Proteome dynamics in complex organisms: using stable isotopes to monitor individual protein turnover rates

The complete definition of changes in a proteome requires information about dynamics and specifically the rate at which the individual proteins are turned over intracellularly. Whilst this can be achieved in single-cell culture using stable isotope precursors, it is more challenging to develop methods for intact animals. In this study, we show how dietary administration of stable isotope-labelled amino acids can obtain information on the relative rates of synthesis and degradation of individual proteins in a proteome. The pattern of stable isotope-labelling in tryptic peptides can be deconstructed to yield a highly reliable measure of the isotope abundance of the precursor pool, a parameter that is often difficult to acquire. We demonstrate this approach using chickens fed a semisynthetic diet containing [(2)H(8)]valine at a calculated relative isotope abundance (RIA) of 0.5. When the labelling pattern of gel-resolved muscle proteins was analyzed, the intracellular precursor isotope abundance was 0.35, consistent with dilution of the amino acid precursor pool with unlabelled amino acids derived from degradation of pre-existing proteins. However, the RIA was stable over an extended labelling window, and permitted calculation of the rates of synthesis and degradation of individual proteins isolated by gel electrophoresis. For the first time, it is feasible to contemplate the analysis of turnover of individual proteins in intact animals.     

Harmonizing Labeling and Analytical Strategies to Obtain Protein Turnover Rates in Intact Adult Animals

Changes in the abundance of individual proteins in the proteome can be elicited by modulation of protein synthesis (the rate of input of newly synthesized proteins into the protein pool) or degradation (the rate of removal of protein molecules from the pool). A full understanding of proteome changes therefore requires a definition of the roles of these two processes in proteostasis, collectively known as protein turnover. Because protein turnover occurs even in the absence of overt changes in pool abundance, turnover measurements necessitate monitoring the flux of stable isotope–labeled precursors through the protein pool such as labeled amino acids or metabolic precursors such as ammonium chloride or heavy water. In cells in culture, the ability to manipulate precursor pools by rapid medium changes is simple, but for more complex systems such as intact animals, the approach becomes more convoluted. Individual methods bring specific complications, and the suitability of different methods has not been comprehensively explored. In this study, we compare the turnover rates of proteins across four mouse tissues, obtained from the same inbred mouse strain maintained under identical husbandry conditions, measured using either [¹³C₆]lysine or [²H₂]O as the labeling precursor. We show that for long-lived proteins, the two approaches yield essentially identical measures of the first-order rate constant for degradation. For short-lived proteins, there is a need to compensate for the slower equilibration of lysine through the precursor pools. We evaluate different approaches to provide that compensation. We conclude that both labels are suitable, but careful determination of precursor enrichment kinetics in amino acid labeling is critical and has a considerable influence on the numerical values of the derived protein turnover rates.     

Turnover of the human proteome: determination of protein intracellular stability by dynamic SILAC

The proteome of any system is a dynamic entity, such that the intracellular concentration of a protein is dictated by the relative rates of synthesis and degradation. In this work, we have analyzed time-dependent changes in the incorporation of a stable amino acid resolved precursor, a protocol we refer to as "dynamic SILAC", using 1-D gel separation followed by in-gel digestion and LC-MS/MS analyses to profile the intracellular stability of almost 600 proteins from human A549 adenocarcinoma cells, requiring multiple measures of the extent of labeling with stable isotope labeled amino acids in a classic label-chase experiment. As turnover rates are acquired, a profile can be built up that allows exploration of the 'dynamic proteome' and of putative features that predispose a protein to a high or a low rate of turnover. Moreover, measurement of the turnover rate of individual components of supramolecular complexes provides a unique insight in processes of protein complex assembly and turnover.     

Identification of [1-14C]pantothenic-acid-mediated modified mitochondrial proteins

The in vivo administration of [1-14C]pantothenic acid, which is the precursor of coenzyme A, resulted in the radioactive labelling of several mitochondrial proteins in rat liver. The incorporated radioactivity could be released by glutathione or 2-mercaptoethanol. Two mitochondrial matrix proteins acetyl-CoA acetyltransferase (liver and heart), an enzyme involved in the biosynthesis or degradation of ketone bodies, and 3-oxoacyl-CoA thiolase (liver), a protein participating in fatty acid oxidation were identified as modified proteins. The radioactivity was localized exclusively in forms A1 and A2 indicating that these forms represent the modified states of the acetyl-CoA acetyltransferase protein. Kinetics of incorporation of radioactivity revealed an accumulation of the modified forms. The ratio of specific radioactivities of A2 compared to A1 was 2.41 +/- 0.15 (n = 10). After in vivo labelling with [14C]leucine, the specific radioactivity of acetyl-CoA acetyltransferase depended on the state of the enzyme protein. The unmodified enzyme exhibited a lower specific radioactivity than its modified forms suggesting different turnover rates of these proteins.     

The extent and nature of protein degradation in the tissues during development

Protein turnover, defined as the degradation and replacement of proteins, appears to vary between most adult species in the same way as metabolic rate, i.e. as W0.75, although it may be a little lower in man. During development in the rat it also varies as metabolic rate. Thus P Total = 14.7 W0.53kg per day. Most of this turnover occurs in nonmuscle tissues (P = 11.3 W0.50kg per day) with protein turnover in muscle described by P = 3.53 W0.69kg per day. Mechanisms for protein degradation in liver and muscle involve lysosomes although the morphology of the lysosomal system in muscle is different from that in liver. However, heterogeneous turnover is a feature of proteins in both issues including the principal myofibrillar proteins. While the reaction order of protein synthesis can reasonably be described as zero order--a fixed rate per unit of DNA--there is less certainty about degradation. It is postulated that structural and functional characteristics of the cytoplasm of cells determine the accessibility of cellular protein to the degrading system. As a result, a first order rate for a particular cell type is fixed, and this determines the magnitude of the protein-DNA ratio or the functional-cell size. The first order degradation rate of the cytoplasmic protein also determines the specific activity of the degrading enzymes.     

Role of the calpain system in muscle growth.

Muscle protein degradation has an important role in rate of muscle growth. It has been difficult to develop procedures for measuring rate of muscle protein degradation in living animals, and most studies have used in vitro systems and muscle strips to determine rate of protein degradation. The relationship between results obtained by using muscle strips and rate of muscle protein turnover in living animals is unclear because these strips are in negative nitrogen balance and often develop hypoxic cores. Also, rate of protein degradation is usually estimated by release of labeled amino acids, which reflects an average rate of degradation of all cellular proteins and does not distinguish between rates of degradation of different groups of proteins such as the sarcoplasmic and the myofibrillar proteins in muscle. A number of studies have suggested that the calpain system initiates turnover of myofibrillar proteins, which are the major group of proteins in striated muscle, by making specific cleavages that release thick and thin filaments from the surface of the myofibril and large polypeptide fragments from some of the other myofibrillar proteins. The calpains do not degrade myofibrillar proteins to small peptides or to amino acids, and they cause no bulk degradation of sarcoplasmic proteins. Hence, the calpains are not directly responsible for release of amino acids during muscle protein turnover. Activity of the calpains in living cells is regulated by calpastatin and Ca2+, but the nature of this regulation is still unclear.     

A proteomics strategy for determining the synthesis and degradation rates of individual proteins in fish

In order to study the protein dynamics in the tissues of fish we have developed a proteomics-based strategy to determine the rates of synthesis and degradation of individual proteins. We have demonstrated the feasibility of this approach by measuring the turnover of multiple isoforms of parvalbumin (β1-7) in the skeletal muscle of common carp (Cyprinus carpio). A stable isotope-labelled amino acid ([(2)H(7)] l-leucine) was administered to the carp via the diet and its incorporation into the isoforms of parvalbumin in muscle over time was monitored by LC-MS analysis of signature peptides. The relative isotope abundance was calculated and used to deconvolute the data. The β7 parvalbumin isoform had a rate of synthesis that was greater than the rate of degradation. In contrast the rate of degradation of the β5 isoform exceeded its rate of synthesis, whilst the analysis revealed that the other parvalbumin β-isoforms (β1, β2, β3, β4 and β6) had a rate of synthesis that was equal to the rate of degradation. This work has addressed a number of technical challenges and represents the first study to use proteomic approaches to measure the turnover of individual proteins in fish.     

Proteome Dynamics: Tissue Variation in the Kinetics of Proteostasis in Intact Animals

Understanding the role of protein turnover in the maintenance of proteostasis requires accurate measurements of the rates of replacement of proteins in complex systems, such as intact animals. Moreover, any investigation of allometric scaling of protein turnover is likely to include species for which fully annotated proteomes are not available. We have used dietary administration of stable isotope labeled lysine to assess protein turnover rates for proteins from four tissues in the bank vole, Myodes glareolus. The annotated genome for this species is not available, so protein identification was attained through cross-species matching to the mouse. For proteins for which confident identifications were derived, the pattern of lysine incorporation over 40 days was used to define the rate of synthesis of individual proteins in the four tissues. The data were heavily filtered to retain a very high quality dataset of turnover rates for 1088 proteins. Comparative analysis of the four tissues revealed different median rates of degradation (kidney: 0.099 days⁻¹; liver 0.136 days⁻¹; heart, 0.054 days⁻¹, and skeletal muscle, 0.035 days⁻¹). These data were compared with protein degradation rates from other studies on intact animals or from cells in culture and indicate that both cell type and analytical methodology may contribute to variance in turnover data between different studies. These differences were not only due to tissue-specific proteins but were reflected in gene products common to all tissues. All data are available via ProteomeXchange with identifier PXD002054.Proteostasis balances the opposing contributions of protein synthesis and protein degradation in the maintenance or adjustment of the intracellular abundance of a protein. Accurate determination of the net contribution of these two processes requires accurate determination of at least two of the three parameters of synthesis rate, degradation rate, and protein pool size. Moreover, these parameters need to be recoverable at proteome scales, extending to many proteins in a parallel analysis within a single experiment. Because synthesis and degradation can still occur even when the protein concentration is unchanging, it is necessary to monitor the flux through the protein pool by a tracer, and in a mass spectrometry-driven proteomics context, this involves the incorporation of a stable isotope label. The tracer can be administered as a metabolic precursor (1, 2), an amino acid (3–5), a microbially sourced diet uniformly labeled with ¹⁵N, or by administration of [²H₂]O in drinking water (6–9).Many studies of proteome dynamics have been conducted in mammalian cells in culture (for reviews see (10, 11)). The experimental convenience of effecting rapid switching between a labeled and a subsequent unlabeled precursor pool by medium exchange is, however, offset by the fact that rapidly dividing cells are able to “solve” the problem of protein level adjustment by dilution into progeny cells. This dilution of the isotopically labeled pool not only restricts the scope to monitor the labeled pool but also may be focusing turnover studies on cells that bear little resemblance in their protein turnover to the same or similar cells in a tissue (11, 12). There is therefore a requirement to determine protein turnover in intact animals, which imposes considerable complexity in experimental design and data analysis (13–16). In tissues, protein turnover is substantially slower than in cells in culture (12, 17), and it is necessary to administer label for extended periods, rendering oral (food or drinking water) administration as the only feasible option.Measurement of turnover in rapidly growing cells in culture suffers from the rapid loss or gain of label as a consequence of growth and, thus, dilution of the labeled protein pool. By contrast, measurement of turnover in animal tissues, particularly in nongrowing individuals, requires a different strategy (13, 14, 16, 18–20). It is challenging and prohibitively expensive to label animals fully over multiple generations and subsequently monitor the loss of label over time. Further, a strategy that measures the transition between fully labeled and fully unlabeled proteins requires specialist, completely labeled diets that differ substantially from normal laboratory diets. To circumvent such difficulties, we have developed a strategy based on the addition of a single stable isotope labeled amino acid to a laboratory diet, such that the isotopic enrichment of the total amino acid in the diet would be ∼0.5. The precise degree of dietary labeling is not critical, as this is revealed during analysis. Animals are acclimated to the modified diet containing nonlabeled amino acid before being transferred to the same composition, labeled diet. Subsequently, incorporation of label into the body precursor pool can be monitored noninvasively by measurement of the relative isotope abundance (RIA)¹ of secreted proteins, particularly those released in urine (16). We have previously used the essential amino acid, valine, to measure protein turnover in the house mouse, Mus musculus domesticus (16). The valine was administered by supplementation of a standard laboratory diet by incorporation of crystalline [²H₈]valine to the same level as originally present in the diet (in protein bound or free form). Thus, the dietary RIA for the valine was set to a nominal value of 0.5. This approach worked very well, apart from an additional (but surmountable, (16)) complication due to partial transamination of the valine that led to loss of the alpha carbon deuteron to form a mixture of [²H₈] and [²H₇]valine. In this study, to simplify the strategy for determination of protein turnover rates, we have substituted [¹³C₆]lysine for the [²H₈]valine used previously. Lysine is also an essential amino acid, and so the RIA of the precursor pool cannot be reduced by biosynthesis de novo. Moreover, the labeling at the six carbon atoms precludes complications due to metabolic loss of specific atom centers. Finally, approximately half of the tryptic peptides (those that are lysine-terminated or which contain an internal LysPro sequence) should yield informative turnover data, although all tryptic peptides (both lysine and arginine terminated) can of course be used for protein identification.We are interested in the allometric scaling of proteome turnover, which will require approaches that recover high-quality turnover rates from species for which fully annotated proteomes do not exist. To test the feasibility of this approach, we selected as our experimental system a rodent of similar body mass to the house mouse, the bank vole Myodes glareoulus. The annotated genome sequence of this rodent is not available, and thus, the measurement of protein turnover in this species brings two challenges: that of cross-species identification and also the recovery of species-specific turnover parameters. Finally, we have provided a robust analytical approach to the determination of protein turnover rates using the statistical package R that is thus amenable to use by all groups working in the field.     

Diurnal response in endogenous amino acid oxidation of meal-fed rats.

A model has been developed to measure the effects of dietary protein on daily fluctuations in the rate of endogenous amino acid oxidation in meal-fed and starved rats. In addition, N tau-methylhistidine and hydroxyproline were utilized to determine changes in the rate of degradation of myofibrillar and collagen proteins. In rats meal-fed a normal diet of 18% (w/w) casein, a diurnal response was observed in rate of oxidation of radioactive amino acids contained in endogenous labelled body protein, with a nadir 16--20 h and maximum 4--8 h after beginning the feeding. This observation in part may be related to alterations in flux of amino acids from non-hepatic tissues to site of oxidation in liver, as well as alterations in rates of amino acid oxidation after a protein meal. When meal-fed a 70% protein diet, the maximal rates of endogenous amino acid oxidation were significantly increased by 4--8 h after meal-feeding, with no change in fractional rates of degradation of myofibrillar- or collagen-protein breakdown. This could suggest increases in activities of enzymes involved in amino acid oxidation, in rats meal-fed 70% compared with 18% dietary protein. In contrast, meal-feeding of a protein-free diet muted the diurnal response in the rate of oxidation of endogenously labelled amino acids, which correlated with a decrease in the fractional rate of degradation of myofibrillar or collagen protein. Thus dietary protein is apparently responsible for the observed diurnal rhythm rhythms in the rate of amino acid oxidation, whereas carbohydrates tend to mute the response.     

Problems associated with the labelling of RNA with radioactive precursors in vivo (author's transl)]

The radioactivity of RNA, DNA and proteins in the liver, muscles and cerebrum of 30-day-old rats after labelling with [3H]uridine, [14C]uridine, [3H]cytidine or [3H]orotic acid was measured. It was found that after administration of [3H]uridine, the proteins were 5 - 10 times more radioactive than the RNA. After administration of [14C]uridine, the proteins were 1 - 2 times more heavily labelled than the RNA. Hydrolysis of the proteins followed by chromatography of the amino acids revealed that the protein labelling was mostly due to [3H]glutamate. In the liver, [3H]orotic acid produced very specific labelling of the RNA. The radioactivity of the proteins is very slight. However, the specific labelling of the RNA in the muscles and cerebrum is not so pronounced with this precursor. [3H]Cytidine is an ideal precursor for RNA. The labelling of protein in all three organs examined is very slight, and furthermore, the specific activity of the RNA is 10 - 20 times higher than after labelling with uridine. We were also able to show that after labelling with radioactive uridine, the method of isolation of RNA by alkaline hydrolysis gives incorrect results, because [3H]amino acids interfere with the measurement of the specific activity of the RNA. The heavy labelling of proteins by [3H]-uridine must also be taken into account in histoautoradiography, because our experiments showed that in liver, the proteins in the cell nucleus are 3 times as radioactive as the nucleic acids. The particulate components of the cytoplasm are even 20 times more radioactive than the nucleic acids.     

The effect of thiamine deficiency on the turnover of lactate dehydrogenase in mouse tissues

• 1.1. Groups of mice were subjected to different degrees of thiamine deprivation in their diet. In particular, the effects of complete thiamine deficiency and a continuation of minimal nutritional levels of thiamine were compared.
• 2.2. The effects of these treatments on the turnover characteristics of lactate dehydrogenase and total soluble protein have been studied by means of double labelling experiments, and determinations of the relative emphases of synthesis and degradation of these tissue components.
• 3.3. Marked divergences from normal were apparent with each of these nutritional regimens-complete thiamine deficiency causing a considerably increased rate of degradation for both total protein and lactate dehydrogenase in all tissues; whereas maintenance of minimal levels of thiamine led to increased degradation of total protein in liver, but reduced rates of degradation for lactate dehydrogenase in brain, heart and liver.
• 4.4. The significance of these results has been discussed in relation to the relative influence of vitamin and calorie deficiencies on turnover parameters, the individuality of specific tissue behaviour, differences in protein redistribution in response to separate physiological perturbations, and the role of thiamine in specific proteolysis.

     

Effect of administration of diethylhexyl phthalate on the function and turnover of rat hepatic mitochondria

Administration of the widely used plasticizer di(2-ethylhexyl)phthalate (2% w/w) in the diet to the rat caused proliferation of mitochondria in the liver. The number of mitochondria as well as the amount of protein recovered in the organellar fraction was doubled. Mitochondria isolated from the livers of treated animals showed decreased (50%) respiratory activity. The content and activity of cytochrome oxidase were also decreased. The specific incorporation of amino acids into the proteins of whole liver and of mitochondria was not increased in plasticizer-treated animals. Isolated mitochondria also did not show any difference in the rate of incorporation of amino acids into proteins. The half-lives of whole liver proteins and of mitochondria were increased in plasticizer-fed animals. The half-life of cytochrome oxidase, however, was unaffected by the treatment. The pattern of double labeling of mitochondrial proteins confirmed decreased turnover in plasticizer-treated animals.     

A direct effect of growth hormone on the incorporation of precursors into proteins and nucleic acids of perfused rat liver

1. The livers of rats were perfused in situ. When the amino acid concentration in the perfusing medium was that present in rat plasma, the addition of growth hormone to the medium stimulated the incorporation of labelled amino acids into liver protein only marginally and not to a statistically significant extent. When, however, the amino acid concentration was raised to three times that present in rat plasma, growth hormone significantly and substantially stimulated amino acid incorporation into protein within 30min. of perfusion of normal rat liver. 2. A significant effect of growth hormone on labelling of normal rat-liver protein was seen with concentrations not much greater than those reported to be present in rat plasma. 3. The labelling of nucleic acids of normal and hypophysectomized rat liver by [(3)H]orotic acid was enhanced by addition of growth hormone to the perfusing medium when normal concentrations of amino acids were used. 4. At elevated concentrations of amino acids, growth hormone stimulated labelling of nucleic acids of hypophysectomized rat liver at 30 and 60min. of perfusion. Under these conditions, nucleic acids of normal rats were labelled to about the same extent in control and hormone-treated livers at 30min. and, because of a fall in the radioactivity of the control livers, there was more labelled nucleic acids in growth-hormone-treated livers at 60min. than in the control livers. 5. Growth hormone, unlike insulin, had no inhibitory effect on the release of glucose by the perfused liver. 6. It is concluded that growth hormone can stimulate the incorporation of precursor into proteins and nucleic acids of liver directly and without the mediation of other organs or of insulin.     

SILAC zebrafish for quantitative analysis of protein turnover and tissue regeneration

Defective tissue regeneration is thought to contribute to several human diseases, including neurodegenerative disorders, heart failure and various lung diseases. Boosting the regenerative capacity has been suggested a possible therapeutic approach. Methods to metabolically label newly synthesized proteins in vivo with stable isotopic forms of amino acids holds promise for the study of protein turnover and tissue regeneration that are fundamental to the sustained life of all organisms. Here, we used the "stable isotope labeling with amino acids in cell culture" (SILAC) approach to explore normal protein turnover and tissue regeneration in adult zebrafish. The ratio of labeled and unlabeled proteins/peptides in specific organs of zebrafish fed a SILAC diet containing (13)C(6)-labeled lysine was determined by liquid chromatography and tandem mass spectrometry. Labeling was highest in tissues with high regenerative capacity, including intestine, liver, and fin, whereas brain and heart displayed the lowest labeling. Proteins with high degree of labeling were mainly involved in catalytic or transport activity pathways. The technique also verified increased protein synthesis during regeneration of the caudal fin following amputation. This newly developed SILAC zebrafish model constitutes a novel tool to analyze tissue regeneration in an animal model amenable to genetic and pharmacologic manipulation.     

Topograph,a Software Platform for Precursor Enrichment Corrected Global Protein Turnover Measurements

Defects in protein turnover have been implicated in a broad range of diseases, but current proteomics methods of measuring protein turnover are limited by the software tools available. Conventional methods require indirect approaches to differentiate newly synthesized protein when synthesized from partially labeled precursor pools. To address this, we have developed Topograph, a software platform which calculates the fraction of peptides that are from newly synthesized proteins and their turnover rates. A unique feature of Topograph is the ability to calculate amino acid precursor pool enrichment levels which allows for accurate calculations when the precursor pool is not fully labeled, and the approach used by Topograph is applicable regardless of the stable isotope label used. We validate the Topograph algorithms using data acquired from a mouse labeling experiment and demonstrate the influence that precursor pool corrections can have on protein turnover measurements.Methods of measuring protein synthesis and degradation using stable or radioactive isotope labels have existed for decades. The isotope label is introduced in the form of a labeled amino acid or amino acid precursor, and the incorporation or removal of that label from protein is used to estimate average protein turnover rates (1, 2). Historically, the amount of stable isotope label incorporated into a protein is measured by enriching for the protein (e.g. affinity chromatography, gel electrophoresis, and other biochemical methods), hydrolyzing the protein to amino acids, derivatizing the amino acids, and measuring the labeled amino acid by gas chromatography-mass spectrometry or gas chromatography-combustion-isotope ratio mass spectrometry (3, 4). More recently, proteomics methods have been developed that measure the labeled amino acid on the peptide level, eliminating the need for a protein enrichment step and enabling the monitoring of many proteins in a single experiment (5).Proteomics approaches to measuring protein turnover rates in mice have been accomplished by the introduction of a ¹⁵N stable isotope label. The labeled diets were created by supplementing a protein-free diet with a ¹⁵N enriched protein source. Price et al. (6) generated ¹⁵N-labeled protein from the alga, Spirulina platensis and Zhang et al. (7) introduced ¹⁵N-label in the form of lysate from the bacterium, Ralstonia eutropha. An advantage of using complete ¹⁵N labeling is the rapid incorporation of ¹⁵N and separation of isotope distributions between labeled and natural isotope abundance peptides, which reduces the need to deconvolute the two distributions. However, current methods require that the dietary protein content be derived from bacterial or alga lysate, a diet that is not normally fed to laboratory mice. As a result, measurements of protein turnover may not reflect conventional mouse model systems because of effects of diet on protein and amino acid metabolism. A more recent work by Claydon et al. (8) demonstrated a stable isotope labeling method by supplementing labeled valine into a standard mouse diet.The complex data generated from these analyses creates a data processing and analysis challenge; exemplified by recent software platforms that have been developed. Guan et al. (9) and Hoopmann et al. (10) demonstrated data analysis pipelines for ¹⁵N labeled SILAM and SILAC experiments. Here we describe the software platform, Topograph, we have developed for the analysis of liquid chromatography-tandem MS (LC-MS/MS) data from samples with isotopic labels. Topograph is able to deconvolute the complex spectra that may result from overlapping isotope distributions, regardless of the isotope label used. More uniquely, Topograph is able to calculate the relative isotope abundance (RIA)¹ of the amino acid precursor pool, which is necessary to correctly determine the amount of newly synthesized peptide and to subsequently calculate peptide and protein turnover rates.     

Mitochondrial turnover in liver is fast in vivo and is accelerated by dietary restriction: application of a simple dynamic model

'Mitochondrial dysfunction', which may result from an accumulation of damaged mitochondria in cells due to a slowed-down rate of mitochondrial turnover and inadequate removal of damaged mitochondria during aging, has been implicated as both cause and consequence of the aging process and a number of age-related pathologies. Despite growing interest in mitochondrial function during aging, published data on mitochondrial turnover are scarce, and differ from each other by up to one order of magnitude. Here we demonstrate that re-utilization of the radioactively labelled precursor in pulse-chase assays is the most likely cause of significant overestimation of mitochondrial turnover rates. We performed a classic radioactive label pulse-chase experiment using (14)C NaHCO(3), whose (14)C is incorporated into various amino acids, to measure mitochondrial turnover in mouse liver. In this system, the activity of the urea cycle greatly limited arginine dependent label re-utilization, but not that of other amino acids. We used information from tissues that do not have an active urea cycle (brain and muscle) to estimate the extent of label re-utilization with a dynamic mathematical model. We estimated the actual liver mitochondrial half life as only 1.83 days, and this decreased to 1.16 days following 3 months of dietary restriction, supporting the hypothesis that this intervention might promote mitochondrial turnover as a part of its beneficial effects.     

Effects of niacin deficiency on the relative turnover rates of proteins in various tissues of Japanese quail

• 1.1. The effects of niacin deficiency on the relative turnover rates of proteins in various tissues of Japanese quail were investigated.
• 2.2. The level of liver NAD was not affected by niacin deficiency whereas the level of pectoral muscle NAD was markedly reduced.
• 3.3. In all dietary treatments the liver had the highest turnover rates of proteins, heart and brain had intermediate rates, and pectoral muscle had the lowest rates.
• 4.4. Relative turnover rates of proteins in all tissues (particularly pectoral muscle) of the niacin deficient group were significantly higher than those of pair-fed control group, although there were no significant differences in turnover rate between pair-fed control and control groups.
• 5.5. The high turnover rate of proteins in niacin deficiency was primarily attributed to enhanced degradation rate of proteins rather than enhanced synthesis rate of proteins.
• 6.6. Optical density scanning (or densitometric) of water-soluble pectoral muscle proteins separated by isoelectric focusing revealed several additional minor protein bands between major protein bands in the niacin deficient group which were more pronounced in the acidic region of the gel.
• 7.7. These results suggest that proteins with a low pI value in pectoral muscle of the niacin deficient animal are highly sensitive to protein degradation.

     

Amino acid requirement for the growth-hormone stimulation of incorporation of precursors into protein and nucleic acids of liver slices

1. Incorporation of [(14)C]leucine into protein in rat liver slices, incubated in vitro, increased as the concentration of unlabelled amino acids in the incubation medium was raised. A plateau of incorporation was reached when the amino acid concentration was 6 times that present in rat plasma. Labelling of RNA by [(3)H]orotic acid was not stimulated by increased amino acid concentration in the incubation medium. 2. When amino acids were absent from the medium, or present at the normal plasma concentrations, no effect of added growth hormone on labelling of protein or RNA by precursor was observed. 3. When amino acids were present in the medium at 6 times the normal plasma concentrations addition of growth hormone stimulated incorporation of the appropriate labelled precursor into protein of liver slices from normal rats by 31%, and into RNA by 22%. A significant effect was seen at a hormone concentration as low as 10ng/ml. 4. Under the same conditions addition of growth hormone also stimulated protein labelling in liver slices from hypophysectomized rats. Tissue from hypophysectomized rats previously treated with growth hormone did not respond to growth hormone in vitro. 5. No effect of the hormone on the rate or extent of uptake of radioactive precursors into acid-soluble pools was found. 6. Cycloheximide completely abolished the hormone-induced increment in labelling of both RNA and protein. 7. It was concluded that, in the presence of an abundant amino acid supply, growth hormone can stimulate the synthesis of protein in rat liver slices by a mechanism that is more sensitive to cycloheximide than is the basal protein synthesis. The stimulation of RNA labelling observed in the presence of growth hormone may be a secondary consequence of the hormonal effect on protein synthesis. 8. The mechanism of action of growth hormone on liver protein synthesis in vitro was concluded to be similar to its mechanism of action in vivo.     

Protein degradation in skeletal muscle: implications of a first order reaction for the degradative process

The rate of protein degradation is usually thought to be first order, i.e. determined by the nature of the protein as a substrate. It is not immediately apparent if this is the case for the overall process in the cell since rates of turnover of individual proteins may vary between tissues. In muscle the characteristics of protein turnover in relation to DNA-unit size have led to the development of a model for protein turnover in which degradation rates are determined by the rate of dissociation of protein subunits from the myofibrillar matrix. This is a necessary step if heterogeneous turnover occurs and if degradation and resynthesis of myofibrillar proteins occurs peripherally to the myofibril. As a result a first order rate can be envisaged so that during muscle growth the protein mass per unit DNA increases to a characteristic amount thus determining the specific activity of the degrading system. Such a mechanism may apply to all cells.