protein synthesis by 50%. This is the result of a decrease in the translation efficiency of total mRNA from 5 to 3 polypeptides/message min-1 and is consistent with a reduction in the initiation rate. In contrast, the 70% decrease in albumin synthesis was a result of a reduced number of functional albumin messages/cell. The translation efficiency of these albumin messages remained unchanged at 1.

The effect of serum deprivation on the initiation of protein synthesis in mouse neuroblastoma cells

Growth of mouse neuroblastoma cells becomes stationary when cultured in serum-free medium. Within 60 h, the protein-synthesizing capacity of the cells declines to 25% as compared to that of exponentially growing cells. The transitional activity of the crude ribosomal salt washes from serum-deprived and control cells was compared in in vitro protein-synthesizing pH 5 systems. It appears that the ribosomal salt wash from serum-deprived cells has significantly (70%) lost its ability to support the translation of neuroblastoma poly(A)+ RNA. This activity of the ribosomal wash from serum-deprived cells can be restored to control level with rabbit reticulocyte initiation factor eIF-4B only. The ability of the ribosomal wash from serum-deprived cells to support the translation of encephalomyocarditis virus (EMC) and Semliki Forest virus (SFV) 42 S mRNA was tested. We found that EMC-mRNA is efficiently translated with the ribosomal salt wash from serum-deprived cells, whereas on the other hand the translation of SFV 42 S mRNA is severely impaired. Therefore, we conclude that in serum-deprived neuroblastoma cells protein synthesis is regulated in both a quantitative and a qualitative way. Modulation of the activity of initiation factor of protein synthesis eIF-4B is at least partly responsible for the observed (selective) blockade of protein synthesis in serum-deprived cells.

Translation is a non-uniform process. Effect of tRNA availability on the rate of elongation of nascent polypeptide chains

We reported elsewhere (Varenne et al., 1982) that, during synthesis of a number of colicins in Escherichia coli, intermediate nascent chains of discrete sizes accumulated, suggesting a variable rate of translation. In this paper, a detailed analysis provides arguments that this phenomenon, at least for the proteins under study, is not related to aspects of messenger RNA such as secondary structure. It is linked to the difference in transfer RNA availability for the various codons. Experimental analysis of translation of other proteins in E. coli confirms that the main origin for the discontinuous translation in the polypeptide elongation cycle is the following. For a given codon, the stochastic search of the cognate ternary complex (aminoacyl-tRNA-EF-Tu-GTP) is the rate-limiting step in the elongation cycle: transpeptidation and translocation steps are much faster. The degree of slackening in ribosome movement is almost proportional to the inverse of tRNA concentrations. The verification of this model and its possible physiological significance are discussed.

Effect of ethanol metabolism on initiation of protein synthesis in rat hepatocytes

Rat liver parenchymal cells were incubated in the presence and absence of ethanol (80 mM). Polysomes were isolated and analysed on sucrose gradients. Ethanol was shown to inhibit the incorporation of 14C-valine into proteins, result in a shift in the distribution of polysomes towards smaller sizes, inhibit the formation of 40S initiation complexes, and diminish the concentration of glucose-6-phosphate in the hepatocytes. Addition of 4-methylpyrazole (0.5 mM) partially prevented the inhibition of protein synthesis and completely restored the polysomal distribution. It is concluded that ethanol inhibits protein synthesis partly by a mechanism linked to ethanol metabolism. This effect takes place at the level of initiation and may be mediated by a reduced gluconeogenesis.

The rate of initiation of alpha- and beta-globin mRNA translation is modulated by 50 kDa, 28-kDa and 24-kDa polypeptide-containing fractions

The relative rates of initiation of alpha- and beta-globin mRNA translation in a Krebs II ascites cell-free system are differently modulated by a 50-kDa protein and two fractions containing either a 28-kDa or a 24-kDa polypeptide. Each of these fractions stimulated a discrete step that limits initiation of protein synthesis, but other rate-limiting steps take place upstream and/or downstream, resulting in characteristic kinetics of the stimulation of alpha- and beta-globin synthesis. The ascites extracts appear to be deficient in these activities.

Adenovirus VAI RNA facilitates the initiation of translation in virus-infected cells

The adenovirus VAI RNA is a small polymerase III-transcribed species that is required for optimal translation of mRNAs late after infection. Mutant dl331 fails to produce this RNA species and, as a result, grows poorly. Mutant-infected cells contain normal levels of late mRNAs, but reduced levels of polypeptides are synthesized late after infection. Translational elongation occurs at normal rates in mutant, as compared to wild-type, virus-infected cells. Initiation of translation occurs with reduced efficiency in dl331 -infected cells. VAI RNA is required for formation of a stable 48S preinitiation complex and very likely functions to facilitate the interaction between 43S preinitiation complex and mRNA to form the 48S species.

Mechanism of inhibition of polypeptide chain initiation in heat-shocked Ehrlich ascites tumour cells

The rate of polypeptide synthesis is inhibited by 80% in Ehrlich cells incubated at 43 degrees C compared to those at 37 degrees C. The regulatory site of translation resides at polypeptide chain initiation. Polypeptide synthesis does not recover at the higher temperature; however, the inhibition is reversed by returning the cells to 37 degrees C. Neither new RNA synthesis or protein synthesis is required for recovery at 37 degrees C, eliminating degradation of mRNA and irreversible denaturation of a protein essential for polypeptide chain initiation. The concentration of 40-S initiation complexes was found to be reduced markedly in heat-shocked cells compared to controls. This was confirmed in the cell-free protein-synthesizing systems prepared from heat-shocked and control cells. Reversible alteration in the activity of components affecting eIF2 function is, therefore, a likely mechanism of regulation in heat-shocked Ehrlich cells. In extracts from heat-shocked cells, Met-tRNA synthetase activity was unaltered compared to control extracts.

Coordinate regulation of polypeptide chain initiation and elongation in rabbit reticulocytes

Under normal conditions, reticulocytes synthesize alpha- and beta-globin polypeptides at equal rates. Incubation in the absence of hemin or under anoxia or hypertonic stress (100 mM excess NaCl) reduces the rate of protein synthesis to 30-50% of control levels. However, only hemin deprivation causes a reduction in polyribosome size and preferential inhibition of alpha-globin synthesis consistent with specific reduction in the rate of polypeptide chain initiation. Polyribosomal profiles are unaffected by anoxic or hypertonic stress and the ratio of alpha:beta globin synthesis remains close to unity. Measurement of ribosome transit time indicates that anoxic or hypertonic stress causes a decrease in the rate of polypeptide chain elongation that varies with the degree of inhibition of protein synthesis. Ribosomes isolated from stressed cells exhibit a reduced ability to bind 35S-met-tRNAf, suggesting that the ability to form initiation complexes is also impaired. These results suggest that reticulocytes, unlike nucleated cell lines, can coordinately reduce rates of initiation and elongation in response to certain physiological stresses.

An in vitro amino acid incorporation method for assessing the status of in vivo protein synthesis

A quantitative in vitro amino acid incorporation assay is described which can be used to assess the status of in vivo protein synthesis. The preparation and incubation conditions employed result in constant precursor specific activity and limit amino acid incorporation to completion of nascent peptide chains. Results obtained with this method correlate well with measurements of polyribosome profiles using sucrose gradient centrifugation. The assay is easily applied to a large number of samples, and requires only a fraction of the time and tissue necessary for conventional measures of polysome aggregation. The method has been found suitable for studies of protein synthesis in mouse brain and liver, and in gerbil brain, but not in mouse kidney. Products of in vitro protein synthesis can be separated by standard electrophoretic techniques, allowing a characterization of proteins whose mRNAs are actively translated in vivo.

The regulation of ribosomal protein S-6 phosphorylation in Xenopus oocytes: a potential role for intracellular pH

The intracellular pH of full-grown Xenopus oocytes increases from 7.2 to 7.6 in response to progesterone stimulation. Phosphorylation of the 40 S ribosomal protein S-6 increases six- to eightfold in these stimulated cells and this phosphorylation coincides with the intracellular alkalization. This is followed by a two- to threefold increase in the protein synthetic rate. Progesterone-treated cells cultured in choline chloride substituted Na-free medium fail to alkalize and S-6 is not phosphorylated. Weak bases, such as trimethylamine, methylamine, and procaine, artificially alkalize the cell cytoplasm and stimulate S-6 phosphorylation in medium containing or lacking sodium. The methylxanthine theophylline, suppresses S-6 phosphorylation and inhibits protein synthesis. This inhibition does not appear to involve cAMP. Rather, theophylline acidifies the oocyte cytoplasm. Thus, S-6 phosphorylation appears to be regulated by the intracellular pH of the cell. In addition, the level of protein synthesis in the oocyte seems to be correlated with the level of S-6 phosphorylation.

Early and late functions in a bipartite RNA virus: evidence for translational control by competition between viral mRNAs

It has been shown previously that Drosophila cells infected with black beetle virus synthesize an early viral protein, protein A, a putative element of the viral RNA polymerase. Synthesis of protein A declines sharply by 6 h postinfection, whereas synthesis of viral coat protein alpha continues for at least 14 h. The early shutoff in protein A synthesis occurred despite the presence of equimolar proportions of the mRNAs for proteins A and alpha, RNAs 1 and 2, respectively. We have now been able to mimic this translational discrimination in a cell-free protein-synthesizing system prepared from infected or uninfected Drosophila cells, thus allowing further analysis of the mechanism by which translation of RNA 1 is selectively turned off. The results revealed no evidence for control by virus-encoded proteins or by virus-induced modification of mRNAs by the cell-free system. Rather, with increasing RNA concentration, viral RNA 1 was outcompeted by its genomic partner, RNA 2. This suggests that the early shutoff in intracellular synthesis of protein A is due to decreasing ability of RNA 1 to compete for a rate-controlling translational factor(s) as the concentration of viral RNAs accumulates within the infected cell.

Computer simulation of ribosome editing

A stochastic model of protein synthesis was modified by including the process of dissociating peptidyl-tRNA from ribosomes. To simulate ribosome editing, the probability of dissociation was assumed to be high if the peptidyl-tRNA was erroneous; that is, if it resulted from transfer of a peptide to an aminoacyl-tRNA that was inappropriate relative to the mRNA codon. The effects of amino acid starvation on protein synthesis were simulated both by increasing the probability of such erring at and by reducing the conditional probability of elongation at "hungry" codons, those whose correct amino acid was in short supply. These probabilities were varied systematically to simulate tryptophan limitation during synthesis of coat protein from bacteriophage MS2. Significant reduction, during starvation, in the synthesis of complete coat protein required large reductions in the probability of elongation at hungry codons but only small increases in the probability of erring. Enhanced dissociation of peptidyl-tRNA during starvation, followed rapidly by dissociation of ribosomes from mRNA, led to reductions in mean polysome size, a result that had been interpreted by others as due to some effect of starvation on the initiation of protein synthesis. Results from experiments by Goldman (1982) on the cell-free synthesis of MS2 coat protein during tryptophan starvation could be mimicked in detail by the computer simulations. A simple competition between correct and erroneous amino acids was sufficient to explain the tryptophan dependence of complete coat protein and internal peptide syntheses. Values for the Michaelis constants were derived from the computer simulations.

Control of RNA and protein synthesis by the concentration of Trp-tRNATrp in Escherichia coli infected with bacteriophage MS2

The effect of varying the concentration of Trp-tRNATrp in Escherichia coli infected with bacteriophage MS2 has been studied by varying the amount of exogenously added tryptophan (Trp) to cells bearing a mutation which results in a tryptophanyl-tRNA synthetase with a higher Km value for Trp. The phenotype of the mutant has been confirmed by measuring the level of tRNATrp which can be aminoacylated in vivo, and the mutant has also been shown to have elevated tRNATrp levels compared to wild-type. The growth of MS2 decreases continuously with decreasing Trp concentration (and hence, decreasing Trp-tRNATrp concentration). This appears to be due to reduced gene expression, since at later times in infection the amount of MS2 coat protein synthesized likewise decreases continuously with decreasing Trp concentration. However, there is little decrease in the amount of coat protein or replicase synthesized during the first few minutes after the Trp concentration shift. A continuous increase in the average polysome size distribution is seen as the Trp concentration is decreased. MS2 RNA synthesis also decreases continuously with decreasing Trp concentration, and is shut off in the absence of Trp. This does not seem to be due to ppGpp as these cells are functionally relaxed under these conditions, nor does it seem to be due to degradation of pre-existing template. Addition of chloramphenicol abolishes the effect of Trp concentration on RNA synthesis. The data are consistent with a model in which ribosomes pause at Trp codons in the absence of Trp-tRNATrp, while other ribosomes queue behind and continue to load onto the message. The reduction of RNA synthesis would then be a consequence of coupling to translation.

Translational barrier in central region of encephalomyocarditis virus genome. Modulation by elongation factor 2 (eEF-2)

A fractionated cell-free system from Krebs-2 cells was prepared which contained ribosomes and a high-speed supernatant. When this system was programmed with encephalomyocarditis virus RNA, the synthesis of a precursor of capsid proteins, polypeptide preA, proceeded at a rate not very different from that observed in unfractionated extracts, whereas the synthesis of more distally encoded proteins, in particular polypeptide F, was greatly retarded, if not abolished. A protein was purified from the cytoplasmic extracts of Krebs-2 cells which greatly enhanced production of polypeptide F as well as other noncapsid proteins in the fractionated system. By several criteria, this protein was identified as eukaryotic elongation factor 2 (eEF-2). By using the ADP-ribosylation assay, it was found that the fractionated system contained about 15% of the amount of eEF-2 present in the unfractionated extracts. The results suggest that changes in the eEF-2 content may affect the elongation rate differently at different regions of the RNA template.

Alteration of tRNA modification in eukaryotes: causes and consequences

To evaluate the role of the modified nucleosides in tRNA function, especially their involvement in regulatory mechanisms of development, differentiation, or neoplastic transformation we use the following organisms: eubacteria, the slime mold D. discoideum, the topminnow Xiphophorus, and mice. Ribosylthymine, a common modified nucleoside at position 54 in tRNAs of prokaryotes and the major class of eukaryotic elongator tRNAs, is involved in the binding to the ribosomal A-site and is important for the proper functioning of tRNA during translation. Alterations in the extent of this modification occur early in the development of D. discoideum. The fully methylated species are found on polysomes, actively synthesizing protein. The partially methylated tRNAs accumulate in the nuclei, and might be involved in regulatory mechanisms at the transcriptional level. The Q base, a modified deazaguanine derivative, is present at position 34, the first position of the anticodon of tRNAAsn, tRNATyr, and tRNAHis. Alterations in the extent of this modification occur in corresponding tRNAs during the first minutes after the onset of development in D. discoideum and before final differentiation into spores, indicating that Q is important for developmental processes. Changes in the modification of G34 to Q34 in specific tRNAs of the melanophoric system of the topminnow Xiphophorus further support the view that Q is necessary in differentiation. In plasmacytomas and in Ehrlich ascites tumor cells of mice, the amount of unmodified G34 in corresponding tRNAs is correlated to the growth rate, density, or age of the tumor cells.

Initiation reactions in the mRNA-dependent reticulocyte lysate

Reticulocyte lysates depleted of mRNA by digestion with micrococcal nuclease still show an unexpectedly high rate of formation of 80 S initiation complexes. Formation of these complexes is sensitive to all inhibitors of the normal protein synthesis initiation process tested. Such lysates contain high concentrations of mRNA fragments which can be utilized for initiation, with which exogenous mRNA must compete. As a consequence of this competition, mRNAs that are weak initiators may be translated poorly by this system even at low exogenous mRNA concentrations.

Positive and negative cAMP-mediated control of tyrosine aminotransferase synthesis in Reuber H35 hepatoma cells

Induction of L-tyrosine:2-oxoglutarate aminotransferase (EC 2.6.1.5) by N6,O2'-dibutyryl-adenosine 3',5'-monophosphate (Bt2cAMP) in Reuber H35 hepatoma cells reaches a maximum value between 3-5 h after addition of Bt2cAMP and subsequently decreases in the continuous presence of Bt2cAMP. We have investigated the kinetics of the increase, i.e. induction, and the decrease, i.e. the repressed state, of the tyrosine-aminotransferase-synthesizing system under these conditions. Our experimental results are as follows. 1. The repressed state of the tyrosine-aminotransferase-synthesizing system is not caused by a decrease in the intracellular cAMP concentration. 2. The repressed state is inhibited by actinomycin D (while induction is not inhibited). 3. During the repressed state no effect of dexamethasone on tyrosine aminotransferase synthesis is found, while during induction Bt2cAMP and dexamethasone act synergistically. 4. Longer starvation of the cells in serum-free medium has no influence on the kinetics of the induction/repressed state curve. From these results we have concluded that the mechanism of the transition to the repressed state of the tyrosine-aminotransferase-synthesizing system is essentially different from the mechanism of deinduction which occurs after removal of the inducer. Moreover, the repressed state of the system is a phenomenon which is induced by Bt2cAMP separately from induction at a different level of protein synthesis.

Translational elongation rate changes in encephalomyocarditis virus-infected and interferon-treated cells

Infection of mouse L cells with encephalomyocarditis virus results in a rapid inhibition of host protein synthesis before the synthesis of viral proteins. Although no alterations in initiation factor activities have been demonstrated in encephalomyocarditis virus-infected mouse cells, a defect in polypeptide chain elongation has been shown to occur in infected cell extracts. We investigated the significance of this elongation defect in the host shutoff phenomenon in vivo. Average polypeptide chain elongation rates were measured at various times after infection. Interferon was used as a reagent to separate temporarily the virus-induced alterations. Encephalomyocarditis virus infection of L cells was shown to lead to a progressive reduction in the elongation rate. Whereas interferon pretreatment delayed the decrease in elongation rate in a dose-dependent manner, it failed to alter the kinetics of host shutoff, suggesting that slowing of elongation steps played no significant role in this phenomenon. In addition, interferon pretreatment of either mock-infected or virus-infected cells led to no elongation defect that could be attributed to interferon action.

Reduced aminoacylation of asparagine-transfer RNA early in the developmental cycle of Dictyostelium discoideum: modification pattern and possible significance of the uncharged isoacceptor tRNAAsn3

Changes in the patterns of isoacceptors of tRNAAsn and alterations in modification of the guanine residue 34, the first position of the anticodon of tRNAAsn, have been observed in eukaryotes during differentiation. We use Dictyostelium discoideum as a model system to elucidate the possible involvement of tRNAAsn in developmental processes. Vegetative amoebae were induced to undergo developmental transition by nutrient starvation. Since amino acid starvation alone is a specific stimulus initiating development and unacylated tRNAs might be involved in control mechanisms of protein synthesis, the level of aminoacylation of tRNAAsn isoacceptors has been investigated. As early as two minutes after the onset of development, the aminoacylation of tRNAAsn specifically was reduced to about 30%, whereas at the same time 10 other tRNA species were found to be charged normally, i.e. to 70-100%. One of the two major isoacceptors, tRNAAsn3, was completely deacylated, whereas the other one, tRNAAsn2, accounted for the residual aminoacylation. Analyses of the modified nucleosides of highly purified tRNAAsn2 and tRNAAsn3 are respectively, show that both isoacceptors are identical in their modification patterns except for the modification at the first position of the anticodon; tRNAAsn2 comprises queuine (Q), 7-[(4,5-cis-dihydroxy-2-cyclopenten-1-ylamino)methyl]-7-deazaguanine, whereas tRNAAsn3 contains guanine.

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.