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

ABSTRACT: 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.

SUBMITTER: Roodyn DB

PROVIDER: S-EPMC1264760 | biostudies-other | 1965 Dec

REPOSITORIES: biostudies-other

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A critical study of amino acid incorporation into protein by isolated liver mitochondria from adult rats.

Project description:1. Mitochondria were isolated from rat liver in a way that kept bacterial contamination at a minimum. 2. The activity of oxidative phosphorylation was unchanged under these conditions, whereas the ability of the preparations to incorporate amino acids into protein was insignificant, though it could be enhanced somewhat by the presence of EDTA. This enhancement was sensitive to ribonuclease. 3. The active time of incorporation did not exceed 15min. at 30 degrees . 4. Microsomal contamination, as measured by glucose 6-phosphatase activity, was about 5%. 5. The ability of isolated bacteria to incorporate amino acids into protein was greatly enhanced by the addition of mitochondria or heat-inactivated mitochondria. 6. A correlation was found between the growth rate of bacteria and the amino acid-incorporating activity. 7. Amino acid incorporation by combined mitochondrial-bacterial systems was inhibited by 2,4-dinitrophenol. 8. The results confirm and extend the earlier findings made in our Laboratory that isolated liver mitochondria, when free from contaminating bacteria and obtained from adult rats, are not able to catalyse the incorporation of amino acids into protein at a measurable rate. 9. The results are discussed with special emphasis on the validity of these findings.

| S-EPMC1270623 | biostudies-other

Importance of the osmolarity of the incubation medium on amino acid incorporation into protein by isolated rat liver mitochondria.

Project description:1. Incorporation of [(14)C]leucine into protein by isolated rat liver mitochondria was examined by using incubation media similar to those used by Sandell, Löw & Decken (1967) (medium A) and Roodyn, Reis & Work (1961) (medium B). The incorporation process was found to be almost completely inhibited in medium A. 2. By decreasing the amount of sucrose and omitting tris-hydrochloric acid from medium A, incorporation proceeded at a rate higher than that found in medium B. It was found that the inhibitory action of medium A was due to its high osmolarity. 3. Oxidative phosphorylation and RNA synthesis by the isolated mitochondria proceeded at the same rate in media essentially the same as media A and B. 4. There was a partial inhibitory action of medium A on leucine uptake by the mitochondria and also on the formation of leucyl-transfer-RNA. The major block of inhibition by the hyperosmolarity of medium A seemed to be located at a later step of protein synthesis involving mitochondrial ribosomes. 5. Protein synthesis by Escherichia coli B was only slightly inhibited, if at all, in hyperosmotic media in which protein synthesis by isolated mitochondria was completely stopped.

| S-EPMC1187594 | biostudies-other

THE STIMULATION BY TREATMENT IN VIVO WITH TRI-IODOTHYRONINE OF AMINO ACID INCORPORATION INTO PROTEIN BY ISOLATED RAT-LIVER MITOCHONDRIA.

Project description: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.

| S-EPMC1206597 | biostudies-other

Amino acid production in isolated rat liver mitochondria.

Project description:Amino acid analyses of mitochondrial membranes are compared with the amino acid composition of whole mitochondria (Alberti, 1964) and found to be very similar except in the cystine content. The composition of the endogenous amino acids found in freshly prepared mitochondria has been established and shown to differ considerably from the amino acid composition of membranes or whole mitochondria. The amino acids produced during anaerobic incubation of mitochondria at pH7.4, on the other hand, resemble the membrane in composition, supporting the view that neutral proteinase activity is responsible for their appearance. Aerobic incubation produces a similar pattern of amino acids except that amino acids such as proline, serine, asparagine, glutamic acid and glutamine, which can be metabolically utilized under aerobic conditions, are present to a smaller extent. The presence of large relative concentrations of endogenous taurine, cysteic acid and oxidized glutathione and the accumulation of taurine during incubation is found. The selective retention of taurine and cysteic acid within the mitochondria is established. It is proposed that the first step in the degeneration of isolated mitochondria results from lipid hydroperoxide accumulation caused by the lack of glutathione reductase in isolated mitochondria.

| S-EPMC1177828 | biostudies-other

Increasing the fidelity of noncanonical amino acid incorporation in cell-free protein synthesis.

Project description:BackgroundCell-free protein synthesis provides a robust platform for co-translational incorporation of noncanonical amino acid (ncAA) into proteins to facilitate biological studies and biotechnological applications. Recently, eliminating the activity of release factor 1 has been shown to increase ncAA incorporation in response to amber codons. However, this approach could promote mis-incorporation of canonical amino acids by near cognate suppression.MethodsWe performed a facile protocol to remove near cognate tRNA isoacceptors of the amber codon from total tRNAs, and used the phosphoserine (Sep) incorporation system as validation. By manipulating codon usage of target genes and tRNA species introduced into the cell-free protein synthesis system, we increased the fidelity of Sep incorporation at a specific position.ResultsBy removing three near cognate tRNA isoacceptors of the amber stop codon [tRNALys, tRNATyr, and tRNAGln(CUG)] from the total tRNA, the near cognate suppression decreased by 5-fold without impairing normal protein synthesis in the cell-free protein synthesis system. Mass spectrometry analyses indicated that the fidelity of ncAA incorporation was improved.ConclusionsRemoval of near cognate tRNA isoacceptors of the amber codon could increase ncAA incorporation fidelity towards the amber stop codon in release factor deficiency systems.General significanceWe provide a general strategy to improve fidelity of ncAA incorporation towards stop, quadruplet and sense codons in cell-free protein synthesis systems. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue.

| S-EPMC5457342 | biostudies-literature

MS-READ: Quantitative measurement of amino acid incorporation.

Project description:Ribosomal protein synthesis results in the genetically programmed incorporation of amino acids into a growing polypeptide chain. Faithful amino acid incorporation that accurately reflects the genetic code is critical to the structure and function of proteins as well as overall proteome integrity. Errors in protein synthesis are generally detrimental to cellular processes yet emerging evidence suggest that proteome diversity generated through mistranslation may be beneficial under certain conditions. Cumulative translational error rates have been determined at the organismal level, however codon specific error rates and the spectrum of misincorporation errors from system to system remain largely unexplored. In particular, until recently technical challenges have limited the ability to detect and quantify comparatively rare amino acid misincorporation events, which occur orders of magnitude less frequently than canonical amino acid incorporation events. We now describe a technique for the quantitative analysis of amino acid incorporation that provides the sensitivity necessary to detect mistranslation events during translation of a single codon at frequencies as low as 1 in 10,000 for all 20 proteinogenic amino acids, as well as non-proteinogenic and modified amino acids. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue.

| S-EPMC5524608 | biostudies-literature

Perturbation of Short Hydrogen Bonds in Photoactive Yellow Protein via Noncanonical Amino Acid Incorporation.

Project description:Photoactive yellow protein (PYP) is a small photoreceptor protein that has two unusually short hydrogen bonds between the deprotonated p-coumaric acid chromophore and two amino acids, a tyrosine and a glutamic acid. This has led to considerable debate as to whether the glutamic acid-chromophore hydrogen bond is a low barrier hydrogen bond, with conflicting results in the literature. We have modified the p Ka of the tyrosine by amber suppression and of the chromophore by chemical substitution. X-ray crystal structures of these modified proteins are nearly identical to the wild-type protein, so the heavy atom distance between proton donor and acceptor is maintained, even though these modifications change the relative proton affinity between donor and acceptor. Despite a considerable change in relative proton affinity, the NMR chemical shifts of the hydrogen-bonded protons are only moderately affected. QM/MM calculations were used to explore the protons' potential energy surface and connect the calculated proton position with empirically measured proton chemical shifts. The results are inconsistent with a low barrier hydrogen bond but in all cases are consistent with a localized proton, suggesting an ionic hydrogen bond rather than a low barrier hydrogen bond.

| S-EPMC7061054 | biostudies-literature

Site-Specific Incorporation of a Photoactivatable Fluorescent Amino Acid.

Project description:Photoactivatable fluorophores are emerging optical probes for biological applications. Most photoactivatable fluorophores are relatively large in size and need to be activated by ultraviolet light; this dramatically limits their applications. To introduce photoactivatable fluorophores into proteins, recent investigations have explored several protein-labeling technologies, including fluorescein arsenical hairpin (FlAsH) Tag, HaloTag labeling, SNAPTag labeling, and other bioorthogonal chemistry-based methods. However, these technologies require a multistep labeling process. Here, by using genetic code expansion and a single sulfur-for-oxygen atom replacement within an existing fluorescent amino acid, we have site-specifically incorporated the photoactivatable fluorescent amino acid thioacridonylalanine (SAcd) into proteins in a single step. Moreover, upon exposure to visible light, SAcd can be efficiently desulfurized to its oxo derivatives, thus restoring the strong fluorescence of labeled proteins.

| S-EPMC8011588 | biostudies-literature

Virulence-affecting amino acid changes in the PA protein of H7N9 influenza A viruses.

Project description:Novel avian-origin influenza A(H7N9) viruses were first reported to infect humans in March 2013. To date, 143 human cases, including 45 deaths, have been recorded. By using sequence comparisons and phylogenetic and ancestral inference analyses, we identified several distinct amino acids in the A(H7N9) polymerase PA protein, some of which may be mammalian adapting. Mutant viruses possessing some of these amino acid changes, singly or in combination, were assessed for their polymerase activities and growth kinetics in mammalian and avian cells and for their virulence in mice. We identified several mutants that were slightly more virulent in mice than the wild-type A(H7N9) virus, A/Anhui/1/2013. These mutants also exhibited increased polymerase activity in human cells but not in avian cells. Our findings indicate that the PA protein of A(H7N9) viruses has several amino acid substitutions that are attenuating in mammals.Novel avian-origin influenza A(H7N9) viruses emerged in the spring of 2013. By using computational analyses of A(H7N9) viral sequences, we identified several amino acid changes in the polymerase PA protein, which we then assessed for their effects on viral replication in cultured cells and mice. We found that the PA proteins of A(H7N9) viruses possess several amino acid substitutions that cause attenuation in mammals.

| S-EPMC3957961 | biostudies-literature

O-Methyltransferase-Mediated Incorporation of a ?-Amino Acid in Lanthipeptides.

Project description:Lanthipeptides represent a large class of cyclic natural products defined by the presence of lanthionine (Lan) and methyllanthionine (MeLan) cross-links. With the advances in DNA sequencing technologies and genome mining tools, new biosynthetic enzymes capable of installing unusual structural features are continuously being discovered. In this study, we investigated an O-methyltransferase that is a member of the most prominent auxiliary enzyme family associated with class I lanthipeptide biosynthetic gene clusters. Despite the prevalence of these enzymes, their function has not been established. Herein, we demonstrate that the O-methyltransferase OlvSA encoded in the olv gene cluster from Streptomyces olivaceus NRRL B-3009 catalyzes the rearrangement of a highly conserved aspartate residue to a ?-amino acid, isoaspartate, in the lanthipeptide OlvA(BCSA). We elucidated the NMR solution structure of the GluC-digested peptide, OlvA(BCSA)GluC, which revealed a unique ring topology comprising four interlocking rings and positions the isoaspartate residue in a solvent exposed loop that is stabilized by a MeLan ring. Gas chromatography-mass spectrometry analysis further indicated that OlvA(BCSA) contains two dl-MeLan rings and two Lan rings with an unusual ll-stereochemistry. Lastly, in vitro reconstitution of OlvSA activity showed that it is a leader peptide-independent and S-adenosyl methionine-dependent O-methyltransferase that mediates the conversion of a highly conserved aspartate residue in a cyclic substrate into a succinimide, which is hydrolyzed to generate an Asp or isoAsp containing peptide. This overall transformation converts an ?-amino acid into a ?-amino acid in a ribosomally synthesized peptide, via an electrophilic intermediate that may be the intended product.

| S-EPMC6812601 | biostudies-literature

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