Turnover and Exchange of Ribosomal Proteins from Rat Liver

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.

•

Controlled comparison of heavy water or amino acid labeling for protein turnover.

•

Delays in amino acid precursor labeling mostly affect high turnover proteins

•

Both methods produced similar turnover rates after adjustment of precursor kinetics.

•

Recommendations for analytical workflows for protein turnover studies in animals.

Question-driven stepwise experimental discoveries in biochemistry: two case studies

Philosophers of science diverge on the question what drives the growth of scientific knowledge. Most of the twentieth century was dominated by the notion that theories propel that growth whereas experiments play secondary roles of operating within the theoretical framework or testing theoretical predictions. New experimentalism, a school of thought pioneered by Ian Hacking in the early 1980s, challenged this view by arguing that theory-free exploratory experimentation may in many cases effectively probe nature and potentially spawn higher evidence-based theories. Because theories are often powerless to envisage workings of complex biological systems, theory-independent experimentation is common in the life sciences. Some such experiments are triggered by compelling observation, others are prompted by innovative techniques or instruments, whereas different investigations query big data to identify regularities and underlying organizing principles. A distinct fourth type of experiments is motivated by a major question. Here I describe two question-guided experimental discoveries in biochemistry: the cyclic adenosine monophosphate mediator of hormone action and the ubiquitin-mediated system of protein degradation. Lacking underlying theories, antecedent data bases, or new techniques, the sole guides of the two discoveries were respective substantial questions. Both research projects were similarly instigated by theory-free exploratory experimentation and continued in alternating phases of results-based interim working hypotheses, their examination by experiment, provisional hypotheses again, and so on. These two cases designate theory-free, question-guided, stepwise biochemical investigations as a distinct subtype of the new experimentalism mode of scientific enquiry.

On-Site Ribosome Remodeling by Locally Synthesized Ribosomal Proteins in Axons

Ribosome assembly occurs mainly in the nucleolus, yet recent studies have revealed robust enrichment and translation of mRNAs encoding many ribosomal proteins (RPs) in axons, far away from neuronal cell bodies. Here, we report a physical and functional interaction between locally synthesized RPs and ribosomes in the axon. We show that axonal RP translation is regulated through a sequence motif, CUIC, that forms an RNA-loop structure in the region immediately upstream of the initiation codon. Using imaging and subcellular proteomics techniques, we show that RPs synthesized in axons join axonal ribosomes in a nucleolus-independent fashion. Inhibition of axonal CUIC-regulated RP translation decreases local translation activity and reduces axon branching in the developing brain, revealing the physiological relevance of axonal RP synthesis in vivo. These results suggest that axonal translation supplies cytoplasmic RPs to maintain/modify local ribosomal function far from the nucleolus in neurons.

Invariable stoichiometry of ribosomal proteins in mouse brain tissues with aging

Across phyla, the ribosomes-the central molecular machines for translation of genetic information-exhibit an overall preserved architecture and a conserved functional core. The natural heterogeneity of the ribosome periodically phases a debate on their functional specialization and the tissue-specific variations of the ribosomal protein (RP) pool. Using sensitive differential proteomics, we performed a thorough quantitative inventory of the protein composition of ribosomes from 3 different mouse brain tissues, i.e., hippocampus, cortex, and cerebellum, across various ages, i.e., juvenile, adult, and middle-aged mouse groups. In all 3 brain tissues, in both monosomal and polysomal ribosome fractions, we detected an invariant set of 72 of 79 core RPs, RACK1 and 2 of the 8 RP paralogs, the stoichiometry of which remained constant across different ages. The amount of a few RPs punctually varied in either one tissue or one age group, but these fluctuations were within the tight bounds of the measurement noise. Further comparison with the ribosomes from a high-metabolic-rate organ, e.g., the liver, revealed protein composition identical to that of the ribosomes from the 3 brain tissues. Together, our data show an invariant protein composition of ribosomes from 4 tissues across different ages of mice and support the idea that functional heterogeneity may arise from factors other than simply ribosomal protein stoichiometry.

RACK1 on and off the ribosome

Receptor for activated C kinase 1 (RACK1) is a eukaryote-specific ribosomal protein (RP) implicated in diverse biological functions. To engineer ribosomes for specific fluorescent labeling, we selected RACK1 as a target given its location on the small ribosomal subunit and other properties. However, prior results suggested that RACK1 has roles both on and off the ribosome, and such an exchange might be related to its various cellular functions and hinder our ability to use RACK1 as a stable fluorescent tag for the ribosome. In addition, the kinetics of spontaneous exchange of RACK1 or any RP from a mature ribosome in vitro remain unclear. To address these issues, we engineered fluorescently labeled human ribosomes via RACK1, and applied bulk and single-molecule biochemical analyses to track RACK1 on and off the human ribosome. Our results demonstrate that, despite its cellular nonessentiality from yeast to humans, RACK1 readily reassociates with the ribosome, displays limited conformational dynamics, and remains stably bound to the ribosome for hours in vitro. This work sheds insight into the biochemical basis of RPs exchange on and off a mature ribosome and provides tools for single-molecule analysis of human translation.

Advances in protein turnover analysis at the global level and biological insights

The concept of a dynamic state of body constituents, a precursor of the modern term of proteome dynamics, was conceived over a century ago. But, not until recently can we examine the dynamics of individual "constituents" for example, proteins at a truly global level. The path of advancement in our understanding of protein turnover at the global level is marked by the introduction of some key technological innovations. These methods include the isotopic tracer technique in the 1930s, the two-dimensional gel electrophoresis technique in the 1970s, the sector mass spectrometer that could analyze isotopomers of peptides in the early 1990s, the 2D gel/MALDI-TOF proteomics technology in the late 1990s, the booming liquid chromatography/mass spectrometry proteomics technology in this decade, and the recently emerging protein-tagging approaches that offer single-cell resolution for protein turnover measurements. The long-standing inquiry raised in the 1950s about the existence of a dynamic state in different organisms at different physiological conditions can now be answered with an individual "constituent" resolution on a truly global scale. Now it appears that protein degradation is not necessarily an end to the protein function. Rather, it can be the start of a new function because protein degradation clears the way for the action of other proteins. Protein turnover participates in a multi-layer complex regulatory network and shares equal importance with gene transcription and protein translation. The advances in technologies for protein turnover analysis and the improved understanding of the biological role of protein turnover will likely help to solve some long-standing biomedical problems such as the tuberculosis disease that at the present day still affects one-third of the world population.

Is protein degradation correlated with either the charge or size of Lemna proteins?

Evidence is presented that the organelles of Lemna minor do not degrade as functional units. The proteins of Lemna show wide differences in their rates of degradation and ribulose bisphosphate carboxylase (EC 4.1.1.39) has a particularly slow rate of degradation. Contrary to some earlier evidence, we found no correlation between the rate of soluble-protein degradation and either charge or size of proteins. We could find no correlation between protein degradation and subunit size in any of the organelles of Lemna.

Amino acid incorporation in relation to molecular weight of proteins in young and adult brain

Rates of protein synthesis were studied in immature and adult rat brain tissue. After an amino acid incorporation period, in vivo or in incubated slices from brain, the soluble protein was fractionated according to molecular weight by column chromatography. In examining soluble whole proteins, no direct correlation between molecular weights and synthesis rates could be established; the highest synthesis rates were found in fractions around 70,000 MW and below 10,000. Incorporation into the subunits after fractionation by SDS gel electrophoresis was proportional to subunit molecular weight, with rates of incorporation into the largest subunits being the highest. The results suggest a relationship between turnover rate and structure of subunits of brain proteins.

CTP:phosphocholine cytidylyltransferase in intestinal mucosa

CTP:phosphocholine cytidylyltransferase is thought to be a rate-limiting enzyme in phosphatidylcholine synthesis. This enzyme has not been well studied in intestine. We found that activity was greater in the non-lipid stimulated state (cytosolic form of the enzyme) than any previous tissue investigated (2.7 nM/min per mg protein). On addition of lysophosphatidylethanolamine, the enzyme only increased in activity 2.4-fold which is less than any previously reported tissue on lipid stimulation. As compared to liver, the enzyme was resistant to inhibition by chlorpromazine (gut, 100% activity remaining at 80 microM; 14% in liver). Tetracaine and propranolol were found to be impotent as inhibitors of the intestinal enzyme. Octanol-water partitioning showed that both chlorpromazine and tetracaine were hydrophobic, propranolol was not. pKa studies demonstrated that at the reaction pH, chlorpromazine would be uncharged. Physiologic experiments in which de novo phosphatidylcholine synthesis was either stimulated by bile duct fistulization and triacylglycerol infusion or suppressed by including phosphatidylcholine in a lipid infusion demonstrated that the enzyme (cytosolic enzyme) responded by decreasing Vmax but that the Km remained the same. In sum, these studies suggest that CTP:phosphocholine cytidylyltransferase in intestine is unique as compared to other tissues and that its response to a physiological stimulus is counter to that which would be adaptive.

Ontogenic variations in the interactions of lactate dehydrogenase isozymes with cellular structure

The interactions of the LDH isozymes with cellular structure have been studied in the major tissues of the mouse during development. Overall, there is a clear indication that interactions between LDH and cellular structure are appreciable in all major tissues and at all stages of development, and an analysis of the isozyme status of the enzyme in both soluble and bound compartments has been effected. Information has been provided supporting the preferential binding of the A type activity to actin filaments. The data provided also support the concept of pelletable B type LDH in kidney and brain during the postnatal period. Binding was particularly extensive in the early embryonic stages, and the significance of this phenomenon, and the subcellular interactions observed to varying degrees in all the tissues throughout development, have been discussed in relation to the known metabolic characteristics of these separate tissue situations.

Constancy of ribosomal RNA genes during aging of mouse heart cells and during serial passage of WI-38 cells

The DNA content and ribosomal RNA gene copy number in heart of the inbred mouse strain C57BL/6 were determined at different ages. The DNA content of mouse heart remained constant, at about 150 micrograms DNA per heart, from 1 to 30 mth of age. The number of rRNA genes, as estimated by 28S rRNA . DNA hybridization, was not found to change significantly as a function of age. Likewise, the extent of rRNA hybridization to DNA from cultured human WI-38 cells at early and late passage levels was the same. These data support the notion that genomic rDNA sequences are not lost during in vivo and in vitro aging. However, the rDNA sequences are quite large and numerous small deletions or base pair substitutions would not have been detected in these studies.

Minireview. Roles of turnover and repair of macromolecules and supramolecular structural components

Macromolecules and supramolecular structural components that are incorrectly synthesized or are damaged by radiation or by reactive chemicals are either repaired or selectively degraded and resynthesized. In addition, turnover rates for macromolecules and supramolecular structures can be elevated by alternation of fasting and feeding periods and can be influenced by metabolic regulatory mechanisms which are governed by steady-state concentrations of labile macromolecules.

Effect of phalloidin on liver actin distribution, content, and turnover

Phalloidin increases F-actin microfilament content and actin-directed immunofluorescence in hepatocytes in vivo and also increases actin polymerization and the stability of F-actin in vitro. We studied the sensitivity of immunofluorescent staining of actin to an actin depolymerizing factor (ADF) as well as actin content, degree of polymerization, and turnover in livers of in vivo phalloidin-treated rats. Pretreatment with ADF abolished anti-actin antibody (AAA) staining of normal liver but did not modify staining of livers from phalloidin-treated animals. Planimetric analyses of SDS-polyacrylamide gels showed the percent actin of total protein was increased by approximately 40% and the absolute amount of actin by approximately 43%, ten days after daily phalloidin treatment (50 micrograms/100 gm body weight). Similar but smaller changes could be seen after one day of treatment. Ultracentrifugational analyses of liver extracts indicated no change in the amount or proportion of G-actin but a 194% increase in the proportion of F-actin in ten-day treated animals, changes also apparent in one day animals. Neither the relative fractional rate of actin synthesis nor its synthesis as a percent of total protein synthesis was altered either at one-day or ten-day post-phalloidin treatment. Dualisotope experiments indicated that the rate of actin degradation was decreased selectively in the one- to three-day period following drug treatment. Thus, phalloidin appears to stabilize actin against the depolymerizing actions of ADF, increases the proportion of F-actin without altering the size of the G-actin pool, and causes accumulation of actin by decreasing its relative rate of degradation.

The role of intracellular lysosomal enzymes in the autocellular-surveillance of unhydroxylated collagens in dermal and gingival fibroblasts

The turnover of unhydroxylated collagen was investigated in dermal and gingival fibroblasts derived from C57Bl/6J mice. Unhydroxylated collagen molecules were fostered by the inhibition of prolyl- and lysyl-hydroxylase by the addition of alpha, alpha' dipyridyl. Turnover of collagens was determined by single isotope continuous labeling, double-isotopic labeling, the use of lysosomal pH modulators, and proteinase inhibitors. These studies reveal that the turnover of unhydroxylated collagen is an extracellular event, in spite of the susceptibility of these abnormal structural and conformational proteins to proteolysis; the synthesizing cell does not utilize intracellular lysosomal enzymes as a means of modulating the quantities of non-helical unhydroxylated collagen as an intolerable post-translational error of protein processing.

Two-dimensional electrophoretic analysis of ribosomal proteins from chronically injured liver

Proteins of the small and large ribosomal subunit, isolated at various times from long-term thioacetamide-damaged rat livers, were analysed by two-dimensional polyacrylamide gel electrophoresis and compared with those from normal liver. Chronic hepatic injury induced a number of time-dependent changes of the structural proteins of the small subunit, whereas the proteins of the large subparticle were essentially unaffected. The most significant alterations were an anodical dislocation of protein S6, a strong diminution in the amounts of proteins S9 and S10 and the occurrence of 3 to 4 additional small subunit proteins. By autoradiographic studies it was established that the modifications of S6 were brought about by an enhanced phosphorylation of this protein, which was the earliest sign of a ribosomal alteration in injured liver tissue.

Ribosomal proteins synthesis and exchange in the absence of 28-S and 18-S ribosomal RNA synthesis in L5178Y cells

The effect of the adenosine analogue toyocamycin on ribosomal proteins synthesis and assembly within ribosomal particles was investigated in the murine cells, L5178Y. The analogue was used for periods not exceeding 5 h, at a concentration which permits the synthesis of ribosomal precursor RNA but inhibits the maturation process. The following observations were made: 1. Ribosomal proteins, synthesized de novo in the presence of the drug, were associated with toyocamycin-containing 45-S pre-rRNA in preribosomal-like 80-S ribonucleoproteins which accumulated in the nucleolus. Two-dimensional electrophoresis revealed a full protein complement of these particles, although minor discrepancies were observed in the relative proportions of a limited number of polypeptides. 2. In the absence of 28-S and 18-S rRNA formation, a surprisingly high proportion of newly synthesized ribosomal proteins were incorporated into high-salt washed ribosomal subunits. The extent of individual protein exchange as well as their apparent turnover rates were markedly heterogeneous. Most of these exchangeable proteins were shown to be labeled rapidly in ribosomal subunits of normal cells. Some alternative interpretations of these results are discussed.

Cigarette smoke components and alveolar macrophage protein synthesis

A comparison was made of the effects of acrolein and aqueous cigarette smoke extracts on amino acid incorporation into protein by rabbit pulmonary alveolar macrophages. Studies were on cells maintained in vitro as adherent monolayers. Freshly prepared acrolein inhibited amino acid incorporation by significant amounts after approximately 30 min and aqueous smoke extracts after approximately 15 min of incubation. Fifty percent inhibition by acrolein occurred with a dose of 5.5 microgram acrolein/ml, an amount four times that in the amount of aqueous smoke extract required for 50% inhibition according to previously reported findings. Analysis by a dual-isotope technique and sodium dodecyl sulfate polyacrylamide gel electrophoresis showed the inhibitory effect of acrolein to be nonspecific, as had previously been found for aqueous smoke extracts. The presence of the sulfhydryl reagent cysteine, reduced the inhibitory effect of acrolein by 57.5%, but reduced inhibition induced by aqueous smoke extracts by only 12.2%. These results suggest the effects of acrolein are both quantitatively and qualitatively different than those of aqueous smoke extracts.

Isolation and characterization of free cytoplasmic messenger ribonucleoproteins from rabbit reticulocyte

Free cytoplasmic messenger ribonucleoproteins have been prepared with a high yield in a zonal rotor. They are rapidly labelled by [3H]uridine. Their sedimentation coefficients are 14.6 S and 19.4 S. Their protein contents are higher than in ribosomes, as indicated by a shift towards greater wavelength in their ultraviolet spectra and a buoyant density of 1.39 g cm-2 in CsCl. They do not cross-react with antiribosome antibodies and their protein patterns in sodium dodecylsulfate and two-dimensional polyacrylamide gel electrophoresis are different from ribosomes'. They may contain up to 30 proteins. The proteins are acidic and their molecular weights range from 22 000 to 100 000. When compared to chromatin they behave more like non-histone proteins than histones.

In vivo isotope incorporation patterns into HeLa ribosomal proteins

When cells were incubated with L-[35S] methionine plus L-[Me-3H] methionine, it was found that at least four ribosomal proteins had 3H/35S ratios higher than the rest of the ribosomal proteins, suggesting that they were methylated. The rate of apparent methylation paralleled the rate of amino acid incorporation. Amino acid incorporation into ribosomal proteins revealed several rapidly labeled components. When 3H-labeled amino acid incorporation was chased for 10 min with an excess of non-radioactive amino acids, several proteins reached at least 60% of the specific activity they showed after 150 min of chase. The time lapse between the onset of 3H-labeled amino acid incorporation and arrival at its plateau appeared to differ among various ribosomal proteins of a subunit, suggesting a heterogeneity in the pools of ribosomal proteins.

Liver protein synthesis. Molecular weight distribution of pulse-labeled polypeptide chains in normal and thyroidectomized rats

Equations are presented for determination of elongation rate in vivo for a heterogenous population of polypeptide chain molecular weights. The distribution of pulse-labeled polypeptide chains in rat liver deoxycholate-soluble protein has been obtained by sodium dodecyl sulfate-gel electrophoresis and used to compute a theoretical curve for determination of synthesis time of a 50000 mol. wt. polypeptide chain (tc50). Values of tc50 for normal and thyro-parathyroidectomized Long-Evans male rats were 1.2 and 1.75 min, respectively, representing protein synthetic rates of about 7.5 and 5.1 mg protein/g liver/h. No difference in the molecular weight profile of liver polypeptide chains on the basis of labeling or Amido-black staining was observed between the two groups. The distributions of radioactivity before and after secretion of labeled plasma protein are compared. The role of protein-synthetic rate in the changing enzyme levels associated with thyroid hormone is discussed.

Ribosomal RNA gene dosage as a function of tissue and age for mouse and human

The average number of rRNA genes per haploid genome (rRNA gene dosage) of the cells present in liver and brain was determined throughout the lifespan of the inbred C57BL/6J mouse strain and of human. Ribosomal RNA gene dosage was determined using the RNA-excess DNA - RNA hybridization technique. DNA was extracted and purified using a CsCl/chloroform method with a high percent yield (over 90%) to minimize any possible effects of tissue and age-dependent selective loss or gain of rRNA genes. Radioactive rRNA was from the liver of the youngest age group for either mouse or human in all hybridization experiments, with DNA from the different tissues and age groups being the only variable. In the young mouse (35-49 days), the rRNA gene dosage was 36% higher in brain (114 genes), as compared to liver (84 genes). The rRNA gene dosage remained essentially constant as a function of age for mouse brain; but between the age of about 220 to 440 days, it increased in liver, attaining approximately an equal value to that of brain. No significant difference was found in the rRNA gene dosage of brain or liver between different mice of the same age. In contrast to this result, a significant difference was found between human tissues of similar age. The rRNA gene dosage ranged about 2-fold (148-289) between 2 months to 75 years of age. An age-dependent trend, similar to that for mouse liver, was found when the averages of four different age groups totaling 20 individuals were compared. However, this was not statistically significant. No difference in the rRNA gene dosage as a function of sex or tissue was apparent. Several models are discussed to account for these results.

Enzyme histochemistry as a link between biochemistry and morphology

The presented paper describes the role of enzyme histochemistry in cell biological investigations. In the first chapter a general discussion has been given about enzyme histochemistry as a connecting link between biochemistry and morphology. The methods available for determination of enzymes in a particular cell or cell compartment have been reviewed. In this respect the characteristics of enzyme histochemistry have been discussed. Furthermore, attention has been paid to the possibilities and limitations of enzyme histochemistry. In chapter two a comparison has been made between histochemically judged and biochemically determined enzyme activities. Some fundamental differences between the biochemical and the histochemical approach in cell biological investigations are dealt with. To correlate histochemically and biochemically determined enzyme activities, a description has been given of the application of histochemical methods on isolated fractions and sucrose-ficoll gradients of these fractions. Several experimental results are described concerning the question whether a relation exists between histochemically and biochemically determined activities of respectively alkaline phosphatase, glucose-6-phosphatase, 5'-nucleotidase and 3ss-hydroxysteroid dehydrogenase. From these results the conclusion could be drawn that in general a good correlation exists between histochemically judged activity per volume (area X thickness) and biochemically determined activity per gram tissue. In chapter three the role of enzymes as markers of cellular particles and as parameters of metabolic pathways is described. Histochemical methods are available for most marker enzymes. Only activities of key enzymes can be regarded as parameters of metabolic pathways. The distribution in sucrose-ficoll gradients of enzymes, regarded as markers of mitochondria, lysosomes, endoplasmic reticulum and plasma membranes has been given. The changes occur ing under different experimental conditions for a number of marker enzymes in rat liver are described. Attention has been given to the contibution of enzyme histochemistry in the study of the heterogeneity of mitochondria, the dual localization of some (lysosomal) enzymes, the complexity of the microsomal fraction, the function of the Golgi apparatus and the heterogeneity and function of plasma membranes. Based on these results and on literature findings the possible role of some marker enzymes in cell metabolism has been discussed. In chapter four problems coherent with species and sex differences in enzyme activities are described. The interpretation of histochemical and biochemical results in view of these differences is discussed. Enzymes characteristic for a given cell type -3ss-hydroxysteroid dehydrogenase in steroid producing cells, ATP-ase in liver plasma membrane surrounding the bile canaliculi - do show less variations between species and sexes than enzymes not directly involved in specialized functions...

Biochemical aspects of cell death

Studies of cell injury and death at the molecular and cell-biological level will help to provide methods for the reconstruction of the course of events between the occurrence of primary pathology and the time of investigation. The general role of component turnover, energy metabolism and lysosomes in cellular injury is briefly described.