Heterogeneity of protein turnover in Escherichia coli

Emergent Subpopulation Behavior Uncovered with a Community Dynamic Metabolic Model of Escherichia coli Diauxic Growth

Microbes have adapted to greatly variable environments in order to survive both short-term perturbations and permanent changes. A classical and yet still actively studied example of adaptation to dynamic environments is the diauxic shift of Escherichia coli, in which cells grow on glucose until its exhaustion and then transition to using previously secreted acetate. Here we tested different hypotheses concerning the nature of this transition by using dynamic metabolic modeling. To reach this goal, we developed an open source modeling framework integrating dynamic models (ordinary differential equation systems) with structural models (metabolic networks) which can take into account the behavior of multiple subpopulations and smooth flux transitions between time points. We used this framework to model the diauxic shift, first with a single E. coli model whose metabolic state represents the overall population average and then with a community of two subpopulations, each growing exclusively on one carbon source (glucose or acetate). After introduction of an environment-dependent transition function that determined the balance between subpopulations, our model generated predictions that are in strong agreement with published data. Our results thus support recent experimental evidence that diauxie, rather than a coordinated metabolic shift, would be the emergent pattern of individual cells differentiating for optimal growth on different substrates. This work offers a new perspective on the use of dynamic metabolic modeling to investigate population heterogeneity dynamics. The proposed approach can easily be applied to other biological systems composed of metabolically distinct, interconverting subpopulations and could be extended to include single-cell-level stochasticity. IMPORTANCE Escherichia coli diauxie is a fundamental example of metabolic adaptation, a phenomenon that is not yet completely understood. Further insight into this process can be achieved by integrating experimental and computational modeling methods. We present a dynamic metabolic modeling approach that captures diauxie as an emergent property of subpopulation dynamics in E. coli monocultures. Without fine-tuning the parameters of the E. coli core metabolic model, we achieved good agreement with published data. Our results suggest that single-organism metabolic models can only approximate the average metabolic state of a population, therefore offering a new perspective on the use of such modeling approaches. The open source modeling framework that we provide can be applied to model general subpopulation systems in more-complex environments and can be extended to include single-cell-level stochasticity.

Role of Clp protease subunits in degradation of carbon starvation proteins in Escherichia coli

When deprived of a carbon source, Escherichia coli induces the synthesis of a group of carbon starvation proteins. The degradation of proteins labeled during starvation was found to be an energy-dependent process which was inhibited by the addition of KCN and accelerated when cells were resupplied with a carbon source. The degradation of the starvation proteins did not require the ATP-dependent Lon protease or the energy-independent proteases protease I, protease IV, OmpT, and DegP. During starvation, mutants lacking either the ClpA or ClpP subunit of the ATP-dependent Clp protease showed a partial reduction in the degradation of starvation proteins. Strains lacking ClpP failed to increase degradation of starvation proteins when glucose was added to starving cells. The clpP mutants showed a competitive disadvantage compared with wild-type cells when exposed to repeated cycles of carbon starvation and growth. Surprisingly, the glucose-stimulated, ClpP-dependent degradation of starvation proteins did not require either the ClpA or ClpB protein. The patterns of synthesis of starvation proteins were similar in clpP+ and clpP cells. The clpP mutants had reduced rates of degradation of certain starvation proteins in the membrane fraction when a carbon source was resupplied to the starved cells.

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.

Stringent control and protein synthesis in bacteria

Most bacteria have evolved a number of regulatory mechanisms which allow them to maintain a balanced and rather constant cellular composition in response to nutritional variations. In particular, when the availability of any aminoacyl-tRNA species becomes limiting (namely through amino acid starvation or inactivation of an aminoacyl-tRNA synthetase), several biochemically distinct physiological processes are significantly modified. This coordinate adjustment of cellular activity is termed the "stringent response". Under such conditions of aminoacyl-tRNA limitation, protein synthesis still proceeds, but various quantitative as well as qualitative changes in polypeptide metabolism can be observed. In this review, after a brief recall of the main characteristics of the stringent response, several aspects concerning protein synthesis in deprived bacteria have been presented. First, the rates of residual protein formation, peptide chain growth and protein degradation, and the molecular weight distribution of proteins newly synthesized have been analyzed. Then, the data relative to the biosynthetic regulation of non-ribosomal and ribosomal proteins have been summarized and compared to the results obtained from in vitro experiments using transcription-translation coupled systems. Finally, the problem of translational fidelity during deprivation has been discussed in connection with the metabolic behavior of polysomal structures which are still maintained in cells. The stringent dependence of cellular activity on aminoacyl-tRNA supply is known to be abolished by single-site mutations which confer to bacteria a phenotype referred to as "relaxed". These mutant strains provide an useful analytical tool in the scope of understanding the stringency phenomenon. Therefore, their proteosynthetic activity under aminoacyl-tRNA deprivation has also been studied here, in comparison to that of normal wild-type strains.

Inactivation and partial degradation of phosphoribosylanthranilate isomerase-indoleglycerol phosphate synthetase in nongrowing cultures of Escherichia coli

The stability of tryptophan biosynthetic enzyme activities was examined in cultures of repressor-negative (trpR) strains of Escherichia coli K-12 incubated under conditions of nutrient starvation of chloramphenicol inhibition. The results show that four of the five activities examined are stable under most nongrowing conditions, whereas one activity, indoleglycerol phosphate (InGP) synthetase, carried by the trpC protein, is unstable under most conditions tested. Phosphoribosylanthranilate (PRA) isomerase activity, which is also carried by the trpC protein, is unstable during starvation for ammonium, cysteine, or sulfate but is stable under other nongrowing conditions where InGP synthetase is not. InGP synthetase activity but not PRA isomerase activity is also diminished about twofold in cultures using glycerol as a carbon-energy source. These results indicate that one or both activities of the trpC protein is specifically inactivated under several culture conditions. Experiments with antibodies to the trpC protein show that sulfate-starved and ammonium-starved cultures contain 20 to 40% less immunologically reactive trpC protein than unstarved cultures. This indicates that the trpC protein is probably partially degraded under these conditions. During recovery from sulfate starvation or ammonium starvation, cultures slowly regain normal levels of InGP synthetase and PRA isomerase activities, suggesting that inactivation may be reversible.

An investigation of mistranslation in vivo induced by streptomycin by an examination of the susceptibility of abnormal proteins to degradation

Proteolysis rates in vivo were measured in Escherichia coli cultures during treatment with dihydrostreptomycin and under various other conditions. Dihydrostreptomycin treatment caused an increase in the proteolysis rate, compared to untreated controls. The proteolytic system in vivo responsible for the elevated proteolysis in the early stages of dihydrostreptomycin treatment, or that during canavanine and puromycin treatment, were not inhibited by addition of phenylmethanesulphonyl fluoride. This agent did inhibit proteolysis rates in cultures whose growth was inhibited by starvation, or had been completely stopped by dihydrostreptomycin. It seems, therefore, that the extremely high proteolysis rates in cultures at this stage of dihydrostreptomycin treatment were due to the action of two protease systems: the one concerned with the breakdown of abnormal proteins, and the other concerned with normal protein turnover and active during a non-specific decline of growth. The proteolytic rate at complete growth inhibition brought about by dihydrostreptomycin was intermediate between those induced by canavanine and puromycin at the same stage of treatment. This indicated a similar hierarchy in the extent and nature of abnormality in the proteins synthesized under these conditions. The relationship between the abnormality of proteins induced by dihydrostreptomycin and the importance of this in the antibiotic mechanism is discussed.

Protein synthesis and degradation in a leucine auxotroph of Escherichia coli

The synthesis and degradation of the soluble and sodium dodecyl sulfate-(SDS)-solubilized protein fractions of Escherichia coli were studied in both growing and nongrowing cultures. When separated according to molecular weight on SDS-polyacrylamide gels, the proteins of both fractions of growing cells undergo no measureable differential synthesis or degradation during logarithmic growth. However, when a leucine auxotroph is suspended in medium containing 5.3 muM leucine (a level that will not sustain growth), the SDS-solubilized protein of such a nongrowing culture shows a rapid synthesis of two protein components (32,000 and 12,000 daltons) found only in the out membrane.

The polypeptide chain growth rate in amino acid-starved Escherichia coli determined by a novel method

The proteins synthesized by arginine-requiring Escherichia coli during growth or arginine starvation were characterized by polyacrylamide gel electrophoresis in sodium dodecyl sulfate to give size distributions. The proteins made during amino acid starvation were smaller than those made by growing cells. This was true for otherwise isogenic rel- ("relaxed") and rel+ ("stringent") bacteria. Also using electrophoretic profiles, the peptide chain growth rate was estimated by a novel method based on comparison of theoretically predicted and observed kinetics of pulse labeling protein chains of different sizes. During arginine starvation, the rate was 2--5 amino acids/s for both rel- and rel+ cells, compared to 20 amino acids/s for growing cells. The results rule out chain growth-rate differences as an aspect of the "relaxed" phenomenon.

Physiological consequences of starvation in Pseudomonas putida: degradation of intracellular protein and loss of activity of the inducible enzymes of L-arginine catabolism

We investigated the degradation of radioisotopically labeled intracellular protein in starved, intact cells of Pseudomonas putida P2 (ATCC 25571) and the regulation of this process. Intracellular protein isotopically labeled with L-[4,5-3H]leucine during log-phase growth at 30 C is degraded at rates of 1 to 2%/h in log-phase cells and 7 to 9%/h in starved cells. Rifampin, chloramphenicol, and tosyllysine chloromethylketone lower the rate of protein degradation by starved cells. Addition to starved cells of a nutrient upon which the culture is induced for growth rapidly lowers the rate of protein degradation from 7 to 9%/h to less than 1.5%/h. A nutrient that is oxidized but that cannot immediately support growth also lowers the rate of starvation-induced protein degradation. Proteolytic activity of cell extracts requires a divalent metal ion and may be inhibited up to 60% by tosyllysine chloromethylketone or p-toluenesulfonyl fluoride. Rifampin and chloramphenicol have no effect. In contrast to intact cells, extracts of growing or starving cells degrade protein at equivalent rates. We also investigated the stabilities of the inducible transport system and of four inducible intracellular enzymes of L-arginine catabolism. These include: the membrane-associated, L-arginine-specific transport system; L-arginine oxidase (oxidase); alpha-ketoarginine decarboxylase (decarboxylase); gamma-guanidinobutyraldehyde dehydrogenase ( dehydrogenase); and gamma-guanidinobutyrate amidinohydrolase (hydrolase). In starved cells, the rates of loss of activities were: transport and dehydrogenase activities, stable; oxidase and decarboxylase activities, 20 to 30%/h; hydrolase activity, 5 to 8%/h. Chloramphenicol decreases the rate of loss of oxidase, decarboxylase, and hydrolase activity, whereas p-toluenesulfonyl fluoride lowers the rate of loss of decarboxylase but not of oxidase or hydrolase activity. Addition to starved cells of a nutrient for which they are already induced for growth (e.g., malate, a noninducer of arginine catabolic enzymes) decreases the rate of loss of oxidase and decarboxylase activity but not that of the hydrolase.

Stringent control of intracellular proteolysis in Escherichia coli

Regulation of intracellular proteolysis has been compared during amino acid deficiencies in seven double auxotrophs of Escherichia coli 9723f with a common phenylalanine requirement. Individual deficiencies were either more effective than, less effective, or equal to phenylalanine deficiency in stimulating intracellular proteolysis. For each amino acid, the same relationship prevailed in inhibiting uracil incorporation into nucleic acids, a reaction series regulated by the rel gene for stringent control. The three amino acids least abundant in the cellular protein were the least effective regulators. These findings are interpreted as supportive evidence for stringent control of intracellular proteolysis by the rel gene.

Membrane synthesis in synchronous cultures of Bacillus subtilis 168

Synthesis of bacterial membranes has been investigated in Bacillus subtilis by examining incorporation of amino acids and glycerol into the protein and lipid of membranes of synchronous cultures. A simple reproducible fractionation scheme divides cellular proteins into three classes (i) truly cytoplasmic, (ii) loosely membrane bound, released by chelating agents, and (iii) tightly membrane bound. These comprise approximately 75, 10, and 15%, respectively, of cellular proteins in this organism. Incorporation of radioactivity into these fractions, using steady-state and pulse labeling has been followed during the cell cycle. Cytoplasmic proteins and the loosely membrane-bound proteins are labeled at an exponential rate throughout the cell cycle. The membrane fraction is labeled discontinuously in the cell cycle, with periods of rapid synthesis over the latter part of the cycle and a period with no net synthesis during the early part of the cycle. Pulse labeling indicates that synthesis of membrane occurs at a linear rate that doubles at a fixed time in each cycle, which coincides with the period of zero net synthesis. Rates of membrane synthesis measured by pulse labeling during the period of rapid membrane synthesis are significantly less than indicated by steady-state labeling. These discrepancies are consistent with the hypothesis that during the cell cycle certain proteins are added to the membrane from the cytoplasm and that during the period of zero net synthesis there is an efflux of proteins from the membrane. Evidence in favor of this has been presented. The activity of succinic dehydrogenase (a representative of class c) varies in a step-wise manner with periods of rapid increase, approximately coincident with bursts of membrane protein synthesis, alternating with periods without any increase in activity. The activities of malate dehydrogenase (class a) and reduced nicotinamide adenine dinucleotide dehydrogenase (class b) increased throughout the cell cycle. Phospholipid synthesis is continuous throughout the cell cycle.

Regulation of intracellular proteolysis in Escherichia coli

Individual nitrogenous metabolites have been examined as regulating agents for the breakdown of intracellular proteins in Escherichia coli. Generally, NH(4) (+) is the most effective regulator. Its depletion progressively increases the basal proteolytic rate to maximum in most strains when the doubling time is increased to 2 h. In E. coli 9723, the rate is further increased at longer doubling times. Amino acids have individual effects on intracellular proteolysis. The basal rate in amino acid-requiring auxotrophs of E. coli 9723 is stimulated weakly by starvation for histidine, tryptophan, or tyrosine, moderately by four other amino acid depletions, and more strongly by eight others. The degree of stimulation roughly correlates with the frequency of the amino acid in the cell proteins. Amino acid analogues that incorporate extensively into protein generally slightly inhibit intracellular proteolysis, except for selenomethionine, which is slightly stimulatory. Metabolic inhibitors were studied at graded concentrations. Chloramphenicol inhibits the basal level of intracellular proteolysis when protein synthesis is slightly or moderately inhibited, and stimulates proteolysis slightly at higher levels. Graded inhibition of ribonucleic acid synthesis with rifampin progressively stimulates intracellular proteolysis. Uracil depletion is also stimulatory. Inhibition of deoxyribonucleic acid synthesis with mitomycin C or by thymine starvation slightly inhibits intracellular proteolysis. Intracellular proteolysis is postulated to be regulated primarily by active ribosomal function. At 43 to 45 C, intracellular proteolysis becomes maximally induced and unresponsive to normal regulatory control by metabolites. Most regulation is directed towards the breakdown of the more stable cell proteins. Total proteolysis in all cell proteins is no more than doubled by the most effective conditions of starvation.

Correlation between rates of degradation of bacterial proteins in vivo and their sensitivity to proteases

Experiments were undertaken to test whether the relative rates of degradation of proteins in vivo might correlate with their sensitivity to proteases. Various experimental conditions that promote degradation of proteins in Escherichia coli increased sensitivity of average cell proteins to trypsin or other endoproteases, including incorporation of several aminoacid analogs into the proteins, incorporation of puromycin into the polypeptide chain, or frequent errors in translation. Those abnormal proteins that were degraded most rapidly within the cell appear responsible for the increased protease sensitivity of the cell extract. Normal E. coli proteins that rapidly turn over in growing cells are, on the average, more sensitive to trypsin or Pronase than cell proteins that turn over more slowly. The inherent sensitivity of a protein to proteolytic digestion is thus a major determinant of protein half-lives in vivo.

Disappearance of isocitrate lyase enzyme from cells of Chlorella pyrenoidosa

1. When acetate-adapted cells of Chlorella are suspended in nitrogen-free medium and supplied with glucose, isocitrate lyase activity disappears from the cells at a rate of about 9%/h. This loss of activity is shown to be accompanied by loss of isocitrate lyase protein. 2. When isocitrate lyase activity is assayed in intact cells after freezing and thawing, the rate of loss of activity after addition of glucose approaches 20%/h. 3. It is shown, by using (35)S, that the rate of turnover of isocitrate lyase protein is somewhat lower than that of other major soluble proteins; general protein turnover during nitrogen starvation, and after glucose addition, is too slow to account for the rate of loss of isocitrate lyase protein. 4. Disappearance of isocitrate lyase activity must result from a mechanism that allows degradation of this specific protein under conditions of limiting nitrogen supply.

Steady-state measurement of the turnover of amino acid in the cellular proteins of growing Escherichia coli: existence of two kinetically distinct reactions

Turnover of cellular protein has been estimated in Escherichia coli during continuous exponential growth and in the absence of extensive experimental manipulation. Estimation is based upon the cumulative release into carrier pools of free leucine-1-(14)C over a number of time intervals after its pulsed incorporation into protein. Breakdown rates obtained with other labeled amino acids are similar to those obtained with leucine. Two kinetically separate processes have been shown. First, a very rapid turnover of 5% of the amino acid label occurs within 45 sec after its incorporation, most likely indicating maturative cleavages within the proteins after their assembly. A slower heterogeneous rate of true protein turnover follows, falling by 39% in the remaining proteins for each doubling of turnover time. At 36 C, the total breakdown rate of cellular protein is 2.5 and 3.0% per hr over a threefold range of growth rate in glucose and acetate medium, respectively. This relatively constant breakdown rate is maintained during slower growth by more extensive protein replacement, one fifth of the protein synthesized at any time in the acetate medium being replaced after 4.6 doubling times. Intracellular proteolysis thus appears to be a normal and integral reaction of the growing cell. The total rate equals minimal estimates obtained by others for arrested or decelerated growth but is kinetically more heterogeneous. Quantitatively proteolysis is not directly affected by growth arrestment per se as caused by alpha-methylhistidine, chloramphenicol, or uncouplers of oxidative phosphorylation, but qualitatively it can gradually become more homogeneous kinetically as a secondary event of starvation. Under more extreme conditions as with extensive washing, prolonged phosphorylative uncoupling, or acidification of the growth medium, the proteolytic rate can increase severalfold.

Factors affecting the synthesis and degradation of ribulose-1,5-diphosphate carboxylase in Hydrogenomonas facilis and Hydrogenomonas eutropha

Hydrogenomonas facilis and H. eutropha cultured in fructose medium retained high levels of ribulose-1,5-diphosphate carboxylase only when the following conditions were fulfilled: low aeration, FeCl(3) addition to fructose medium, and cell harvest at or prior to mid-exponential phase of growth. Repression of carboxylase synthesis was demonstrated under conditions of high oxygen tension during growth of H. eutropha on fructose. Upon depletion of fructose in the growth medium, carboxylase activity fell abruptly in both organisms. The decline could not be attributed to a repressive mechanism. Rapid inactivation of carboxylase was promoted by transfer of mid-exponential-phase H. eutropha to a basal salts medium lacking fructose. During severe fructose starvation, N(2), H(2), 80% H(2) to 20% air, 2,4-dinitrophenol, actinomycin D, streptomycin, bicarbonate, and magnesium ion deficiency spared carboxylase. Nitrogen starvation or chloramphenicol afforded no protection during severe starvation. In vitro inactivation was also demonstrated in crude cell-free extracts from nonstarved, fructose-grown H. eutropha. Substrate bicarbonate protected against this loss. Inactivation of the carboxylase could not be demonstrated either by starvation of autotrophically grown cells or in autotrophic extracts. Autotrophic extracts mixed with heterotrophic extracts lost their carboxylase activity, but mixing with heterotrophic extracts that had been heated to 50 C resulted in no loss of activity. Mechanisms are proposed to accommodate these observations.

Response of intracellular proteolysis to alteration of bacterial protein and the implications in metabolic regulation

An assessment has been made of the extent to which the breakdown of microbial cellular proteins is regulated by their metabolic state or function. For this purpose, a number of agents and conditions that alter the synthesis, structure, or utility of cellular protein were examined for the effect on their lability. In Escherichia coli, 5-fluorouracil, p-fluorophenylalanine, norleucine, canavanine, thienylalanine, and puromycin, which engender nonfunctional cellular protein en masse, and ultraviolet irradiation increase the breakdown rate of proteins synthesized in their presence as much as two- to threefold without altering the general capacity for proteolysis. The effects are complicated by, but experimentally distinguishable from, secondary changes in proteolysis that accompany growth inhibition. In contrast, no potentiation of proteolysis is elicited by the presence of suppressor genes, by the administration of heat, or by the biosynthetic alterations attending large changes in the conditions of cultivation or by those attending bacteriophage infection. Thus, although mass perturbations in protein conformation are catabolically distinguishable, the more individual and limited conformational modifications that might occur in disuse do not appear to be the primary determinants of the protein turnover rate. In Bacillus subtilis, turnover synthesis of protein during starvation is as susceptible to treatment with actinomycin D as that during growth. Treatment alters neither the rate of intracellular proteolysis nor the catabolic pattern of the modicum of proteins that are still synthesized. It is concluded that there is no correlation between metabolic stability of protein and the stability of its messenger ribonucleic acid.

Intracellular protein breakdown in growing cells of Escherichia coli

1. When Escherichia coli was grown exponentially in a defined medium at 35 degrees , the rate of protein breakdown was initially rapid, but decreased to 0.6%/hr. after about 30min. The latter rate was maintained for at least 3.5hr. 2. The initial rapid rate may have been due to the presence of a small protein fraction (about 1%) that was degraded with a half-life of 13min. 3. The rate of protein degradation was the same during balanced growth at low rates imposed in a bactogen. However, it increased during the period immediately after a decrease of the growth rate.

Intracellular protein breakdown in non-growing cells of Escherichia coli

1. When Escherichia coli leu(-) was incubated at 35 degrees in a medium based on minimal medium, but with the omission of phosphate ions, or glucose, or NH(4) (+) ions and leucine, intracellular protein was degraded at a rate of about 5%/hr. in each case. If Mg(2+) ions were omitted, however, the rate of degradation was 2.9%/hr. 2. Under certain conditions of incubation, protein degradation was inhibited. The inhibitor was neither NH(4) (+) ions nor amino acids, and its properties were not those of a protein, but it might be an unstable species of RNA. 3. Although a large part of the cell protein was degraded at about 5%/hr. during starvation of NH(4) (+) ions and leucine, some proteins were lost at more rapid rates, whereas others were lost at lower rates or not at all. 4. In particular, beta-galactosidase activity was lost at about 8%/hr. during starvation of NH(4) (+) ions and leucine, whereas d-serine-deaminase and alkaline-phosphatase activities were stable. During starvation of Mg(2+) ions, all three enzyme activities were stable.

Metabolic control of intracellular proteolysis in growing and resting cells of Escherichia coli

Pine, Martin J. (Roswell Park Memorial Institute, Buffalo, N.Y.). Metabolic control of intracellular proteolysis in growing and resting cells of Escherichia coli. J. Bacteriol. 92:847-850. 1966.-Protein breakdown was examined in Escherichia coli under varying conditions of growth and during nutritional deprivation. Optimal breakdown rates, estimated over short time periods of protein synthesis and decay, are invariant and unrepressible by any condition of growth or starvation. A more important aspect of metabolic control is manifest in the selection imposed by the physiological state of the cell for breakdown of limited populations of proteins. During the progress of growth, one-half to three-quarters of the protein susceptible in the resting state is progressively spared, and breakdown is continued in populations that are more selected and more frequently regenerated.