Intracellular protein and nucleic acid turnover in resting yeast cells

Global protein turnover quantification in Escherichia coli reveals cytoplasmic recycling under nitrogen limitation

Protein turnover is critical for proteostasis, but turnover quantification is challenging, and even in well-studied E. coli, proteome-wide measurements remain scarce. Here, we quantify the turnover rates of ~3200 E. coli proteins under 13 conditions by combining heavy isotope labeling with complement reporter ion quantification and find that cytoplasmic proteins are recycled when nitrogen is limited. We use knockout experiments to assign substrates to the known cytoplasmic ATP-dependent proteases. Surprisingly, none of these proteases are responsible for the observed cytoplasmic protein degradation in nitrogen limitation, suggesting that a major proteolysis pathway in E. coli remains to be discovered. Lastly, we show that protein degradation rates are generally independent of cell division rates. Thus, we present broadly applicable technology for protein turnover measurements and provide a rich resource for protein half-lives and protease substrates in E. coli, complementary to genomics data, that will allow researchers to study the control of proteostasis.

The purpose and ubiquity of turnover

Turnover-constant component production and destruction-is ubiquitous in biology. Turnover occurs across organisms and scales, including for RNAs, proteins, membranes, macromolecular structures, organelles, cells, hair, feathers, nails, antlers, and teeth. For many systems, turnover might seem wasteful when degraded components are often fully functional. Some components turn over with shockingly high rates and others do not turn over at all, further making this process enigmatic. However, turnover can address fundamental problems by yielding powerful properties, including regeneration, rapid repair onset, clearance of unpredictable damage and errors, maintenance of low constitutive levels of disrepair, prevention of stable hazards, and transitions. I argue that trade-offs between turnover benefits and metabolic costs, combined with constraints on turnover, determine its presence and rates across distinct contexts. I suggest that the limits of turnover help explain aging and that turnover properties and the basis for its levels underlie this fundamental component of life.

The Metabolic Flux Probe (MFP)-Secreted Protein as a Non-Disruptive Information Carrier for 13C-Based Metabolic Flux Analysis

Novel cultivation technologies demand the adaptation of existing analytical concepts. Metabolic flux analysis (MFA) requires stable-isotope labeling of biomass-bound protein as the primary information source. Obtaining the required protein in cultivation set-ups where biomass is inaccessible due to low cell densities and cell immobilization is difficult to date. We developed a non-disruptive analytical concept for ¹³C-based metabolic flux analysis based on secreted protein as an information carrier for isotope mapping in the protein-bound amino acids. This “metabolic flux probe” (MFP) concept was investigated in different cultivation set-ups with a recombinant, protein-secreting yeast strain. The obtained results grant insight into intracellular protein turnover dynamics. Experiments under metabolic but isotopically nonstationary conditions in continuous glucose-limited chemostats at high dilution rates demonstrated faster incorporation of isotope information from labeled glucose into the recombinant reporter protein than in biomass-bound protein. Our results suggest that the reporter protein was polymerized from intracellular amino acid pools with higher turnover rates than biomass-bound protein. The latter aspect might be vital for ¹³C-flux analyses under isotopically nonstationary conditions for analyzing fast metabolic dynamics.

Transamination governs nitrogen isotope heterogeneity of amino acids in rats

The nitrogen isotope composition (δ¹⁵N) of different amino acids carries different dietary information. We hypothesized that transamination and de novo synthesis create three groups that largely explain their dietary information. Rats were fed with ¹⁵N-labeled amino acids. The redistribution of the dietary ¹⁵N labels among the muscular amino acids was analyzed. Subsequently, the labeling was changed and the nitrogen isotope turnover was analyzed. The amino acids had a common nitrogen half-life of ∼20 d, but differed in δ¹⁵N. Nontransaminating and essential amino acids largely conserved the δ¹⁵N of the source and, hence, trace the origin in heterogeneous diets. Nonessential and nontransaminating amino acids showed a nitrogen isotope composition between their dietary composition and that of their de novo synthesis pool, likely indicating their fraction of de novo synthesis. The bulk of amino acids, which are transaminating, derived their N from a common N pool and hence their δ¹⁵N was similar.

Survival of a psychrophilic marine Vibrio under long-term nutrient starvation

Ant-300, a psychrophilic marine vibrio isolated from the surface water of the Antarctic convergence, was starved for periods of more than 1 year. During the first week of starvation, cell numbers increased from 100 to 800% of the initial number of cells. Fifty percent of the starved cells remained viable for 6 to 7 weeks while a portion of the population remained viable for more than 1 year. During the first 2 days of starvation, the endogenous respiration of the cells decreased over 80%. After 7 days, respiration had been reduced to 0.0071% total carbon respired per hour and remained constant thereafter. After 6 weeks of starvation, 46% of the cellular deoxyribonucleic acid had been degraded. Observation of the cellular deoxyribonucleic acid with Feulgen staining before starvation showed the average number of nuclear bodies per cell varied from 1.44 to 4.02 depending on the age of the culture. A linear relationship was found between the number of nuclear bodies per cell and the increase in cell numbers upon starvation. Our data suggest that Ant-300 is capable of surviving long periods of time with little or no nutrients and is therefore well adapted for the sparse nutrient conditions of the colder portions of the open ocean.

Calculation of the relative metastabilities of proteins in subcellular compartments of Saccharomyces cerevisiae

Background

Protein subcellular localization and differences in oxidation state between subcellular compartments are two well-studied features of the the cellular organization of S. cerevisiae (yeast). Theories about the origin of subcellular organization are assisted by computational models that can integrate data from observations of compositional and chemical properties of the system.

Presentation and implications of the hypothesis

I adopt the hypothesis that the state of yeast subcellular organization is in a local energy minimum. This hypothesis implies that equilibrium thermodynamic models can yield predictions about the interdependence between populations of proteins and their subcellular chemical environments.

Testing the hypothesis

Three types of tests are proposed. First, there should be correlations between modeled and observed oxidation states for different compartments. Second, there should be a correspondence between the energy requirements of protein formation and the order the appearance of organelles during cellular development. Third, there should be correlations between the predicted and observed relative abundances of interacting proteins within compartments.

Results

The relative metastability fields of subcellular homologs of glutaredoxin and thioredoxin indicate a trend from less to more oxidizing as mitochondrion – cytoplasm – nucleus. Representing the overall amino acid compositions of proteins in 23 different compartments each with a single reference model protein suggests that the formation reactions for proteins in the vacuole (in relatively oxidizing conditions), ER and early Golgi (in relatively reducing conditions) are relatively highly favored, while that for the microtubule is the most costly. The relative abundances of model proteins for each compartment inferred from experimental data were found in some cases to correlate with the predicted abundances, and both positive and negative correlations were found for some assemblages of proteins in known complexes.

Conclusion

The results of these calculations and tests suggest that a tendency toward a metastable energy minimum could underlie some organizational links between the the chemical thermodynamic properties of proteins and subcellular chemical environments. Future models of this kind will benefit from consideration of additional thermodynamic variables together with more detailed subcellular observations.

Stability of protein in intestinal epithelial cells

In vivo measurements have revealed a high degree of stability of synthesized protein in rapidly proliferating intestinal epithelial cells. A slow loss of protein has been found during migration of mature cells to the villus tip

Aerobic fermentation and the depletion of the amino acid pool in yeast cells

The amino acid pool of yeast cells, Saccharomyces cerevisiae, incubated with galactose remains at a constant level for 100 minutes. This is 30 minutes beyond the time at which the oxidative phase of the induced-enzyme formation begins. Washed yeast cells, the pools of which have been depleted 60 per cent by incubation with glucose, do not replenish their pools as do washed cells incubated without a substrate. These facts indicate that the induced enzymes are formed at least partially from pool-replenishing amino acids. The time of onset of pool depletion is the time at which the aerobic fermentation phase of induced-enzyme formation begins for cells incubated with galactose. With 0.1 per cent galactose the respiratory phase begins at 100 minutes but no aerobic fermentation nor pool depletion occurs. The rates of respiration and aerobic fermentation are constant for four glucose concentrations from 0.1 to 1.0 per cent. The amount of aerobicfermentation is proportional to the initial concentration of glucose. Amino acid pool depletion occurs for all concentrations but depletion ceases and is followed by pool replenishment after aerobic fermentation is complete. Ultraviolet radiations, which delay the appearance of the respiratory phase of induced-enzyme formation, completely eliminate both the appearance of aerobic fermentation and pool depletion. The results indicate an intimate association between aerobic fermentation and amino acid pool depletion.

REGULATION AND COORDINATION OF PURINE AND PYRIMIDINE BIOSYNTHESES IN YEAST. I. REGULATION OF PURINE BIOSYNTHESIS AND ITS RELATION TO TRANSIENT CHANGES IN INTRACELLULAR NUCLEOTIDE LEVELS

The control of purine biosynthesis in a yeast mutant deficient for uracil, adenine, and histidine has been studied in vivo. The adenine mutation causes accumulation of aminoimidazole ribotide in the cells. The control curve relating steady-state purine nucleotide level in the cell to rate of synthesis in the de novo purine synthetic pathway has been determined. Control in the cell depends on a feedback mechanism involving end-product inhibition. The transient responses of the purine nucleotide pool to changes in adenine input have been studied. Under certain conditions the pool overshoots when shifting from one steady-state to another. Transient changes in nucleotide levels are followed by inverse changes in the rate of attempted de novo purine synthesis. A study of the transient responses of specific intracellular nucleotides suggests that inosinic acid controls the rate of attempted purine synthesis. The transient response of nucleic acid synthesis rate to changes in nucleotide levels was studied and the implications for regulation of nucleic acid synthesis discussed.

Enhanced excretion of intermediates of aromatic amino acid catabolism during chlorophenol degradation due to nutrient limitation in the yeast Candida maltosa

Incubation of phenol-induced cells of the yeast Candida maltosa SBUG 700 with mono- and dichlorophenols resulted in the formation of metabolites of the substrates and of further metabolites not related to the degradation pathway of the substrates. These additional compounds, identified as 4-hydroxyphenylacetic acid (4-HPA), phenylacetic acid (PA), indolylacetic acid (IA) and indolylethanol (i.e.) by means of HPLC and GC/MS, were not excreted in incubation experiments with glucose. The excretion of these metabolites of aromatic amino acid metabolism is not caused by toxic effects of the phenol derivatives, but seems to be a result of carbon and nitrogen starvation of yeast cells.

Catabolite inactivation of the yeast maltose transporter is due to proteolysis

The maltose transport capacity of fermenting Saccharomyces cerevisiae rapidly decreases when protein synthesis is impaired. Using polyclonal antibodies against a recombinant maltose transporter-protein we measured the cellular content of the transporter along this inactivation process. Loss of transport capacity was paralleled by a decrease of cross-reacting material which suggests degradation of the transporter. We also show that in ammonium-starved cells the half-life of the maltose transporter is 1.3 h during catabolism of glucose and > 15 h during catabolism of ethanol.

Control of Saccharomyces cerevisiae carboxypeptidase S (CPS1) gene expression under nutrient limitation

Expression of the vacuolar carboxypeptidase S (CPS1) gene in Saccharomyces cerevisiae is regulated by the availability of nutrients. Enzyme production is sensitive to nitrogen catabolite repression; i.e. the presence of ammonium ions maintains expression of the gene at a low level. Transfer of ammonium-glucose pre-grown cells to a medium deprived of nitrogen causes a drastic increase in CPS1 RNA level provided that a readily usable carbon source, such as glucose or fructose, is available to the cells. Derepression of the gene by nitrogen limitation is cycloheximide-insensitive. Neither glycerol, ethanol, acetate nor galactose support derepression of CPS1 expression under nitrogen starvation conditions. Non-metabolizable sugar analogs (2-deoxyglucose, 6-methyl-glucose or glucosamine) do not allow derepression of CPS1, showing that the process is energy-dependent. Production of carboxypeptidase yscS also increases several-fold when ammonium-pregrown cells are transferred to media containing glucose and a non-readily metabolizable nitrogen source such as proline, leucine, valine or leucyl-glycine. Analysis of CPS1 expression in RAS2+ (high cAMP) and ras2 mutant (low cAMP) strains and in cells grown at low temperature (23 degrees C) and in heat-shocked cells (38 degrees C) shows that steady-state levels of CPS1 mRNA are not controlled by a low cAMP level-signalling pathway.

Turnover of the K+ transport system in Saccharomyces cerevisiae

The stability of the K+ transport system in Saccharomyces cerevisiae has been studied upon inhibition of protein synthesis with cycloheximide. Addition of the antibiotic gave rise to an inactivation of this transport. This activation followed first-order kinetics and was stimulated by the presence of a fermentable substrate. A half-life of about 4 h could be calculated in the presence of glucose. The results indicate that, similarly to sugar carriers, K+ transport system is less stable than the bulk of proteins of this organism.

Adenosine accumulation in Saccharomyces cerevisiae cultured in medium containing low levels of adenine

By monitoring the in vivo incorporation of low concentrations of radiolabeled adenine into acid-soluble compounds, we observed the unusual accumulation of two nucleosides in Saccharomyces cerevisiae that were previously considered products of nucleotide degradation. Under the culture conditions used in the present study, radiolabeled adenosine was the major acid-soluble intracellular derivative, and radiolabeled inosine was initially detected as the second most prevalent derivative in a mutant lacking adenine aminohydrolase. The use of yeast mutants defective in the conversion of adenine to hypoxanthine or to AMP renders very unlikely the possibility that the presence of adenosine and inosine is attributable to nucleotide degradation. These data can be explained by postulating the existence of two enzyme activities not previously reported in S. cerevisiae. The first of these activities transfers ribose to the purine ring and may be attributable to purine nucleoside phosphorylase (EC 2.4.2.1) or adenosine phosphorylase (EC 2.4.2.-). The second enzyme converts adenosine to inosine and in all likelihood is adenosine aminohydrolase (EC 3.5.4.4).

Survival of Saccharomyces cerevisiae Y5 during starvation in the presence of osmotic supports

The viability of starved or dying Saccharomyces cerevisiae Y5 cells was extended for up to 1,500 h by adding osmotic supports (0.6 M sorbitol or mannitol) to the starvation media. Replacement of these polyols with 0.3 M KCl, 0.5 M MgSO4, or 0.2 M MgCl2 postponed the death of cells incubated in N-free medium, but accelerated it in distilled water.

[Intracellular proteolysis]

This article is intended to give an overview of the most significant facts in the area of intracellular proteolysis. It begins with general considerations on the importance and nature of the intracellular proteolytic processes and examples are given of what takes place during both the extensive proteolysis and the limited cleavage of the cellular proteins. We have mentioned the intracellular proteases that have been identified and their established role since the knowledge of the proteases involved in important to understand the mechanisms of these processes.

The ubiquitin-mediated proteolytic pathway and mechanisms of energy-dependent intracellular protein degradation

In this review we briefly describe the lysosomal system, consider the evidence for multiplicity of protein degradation pathways in vivo, discuss in detail the ubiquitin-mediated pathway of intracellular ATP-dependent protein degradation, and also the possible significance of ubiquitin-histone conjugates in chromatin. For detailed discussions of the various characteristics and physiological roles of intracellular protein breakdown, the reader is referred to earlier reviews [1-7] and reports of recent symposia [8-10]. Information on the ubiquitin system prior to 1981 was described in an earlier review [11]. Hershko has briefly reviewed more recent information [12].

Isolation and characterization of aminopeptidase mutants of Saccharomyces cerevisiae

Mutants of Saccharomyces cerevisiae were isolated which have decreased ability to hydrolyze leucine beta-naphthylamide, a chromogenic substrate for amino-peptidases. The mutations were shown by starch gel electrophoresis to affect one of four different aminopeptidases. Mutations affecting a given enzyme belong to a single complementation group. The four genes were symbolized lap1, lap2, lap3, and lap4, and the corresponding enzymes LAPI, LAPII, LAPIII, and LAPIV. Both lap1 and lap4 were mapped to the left arm of chromosome XI, and lap3 was mapped to the left arm of chromosome XIV. Strains which possessed only one of the four leucine aminopeptidases (LAPs) were constructed. Crude extracts from these strains were used to study the properties of the individual enzymes. Dialysis against EDTA greatly reduced the activity of all the LAPs except for LAPIII. Of the cations tested, Co2+ was the most effective in restoring activity. LAPIV was the only LAP reactivated by Zn2+. LAPI was purified 331-fold and LAPII was purified 126-fold from cell homogenates. Both of the purified enzymes had strong activity on dipeptides and tripeptides. The activity levels of the LAPs are strongly dependent on growth stage in batch culture, with the highest levels in early-stationary phase. Strains lacking all four LAPs have slightly lower growth rates than wild-type strains. The ability of leucine auxotrophs to grow on dipeptides and tripeptides containing leucine is not impaired in strains lacking all four LAPs.

Acidification power: indicator of metabolic activity and autolytic changes in Saccharomyces cerevisiae

Acidification power, defined as the sum of the spontaneous pH change determined after suspending yeast cells in water and the substrate-induced pH change after addition of glucose to the resulting suspension, reflects the level of cellular energy sources. Its use as an indicator of metabolic state of the cells was tested during a 120-h aerobic starvation. Its changes coincided with changes in cell viability, initial rate of endogenous oxygen consumption rate, cell ATP, extra- and intracellular buffering capacity, and the ability of cell-free extract to produce acidity by glucose fermentation. It was used as a sensitive marker of metabolic changes occurring during starvation, on treatment with glycolytic and respiratory inhibitors, and at elevated temperature.

Purine metabolism in human lymphocytes

In peripheral human blood lymphocytes the uptake and metabolism of adenine, guanine, and hypoxanthine was investigated. This was achieved by incubation of purified lymphocytes with 14C-purine bases, separation of cells from the incubation medium by a rapid filtration technique, and subsequent separation of the acid soluble material by thin-layer chromatography. No perferential uptake for one of the purine bases was observed. In all cases only traces of 14C-purine bases not added originally and labeled nucleosides could be demonstrated. Approximately 2/3 of adenine and 1/2 of guanine or hypoxanthine were converted to nucleotides. Separation of formed nucleotides showed that adenine and guanine were metabolized mainly to their corresponding nucleotides; hypoxanthine was converted to a considerable amount to adenine nucleotides and only to a small proportion into its own nucleotides. These results demonstrate the predomonance of adenine nucleotide formation in normal human lymphocytes.

Growth and cell division during nitrogen starvation of the yeast Saccharomyces cerevisiae

During nitrogen starvation, cells of the yeast Saccharomyces cerevisiae increased threefold in number, and little ribonucleic acid (RNA) and protein were accumulated. Both RNA and protein were extensivley degraded during starvation, suggesting that intracellular macromolecules could supply most of the growth requirements. The types and proportions of stable RNA synthesized during nitrogen deprivation were characteristic of exponentially growing cells; however, the complement of proteins synthesized was different. We conclude that, once events in the deoxyribonucleic acid division cycle are initiated, cells can complete division with little dependence on continued net cell growth.

Some effects of nitrogen-starvation on nitrogen and carbohydrate metabolism inAnkistrodesmus braunii

Enzymic activities have been measured in cell-free extracts from nitrogen-starved cultures ofAnkistrodesmus braunii. During ten hours of nitrogenstarvation the activities of the enzymes nitrite reductase (E.C.1.6.6.4), glutamic dehydrogenase (E.C.1.4.1.4), glutamine synthetase (E.C.6.3.1.2) and urea amidolyase (E.C.3.5.1.5) were derepressed while the activities of the enzymes malate dehydrogenase (E.C.1.1.1.37) and hexokinase (E.C.2.7.1.1) remained more or less unchanged. In contrast, the photosynthetic capacity of the nitrogen-starved cultures declined rapidly and accompanying this decline were losses in the activities of ribulose diphosphate carboxylase (E.C.4.1.1.39) and triose phosphate-NADP-dehydrogenase (E.C.1.2.1.13).

Control of enzyme synthesis and stability during sporulation in Saccharomyces cerevisiae

Studies were undertaken to understand the control of synthesis, stability and modification of UDP galactose epimerase and DNA-dependent RNA polymerase during sporulation of Saccharomyces cerevisiae. When a pre-induced culture of an inducible strain (wild type) is transferred to sporulation medium, the epimerase is inactivated to an undetectable level within 16 hours. Surprisingly, the addition of cycloheximide, a protein synthesis inhibitor, during sporulation stabilizes the epimerase activity. However, in a constitutive strain, the epimerase continues to be synthesized de novo during sporulation. Since the enzyme is synthesized during both vegatative growth and sporulation constitutively, the controls for synthesis of epimerase must be similar under these physiologically different conditions. After chromatography on DEAE Sephadex, there is no change observed in the elution patterns of RNA polymerase forms extracted from acetate growth vegetative cells, sporulating cells or from mature asci ; in all cases RNA polymerase consists of three forms, Ib, II and III. However, single spore suspension obtained from asci by treatment with zymolase contains a new form with chromatographic properties similar to those of form Ia. Our data suggests that form Ia may be a modification product of from Ib.

Protein degradation and proteinases during yeast sporulation

During ascospore formation in Saccharomyces cerevisiae, at least 60-70% of the pre-existing vegetative protein was broken down at a rather constant rate until the time mature asci appeared. Under the same conditions in a non-sporulating haploid derived from the same strain the rate of protein degradation, although initially comparable to that of sporulating cells, decreased much more rapidly. Proteins synthesized at different times during sporulation had approximately the same degradation rates as the vegetative proteins. Similar rates of degradation were observed for the vegetative proteins in all fractions obtained from cell homogenates by differential centrifugation. Protein breakdown after transfer to sporulation medium was blocked by uncouplers and inhibitors of energy metabolism, and was partially inhibited by cycloheximide. Polyacrylamide gel electrophoresis, in the presence of sodium dodecylsulfate, of the proteins extracted from vegetative cells and from isolated asci and ascospores revealed that ascus formation was accompanied by a shift of the cellular proteins to a lower molecular weight. From several proteinase inhibitors tested, only tosyl-p-lysine chloromethylketone slightly reduced the rate of ascus formation. During sporulation the total activity of proteinase A increased more than twofold with a maximum at 18 h after transfer to sporulation medium. Total proteinase B activity showed a striking increase in the first hours after transfer to sporulation medium and after that remained constant throughout sporulation. The levels of carboxypeptidase Y and of the proteinase B inhibitor were not significantly altered during sporulation. The proteinases and the proteinase B inhibitor were present within the mature ascospore. The proteinases from both vegetative and sporulating cells were eluted with the same ionic strength from DEAE-Sephadex, and they were undistinguishable in their sensitivity to different proteinase inhibitors. No additional proteolytic activities could be detected in sporulating cells using 3H-labelled denatured yeast protein as a substrate.