Effect of aromatic acids on protein synthesis in subcellular preparations from the rat brain.

The incorporation of [3H]phenylalanine, [3H]tyrosine, and [3H]tryptophan into protein and amino acyl-tRNA was studied in cell-free preparations from rat brain. Tyrosine and tryptophan inhibited the incorporation of phenylalanine into protein, and tyrosine inhibited the incorporation of phenylalanine and tryptophan into amino acyl-tRNAs. In most cases, homogentisate, phenylpyruvate, and phenyllactate inhibited the incorporation of phenylalanine, tyrosine, and tryptophan into protein and amino acyl-tRNAs, and the incorporation of phenylalanine into polyphenylalanine. All other protein amino acids, and phenylacetate, salicylate, and benzoate were wholly ineffectual. The results suggest that the formation of amino acyl-tRNAs may have been the step which was affected most by the inhibitors. The incorporation data at different concentrations of the aromatic amino acids were fitted to the simple Michaelis equation. Homogentisate and phenylpyruvate generally tended to reduce both Km and V in the incorporation of aromatic amino acids into protein and amino acyl-tRNAs, even if V decreased more than Km.     

MEASUREMENTS OF RATES OF PROTEIN SYNTHESIS IN RAT BRAIN SLICES

The use of tracer concentrations of labelled amino acids to measure incorporation in incubated slices of brain results in wide fluctuations with time in the specific activity of the precursor. Using concentrations of about 1 mm of labelled amino acid facilitates the accurate measurement of rates of synthesis. These higher precursor levels in the medium decrease the fluctuations in free amino acid specific activity due to dilution by endogenous amino acid and the production of amino acid by protein degradation, and decrease the lag in incorporation due to transport phenomena. Concentrations of 1 mm amino acid in the medium did not inhibit protein synthesis; with valine, leucine, phenylalanine, lysine and histidine, incorporation rates were similar when measured at trace concentrations and at 1 mm medium levels. The source of amino acid for protein synthesis appears to be intracellular. No evidence could be found for the preferential use of extracellular medium amino acid. The rate of incorporation of amino acids in incubated slices of rat brain was 0.087 per cent of the protein amino acid/h.     

In Vitro Protein Synthesis by Plastids of Phaseolus vulgaris: IV. Amino Acid Incorporation by Etioplasts and Effect of Illumination of Leaves on Incorporation by Plastids 1

Protein synthesis in vitro by etioplasts and chloroplasts from Phaseolus vulgaris was examined to study the factors regulating the development of etioplasts into chloroplasts. The properties of incorporation of (14)C-leucine into protein by etioplasts from plants grown 6.5 days in darkness are similar to those of chloroplasts from plants of the same age that were illuminated for 12 hours. However, the rate of incorporation per plastid by chloroplasts is 4 times higher than the rate of amino acid incorporation by etioplasts. When 6-day-old plants are placed in light, this 4-fold increase occurs within 6 hours and is maintained up to 36 hours. The difference in rate of amino acid incorporation into protein between etioplasts and chloroplasts represents a real difference in the ability of etioplasts and chloroplasts to synthesize protein. A difference in pool size of leucine between etioplasts and chloroplasts does not account for the difference in amino acid incorporation between etioplasts and chloroplasts. Also the difference in photosynthetic capabilities of etioplasts and chloroplasts does not account for the difference in the ability to incorporate amino acid into protein. Furthermore, there are no factors in homogenates of etiolated leaves which inactivate amino acid incorporation into protein by chloroplasts. The difference in rates of amino acid incorporation between etioplasts and chloroplasts is correlated with the state of development of the plastids. The plastids have increased ability to incorporate amino acid into protein when the plastids are undergoing growth and differentiation.     

Effect of aromatic acids on protein synthesis in subcellular preparations from the rat brain

The incorporation of [³H]phenylalanine, [³H]tyrosine, and [³H]tryptophan into protein and amino acyl–tRNA was studied in cell-free preparations from rat brain. Tyrosine and tryptophan inhibited the incorporation of phenylalanine into protein, and tyrosine inhibited the incorporation of phenylalanine and tryptophan into amino acyl–tRNAs. In most cases, homogentisate, phenylpyruvate, and phenyllactate inhibited the incorporation of phenylalanine, tyrosine, and tryptophan into protein and amino acyl–tRNAs, and the incorporation of phenylalanine into polyphenylalanine. All other protein amino acids, and phenylacetate, salicylate, and benzoate were wholly ineffectual. The results suggest that the formation of amino acyl–tRNAs may have been the step which was affected most by the inhibitors. The incorporation data at different concentrations of the aromatic amino acids were fitted to the simple Michaelis equation. Homogentisate and phenylpyruvate generally tended to reduce both K_m and V in the incorporation of aromatic amino acids into protein and amino acyl-tRNAs, even if V decreased more than K_m.     

Residue-specific Incorporation of Noncanonical Amino Acids into Model Proteins Using an Escherichia coli Cell-free Transcription-translation System

The canonical set of amino acids leads to an exceptionally wide range of protein functionality. Nevertheless, the set of residues still imposes limitations on potential protein applications. The incorporation of noncanonical amino acids can enlarge this scope. There are two complementary approaches for the incorporation of noncanonical amino acids. For site-specific incorporation, in addition to the endogenous canonical translational machineries, an orthogonal aminoacyl-tRNA-synthetase-tRNA pair must be provided that does not interact with the canonical ones. Consequently, a codon that is not assigned to a canonical amino acid, usually a stop codon, is also required. This genetic code expansion enables the incorporation of a noncanonical amino acid at a single, given site within the protein. The here presented work describes residue-specific incorporation where the genetic code is reassigned within the endogenous translational system. The translation machinery accepts the noncanonical amino acid as a surrogate to incorporate it at canonically prescribed locations, i.e., all occurrences of a canonical amino acid in the protein are replaced by the noncanonical one. The incorporation of noncanonical amino acids can change the protein structure, causing considerably modified physical and chemical properties. Noncanonical amino acid analogs often act as cell growth inhibitors for expression hosts since they modify endogenous proteins, limiting in vivo protein production. In vivo incorporation of toxic noncanonical amino acids into proteins remains particularly challenging. Here, a cell-free approach for a complete replacement of L-arginine by the noncanonical amino acid L-canavanine is presented. It circumvents the inherent difficulties of in vivo expression. Additionally, a protocol to prepare target proteins for mass spectral analysis is included. It is shown that L-lysine can be replaced by L-hydroxy-lysine, albeit with lower efficiency. In principle, any noncanonical amino acid analog can be incorporated using the presented method as long as the endogenous in vitro translation system recognizes it.     

Pools and protein synthesis in mammalian cells.

From the kinetics of incorporation into protein shown by four amino acids and one amino acid analogue in suspension cultured HeLa S-3 cells, two distinctly different patterns were observed under the same experimental conditions. An initial slow exponential incorporation followed by linear kinetics was characteristic of the two non-essential amino acids, glycine and proline, whereas the two essential amino acids studied, phenylalanine and leucine, showed linear kinetics of incorporation with no detectable delay. The analogue amino acid, p-fluorophenylalanine also showed immediate linear kinetics of incorporation. There was a poor correlation between the rate of formation of acid-soluble pools and incorporation kinetics. However, the rate of formation of the freely diffusible pool of amino acids correlated more closely with incorporation kinetics. The lack of direct involvement of the acid-soluble pool in protein synthesis was also demonstrated by pre-loading of pools before treatment of cells with labelled amino acids. The results partially support the hypothesis that precursor amino acids for protein synthesis come from the external medium rather than the acid-soluble pool, but suggest that the amino acid which freely diffuses into the cell from the external medium could also be the source.     

Amphibolic role of the Krebs cycle in the insulin-stimulated protein synthesis.

It has been a generally held view that insulin does not significantly affect the incorporation of amino acids into liver protein. This interpretation was based on data obtained from studies using the branched chain amino acids, which are poorly metabolized by the hepatic tissue. The effect of insulin on 14CO2 formation and protein incorporation of several 1-14C-labeled or U-14C-labeled amino acids was studied in isolated rat hepatocytes and diaphragm pieces. It was shown that insulin enhanced 14CO2 formation and protein incorporation primarily of those carbons of amino acids which are metabolized through the mitochondrial Krebs cycle. Using aminooxyacetic acid (0.5 mM), a potent inhibitor of the transamination reaction, it was shown that there exists an "insulin-sensitive" pool of glutamate which is preferentially utilized for protein synthesis in the presence of insulin. The insulin effect on protein incorporation of 14C-labeled glutamate generated in the Krebs cycle was abolished in the presence of aminooxyacetic acid. We interpret these results to signify that mitochondrial transamination of alpha-ketoglutarate to glutamate is essential for insulin stimulation of 14C incorporation into hepatocyte protein.     

AMINO ACID DISTRIBUTION AND INCORPORATION INTO PROTEINS IN ISOLATED, ELECTRICALLY-STIMULATED CEREBRAL TISSUES

—The uptake of radioactive amino acid by incubated cerebral cortex slices is found to be a first order process. Incorporation of the radioactive amino acid into tissue protein is from a precursor pool that has first equilibrated with the intracellular endogenous free amino acids. Ways of calculating the amino acid incorporation in molar quantities from the observed incorporation of radioactivity are discussed, and it is concluded that the specific radioactivity of the intracellular acid-soluble fraction is the best basis for such estimates. The in vitro incorporation of leucine into tissue protein is estimated to be approximately 1±2 mμnol/mg protein/h, and of valine 0±4 mμmol/mg protein/h. Addition of free amino acids to the media had little or no effect on the calculated rates of incorporation. On incubation for 1 h the total free valine in tissue and medium increased by 0±43 μmol/g and leucine increased by 0±55 μmol/g. Estimates of amino acid incorporation based on the specific radioactivity of the media amino acids can give misleading results if this considerable release of amino acids into the medium is not taken into account. Electrical stimulation of neocortical slices with a variety of types of pulses was either without effect or decreased incorporation into portein. The decrease could not be directly correlated with changes in tissue K⁺ nor with the utilization of ATP. Mild, local stimulation of the lateral olfactory tract of piriform cortex slices was without effect on tissue phosphocreatine, K⁺ or amino acid incorporation.     

Action of light and streptomycin on protein synthesis in cabbage seedlings

The action of light on protein synthesis was examined in the cabbage seedlings, a system extensively used in the studies of anthocyanin synthesis. Continuous red and far red light have no effect on total protein content while they cause a marked decrease in the level of free amino acids in cabbage seedlings. The rate of protein synthesis, measured as incorporation of radioaetively-labelled amino acids into proteins, is clearly stimulated by light. Phytochrome involvement in the light stimulation of the incorporation is also demonstrated by the red-far red reversibility of the response. The relative effectiveness of continuous red and far red light upon the incorporation of amino acids into proteins is affected by the nature of the system used to study the incorporation process. When excised cotyledons and short period of incorporation were used, continuous far red was more effective than red. However, when whole seedlings and long period of incorporation were used, red and far red were equally effective. Streptomycin causes a 10– 15% decrease in the rate of incorporation of amino acids into proteins of all cellular fractions, except the plastid fraction where a much higher inhibition (30%) was observed.     

Evaluation and optimisation of unnatural amino acid incorporation and bioorthogonal bioconjugation for site-specific fluorescent labelling of proteins expressed in mammalian cells

Many biophysical techniques that are available to study the structure, function and dynamics of cellular constituents require modification of the target molecules. Site-specific labelling of a protein is of particular interest for fluorescence-based single-molecule measurements including single-molecule FRET or super-resolution microscopy. The labelling procedure should be highly specific but minimally invasive to preserve sensitive biomolecules. The modern molecular engineering toolkit provides elegant solutions to achieve the site-specific modification of a protein of interest often necessitating the incorporation of an unnatural amino acid to introduce a unique reactive moiety. The Amber suppression strategy allows the site-specific incorporation of unnatural amino acids into a protein of interest. Recently, this approach has been transferred to the mammalian expression system. Here, we demonstrate how the combination of unnatural amino acid incorporation paired with current bioorthogonal labelling strategies allow the site-specific engineering of fluorescent dyes into proteins produced in the cellular environment of a human cell. We describe in detail which parameters are important to ensure efficient incorporation of unnatural amino acids into a target protein in human expression systems. We furthermore outline purification and bioorthogonal labelling strategies that allow fast protein preparation and labelling of the modified protein. This way, the complete eukaryotic proteome becomes available for single-molecule fluorescence assays.     

Amino acid supply and protein metabolism in Ehrlich ascites tumour cells. 2. Incorporation of 14C-tyrosine

The incorporation of 14C-tyrosine into protein of incubated Ehrlich ascites tumour cells was measured over a 10-fold range of external amino acid concentrations, the composition of which simulated that of mouse intraperitoneal fluid. Incorporation was linear with time and the rate of incorporation increased with increasing external amino acid concentration up to at least six times intraperitoneal concentrations. Further increases in external amino acid supply did not yield a concomitant increase in the rate of tyrosine incorporation, a maximum fractional protein synthetic rate of approximately 100% d-1 being achieved. The specific activity of tyrosine in intracellular fluid was approximately 95% of that of extracellular fluid, irrespective of the external amino acid concentration.     

The stimulation by treatment in vivo with tri-iodothyronine of amino acid incorporation into protein by isolated rat-liver mitochondria

1. Normal and thyroidectomized rats were treated with near-physiological doses of tri-iodothyronine. Liver mitochondria were isolated and incubated with radioactive amino acids. In normal rats tri-iodothyronine caused only a slight stimulation of incorporation into mitochondrial protein, but in thyroidectomized animals the incorporation was doubled. 2. There was a lag period of about 36 hr. after injection and the maximum effect was observed after 2 days. 3. Direct addition of tri-iodothyronine to the incubation medium had no effect on mitochondrial incorporation. 4. The incorporation was not due to bacterial, nuclear, lysosomal or microsomal contamination and the labelled particles had sedimentation properties identical with those of mitochondria, as followed by suitable enzyme markers. 5. Thyroid hormone treatment did not cause any marked alterations in the pattern of labelling of submitochondrial fractions and in all cases the most radioactive protein was in an insoluble lipid-rich fraction. The amino acid compositions of the total mitochondrial protein and the more radioactive lipoprotein were also unaltered. 6. Increases in the content of RNA and various cytochromes per mg. of mitochondrial protein were observed after treatment with tri-iodothyronine. These occurred slightly later than the stimulation of amino acid incorporation. 7. No uncoupling of oxidative phosphorylation was observed and the ATP production per mg. of mitochondrial protein increased. 8. It was concluded that tri-iodothyronine stimulated amino acid incorporation into mitochondrial protein and that the result is consistent with the view that treatment with thyroid hormone results in an enhanced selective synthesis of mitochondrial respiratory units.     

Replaceability of amino acids and the self-facilitation of evolution

The self-facilitating aspect of evolution is formulated in terms of measures of amino acid replaceability. The incorporation of highly replaceable amino acids into a protein increases the rate at which it can incorporate highly irreplaceable amino acids. The reality of self-facilitation is supported by sequence data which imply that silent mutations which change the replaceability of codons are subject to selection. There are a number of interesting implications for the dependence of evolutionary rate on protein diversity and variability. In general, the incorporation of low information value amino acids into a protein increases the maximum rate at which the value of the information in the protein can increase.     

NONRIBOSOMAL INCORPORATION OF AMINO ACIDS INTO THE TROPONIN-LIKE PROTEIN FROM SYNAPTOSOMES

A preparation of synaptosomal cytoplasm was isolated from forebrain of young rats and incubated with various amino acids in vitro. Incorporation of amino acids into protein was observed. This incorporation did not occur by ribosomal protein synthesis. The amino acid incorporating system was not stimulated by ATP and was inhibited by calcium. The system incorporated amino acids enzymatically. An electrophoretic analysis of the synaptosomal preparation, following incubation in the presence of radioactive amino acids, showed only three labelled protein species (molecular weights 37,000, 26,000 and 20,000). This incorporation of amino acids was found to have a high degree of specificity for three protein species. Migration of the three protein species was found to be nearly identical to that of rabbit muscle troponin. The proteins incorporating amino acids were also found to have other characteristics of the troponin subunits. A possible role of troponin modification is discussed.     

Further study of factors affecting amino acid incorporation into protein by isolated mitochondria

1. The incorporation of amino acids into protein in isolated mitochondria has now been studied in more detail, and with mitochondria from a range of tissues. 2. Liver mitochondria from newborn rats are twice as active as those from adult rats. 3. The mitochondria are inactivated by excessive homogenization and repeated freezing and thawing. 4. The incorporation is sensitive to conditions of incubation and in particular to the rate of oxygenation, shape of vessel and depth of fluid. Best results are obtained by incubation in flat-bottomed vessels containing suspensions with less than 3mm. depth of fluid. 5. The requirement for oxidizable substrates has been examined with a range of substances, and most of the common energy-yielding metabolites of the mitochondrion are effective. Their activity is greatly influenced by concentration, and some, but not all, of the substrates show optimum concentrations for incorporation with decreased activity at higher concentrations. 6. Some amino acids can act as energy sources for the incorporation. 7. The effect of increasing the concentration of labelled amino acid is different for different amino acids, and complex effects occur on the addition of amino acid mixtures. 8. It is concluded that the amino acid incorporation into protein finally obtained is the result of many interacting factors related to the structural and metabolic state of the mitochondrion.     

Lack of effect of amino acid concentration on protein synthesis in the perfused rat liver.

The effect of increasing the perfusate concentration of amino acids on the incorporation of labelled valine into protein was followed in perfusions of rat livers lasting for 2h. A fixed amount of labelled and unlabelled valine was added to the perfusate as the other amino acids were increased in multiples of the concentrations normally found in rat plasma. Under these conditions no increase in valine incorporation was observed, which appeared to be in conflict with results published by other workers, However, a different method of labelling from that used here was used in the earlier studies. An increasing amount of a labelled amino acid was added as the concentrations of the unlabelled amino acids were increased in the perfusate. An experiment directly comparing to the two labelling methods produced results that indicated that the apparent increase in liver protein synthesis observed by the other workers could have been due to the method of radioisotope addition. It is therefore concluded that increasing the perfusate concentration of amino acids does not increase amino acid incorporation into liver protein.     

Effects of cyclic adenosine 3',5'-monophosphate on amino acid transport and incorporation into protein in the rat aorta.

To assess the effects of cyclic AMP on amino acid transport and incorporation into aortic tissue protein, rat aortic rings were incubated with the cyclic AMP analog, N6-monobutyryl cyclic AMP (MBcAMP), the phosphodiesterase inhibitor, 3-isobutyl-1-methylxanthine (MIX), and radiolabeled amino acids. Subsequently, the aortic rings were homogenized in 5% trichloroacetic acid (TCA) and processed for liquid scintillation counting. Radioactivity present in the TCA supernatant following centrifugation was used to estimate amino acid transport. TCA-precipitable radioactivity was used as a measure of amino acid incorporation into protein. MBcAMP induced an increase in the uptake of [3H]alpha-aminoisobutyric acid into aortic rings and an increase in the incorporation of radiolabeled proline and leucine into TCA-precipitable protein. Similar effects were observed with low concentrations of MIX (0.025-0.25 mM); however, at higher concentrations of MIX, there was an attenuation of the effect or frank inhibition. Maximum stimulation of transport was observed within 90-120 min of the addition of MIX or MBcAMP to the incubation medium, whereas the effect on amino acid incorporation was not detectable until after 12 h of exposure to MIX or MBcAMP. The effects of cyclic AMP on transport were observed in both the tunica media and the tunica adventitia, whereas the effects on amino acid incorporation into protein were observed only in the tunica media. These data are consistent with a possible role for cyclic AMP in promoting changes in the tunica media that could lead to the development of vascular hypertrophy.     

Some paradoxical effects of inhibitors of protein synthesis on protein turnover in cultured human cells

Summary Low concentrations ofcycloheximide, sufficient to block net protein synthesis in growing normal and cancer cells, had no effect on protein turnover, i.e. either the incorporation of labeled amino acids from media lacking other amino acids essential for growth, or the loss to the medium of amino acids from prelabeled cells. At the concentrations that blocked growth, the rate of amino acid incorporation from complete medium was reduced to the “quo;turnover level,” i.e. the rate of incorporation seen in amino acid-deficient media. Protein turnover was inhibited only at higher concentrations of the inhibitor. Qualitatively similar results have been obtained with puromycin, anisomycin, emetin and tylocerebrine.     

Protein synthesis by membrane-bound and free ribosomes of the developing rat cerebral cortex

1. Rates of RNA and protein synthesis were measured in rat cerebral-cortex slices, and compared with amino acid incorporation into protein by membrane-bound and free ribosomes from the same tissue, in the first 3 weeks of life. 2. A rapid age-dependent decline in the incorporation of labelled precursors into both RNA and protein was observed, which was more marked for amino acid incorporation into protein. 3. Although membrane-bound ribosomes comprise only a small fraction of total ribosomes, they were more active in incorporating amino acids into protein than were free ribosomes, especially immediately after birth. The decline in activity with age was more marked in the membrane-bound fraction than in free ribosomes. This loss of activity was largely independent of alterations in soluble factors or endogenous mRNA content and appeared to involve some alteration of the function of the ribosome itself, with relatively small alterations in the ratio of membrane-bound to free ribosomes. 4. Thyroidectomy, performed soon after birth, had no effect on the incorporation of radioactive precursors into RNA or protein by either slices or the cell-free preparations during the first 3-4 weeks of life.