Protein turnover in senescent cultured chick embryo fibroblasts

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.

Active Degradation Explains the Distribution of Nuclear Proteins during Cellular Senescence

The amount of cellular proteins is a crucial parameter that is known to vary between cells as a function of the replicative passages, and can be important during physiological aging. The process of protein degradation is known to be performed by a series of enzymatic reactions, ranging from an initial step of protein ubiquitination to their final fragmentation by the proteasome. In this paper we propose a stochastic dynamical model of nuclear proteins concentration resulting from a balance between a constant production of proteins and their degradation by a cooperative enzymatic reaction. The predictions of this model are compared with experimental data obtained by fluorescence measurements of the amount of nuclear proteins in murine tail fibroblast (MTF) undergoing cellular senescence. Our model provides a three-parameter stationary distribution that is in good agreement with the experimental data even during the transition to the senescent state, where the nuclear protein concentration changes abruptly. The estimation of three parameters (cooperativity, saturation threshold, and maximal velocity of the reaction), and their evolution during replicative passages shows that only the maximal velocity varies significantly. Based on our modeling we speculate the reduction of functionality of the protein degradation mechanism as a possible competitive inhibition of the proteasome.

Nuclear protein accumulation in cellular senescence and organismal aging revealed with a novel single-cell resolution fluorescence microscopy assay

Replicative cellular senescence was discovered some 50 years ago. The phenotypes of senescent cells have been investigated extensively in cell culture, and found to affect essentially all aspects of cellular physiology. The relevance of cellular senescence in the context of age-associated pathologies as well as normal aging is a topic of active and ongoing interest. Considerable effort has been devoted to biomarker discovery to enable the microscopic detection of single senescent cells in tissues. One characteristic of senescent cells documented very early in cell culture studies was an increase in cell size and total protein content, but whether this occurs in vivo is not known. A limiting factor for studies of protein content and localization has been the lack of suitable fluorescence microscopy tools. We have developed an easy and flexible method, based on the merocyanine dye known as NanoOrange, to visualize and quantitatively measure total protein levels by high resolution fluorescence microscopy. NanoOrange staining can be combined with antibody-based immunofluorescence, thus providing both specific target and total protein information in the same specimen. These methods are optimally combined with automated image analysis platforms for high throughput analysis. We document here increasing protein content and density in nuclei of senescent human and mouse fibroblasts in vitro, and in liver nuclei of aged mice in vivo. Additionally, in aged liver nuclei NanoOrange revealed protein-dense foci that colocalize with centromeric heterochromatin.

Energetic stress induces premature aging of diploid human fibroblasts (Wi-38) in vitro

Oxidative phosphorylation is the main endogenous source for the generation of reactive oxygen species (ROS). In order to investigate the influence of enhanced ROS production on the in vitro senescence of Wi-38 fibroblasts, cells were cultivated in medium with elevated (hypertonic) NaCl concentrations. The number of active Na(+)/K(+)-ATPase molecules per cell was found to be increased. A rise in both respiration and glycolysis as evidenced by the increases in oxygen and glucose consumption and lactate production was revealed. Cells stayed alive in medium with NaCl concentrations of up to 0.30 M and could be adapted to growth under these hypertonic conditions (high-NaCl tolerant cells). These cells exhibited an increased cell size and protein content. A growing number of cells showed stress fibers and granulation. The proliferation rate and the maximum number of cumulative population doublings of these high-NaCl tolerant cultures were reduced and saturation density was decreased. Thus, these cells under energetic stress due to increased energy requirements for active ion transport expressed features typical for aging in vitro. We conclude therefore that energetic stress induces premature aging in human diploid fibroblasts.

Age-related alterations in collagen and total protein metabolism determined in cultured rat dermal fibroblasts: age-related trends parallel those observed in rat skin in vivo

The cultured fibroblast has been extensively used as a model system to study aging. However, few studies have examined the veracity of observations obtained in cultured fibroblasts aged in vitro to those made in animal tissues in vivo. This paper compares age-related alterations in collagen metabolism measured in cultured cells with previously reported results in the aging rat (Mays et al. (1991) Biochem. J. 276, 307-313). Age-related changes in collagen synthesis in rat skin fibroblasts in vitro over 30 population doublings were determined based on the production of hydroxy-[14C]proline. Degradation of newly synthesized collagen was based on the appearance of free hydroxy-[14C]proline in the culture system. Total protein synthesis rates were based on the incorporation of [14C]proline into proteins. In vitro rates of collagen synthesis decreased 5-fold over 30 population doublings (P < 0.05). Degradation of newly synthesized collagen increased from 33.0 +/- 0.8% (n = 4, SEM) to 45.2 +/- 1.1% (n = 4; P < 0.05) over the same period, with a maximum after 25 population doublings of 55.8 +/- 1.1% (n = 4). Total protein synthesis rates decreased by one-half over 30 population doublings (P < 0.05). The results indicated that collagen production decreased as cells aged in vitro and that this was due to both changes in synthesis and degradation. The results demonstrate that age-related alterations in collagen and total protein metabolism of skin fibroblasts in culture were similar to those reported previously for skin in vivo, suggesting that for studies of these processes, fibroblasts in culture provide an appropriate model.

Ubiquitin pools, ubiquitin mRNA levels, and ubiquitin-mediated proteolysis in aging human fibroblasts

Senescent cells have less free ubiquitin and more ubiquitin-protein conjugates than do young cells. The ubiquitin-protein conjugates are heterogeneous in size but contain prominent bands at 106, 55, and 22 kDa. The age-related increase in ubiquitin-protein conjugates applies primarily to the 55-kDa band, while the 106-kDa and 22-kDa conjugates change little with age. Ubiquitin mRNA levels do not change with age, and the ability of cells to degrade two proteins that are good substrates for ubiquitin-mediated proteolysis is unaltered by aging. These results indicate that an increase in ubiquitin-protein conjugates does not necessarily reflect alterations in ubiquitin-mediated proteolysis. Furthermore, an overactive pathway of ubiquitin-mediated proteolysis does not appear to contribute to the proliferative arrest in senescent cells.

Cellular senescence: a reflection of normal growth control, differentiation, or aging?

Normal cells, with few exceptions, cannot proliferate indefinitely. Cell populations--in vivo and in culture--generally undergo only a limited number of doublings before proliferation invariably and irreversibly ceases. This process has been termed the finite lifespan phenotype or cellular senescence. There is long-standing, albeit indirect, evidence that cellular senescence plays an important role in complex biological processes as diverse as normal growth control, differentiation, development, aging, and tumorigenesis. In recent years, it has been possible to develop a molecular framework for understanding some of the fundamental features of cellular senescence. This framework derives primarily from the physiology, genetics, and molecular biology of cells undergoing senescence in culture. Our understanding of senescence, and the mechanisms that control it, is still in its infancy. Nonetheless, recent data raise some intriguing possibilities regarding potential molecular bases for the links between senescence in culture and normal and abnormal growth control, differentiation, and aging.

Fibronectin and collagen gene expression during in vitro ageing of pig skin fibroblasts

The fibronectin, collagen type I, and collagen type III genes code for three major proteins of the cell matrix. The age-related alterations in their expression were measured during the in vitro lifespan of pig skin fibroblasts. We observed changes in the transcription rate of these specific genes during ageing. The levels of fibronectin and type III collagen mRNA rose markedly during the senescence phase. The level of collagen type I mRNA decreased during cell ageing, while that of beta-actin did not change. As regards proteins, we observed a sharp increase in the secreted noncollagenous proteins and in the total proteins of the cell layer during senescence. On the contrary, the secretion of the collagenous proteins decreased during senescence. Moreover, most of the newly synthesized molecules of collagen were immediately degraded in the cells, before their extracellular secretion. The terminal phenotype of pig senescent cells was therefore characterized by overexpression of fibronectin and type III collagen genes and reduced expression of the type I collagen gene. Surprisingly, for fibronectin and type III collagen, that terminal phenotype resembled the one normally found in the fibroblasts during the processes of tissue repair, cicatrization, and development.

Differential degradation of intracellular proteins in human skin fibroblasts of mitotic and mitomycin-C (MMC)-induced postmitotic differentiation states in vitro

Rates of degradation of short- and long-lived proteins were analysed in homogeneous fibroblast cultures of mitotic or mitomycin C (MMC)-induced postmitotic states. When the highly mitotic MFII type cells--the major cell type of so called "early passage" or "young" fibroblasts--differentiate into MFIII type cells, the last mitotic fibroblast type, and further into MMC-induced postmitotic fibroblasts, the degradation of short-lived proteins increases by a factor of 1.4, resulting in significantly reduced half-lives of these proteins in the postmitotic fibroblasts. From the highly mitotic MFII to the final postmitotic PMFVI-type cells via the intermediates MFIII, PMFIV and PMFV, the half lives (t1/2) of short-lived proteins decrease by a total of 122 min in average, from 362 to 240 min. Degradation of long-lived proteins did not change significantly from cell type MFII to PMFVI. As analysed by two-dimensional (2D)-gel electrophoresis the half-lives of the mitotic and postmitotic cell-type-specific proteins except one, protein PIVa (33 kDa; Pi 5.0), range between 33.2 h and 62.9 h. Protein PIVa, the first protein specific for postmitotic cells, is initially expressed 18 h after the induction of the postmitotic state by mitomycin C (MMC) and has a half-life of approximately 66 min. This may indicate that protein PIVa could function as one possible regulatory factor controlling the postmitotic differentiation state.

Dual pathways for ribonucleic acid turnover in WI-38 but not in I-cell human diploid fibroblasts

The turnover rates of 3H-labeled 18S ribosomal ribonucleic acid (RNA), 28S ribosomal RNA, transfer RNA, and total cytoplasmic RNA were very similar in growing WI-38 diploid fibroblasts. The rate of turnover was at least twofold greater when cell growth stopped due to cell confluence, 3H irradiation, or treatment with 20 mM NaN3 or 2 mM NaF. In contrast, the rate of total 3H-protein turnover was the same in growing and nongrowing cells. Both RNA and protein turnovers were accelerated at least twofold in WI-38 cells deprived of serum, and this increase in turnover was inhibited by NH4Cl. These results are consistent with two pathways for RNA turnover, one of them being nonlysosomal and the other being lysosome mediated (NH4Cl sensitive), as has been suggested for protein turnover. Also consistent with the notion of two pathways for RNA turnover were findings with I-cells, which are deficient for many lysosomal enzymes, and in which all RNA turnover was nonlysosomal (NH4Cl resistant).

Cellular senescence revisited: a review

The field of cellular senescence (cytogerontology) is reviewed. The historical precedence for investigation in this field is summarized, and placed in the context of more recent studies of the regulation of cellular proliferation and differentiation. The now-classical embryonic lung fibroblast model is compared to models utilizing other cell types as well as cells from donors of different ages and phenotypes. Modulation of cellular senescence by growth factors, hormones, and genetic manipulation is contrasted, but newer studies in oncogene involvement are omitted. A current consensus would include the view that the life span of normal diploid cells in culture is limited, is under genetic control, and is capable of being modified. Finally, embryonic cells aging in vitro share certain characteristics with early passage cells derived from donors of increasing age.

Events blocked in prereplicative phase in senescent human diploid cells, TIG-1, following serum stimulation

When senescent human diploid cells, TIG-1, were stimulated with serum at the end of their proliferative life span, such biochemical events as uptakes of 2-deoxyglucose and uridine, and expression of c-myc, were enhanced. However, RNA synthesis, polyamine accumulation, thymidine uptake and DNA synthesis were not enhanced at all. Protein synthesis increased only moderately as compared with that observed in younger cells. These results indicated that the events in prereplicative phase known to be independent on protein synthesis are induced in senescent cells after the stimulation with serum, whereas those required protein synthesis failed to increase to the same extent as seen in young cells.

Altered degradation of intracellular proteins in aging human fibroblasts

Confluent cultures of fibroblasts at different population doubling levels were incubated with [14C]leucine for 2 days and with [3H]leucine for 2 h to label long-lived and short-lived proteins, respectively. Proteolysis was then measured in the presence of excess unlabeled leucine to prevent reutilization of the isotope. Catabolism of long-lived proteins was reduced in senescent cells when measured in media without fetal bovine serum, insulin, fibroblast growth factor, or dexamethasone. In contrast, degradation of short-lived proteins was increased in senescent cells but only when measured in the presence of serum, hormones, and growth factors. Further experiments with cells of varying ages indicate that in unsupplemented medium half-lives of long-lived proteins lengthened by as much as 20 min per population doubling and in supplemented media half-lives of short-lived proteins decreased by 4 min per population doubling. The reduced catabolism of long-lived proteins in senescent cells cannot be explained by age-related changes in protein secretion or cell death during degradation measurements. These alterations in proteolysis may have major effects on protein content and composition in senescent cells.

Influence of cell density on collagen biosynthesis in fibroblast cultures

Characteristic features of collagen metabolism in human skin fibroblasts were studied in relation to cell density. Measuring peptide-bound hydroxyproline we found that collagen synthesis per cell decreased when cultures approached confluency. On the other hand, the relative rate of collagen synthesis (collagen/total protein) was higher in quiescent than in proliferating cultures. With increasing cell density the proportion of type III collagen in comparison with type I was found to be slightly increased. In addition, in low-density cultures [alpha I(I)]3 collagen trimers were produced in considerable amounts, whereas they were no longer detected in cultures with a high cell density. Although hydroxylation of proline residues was normal in all cell stages, conversion of procollagen into collagen was found to depend strongly on the density at which the cells were investigated. Almost no cleavage of procollagen peptides was observed in rapidly growing cells, whereas highly confluent cell cultures converted most of the newly synthesized procollagen molecules.

Protein turnover and proliferation. Turnover kinetics associated with the elevation of 3T3-cell acid-proteinase activity and cessation of net protein gain

1. At least 95% of the total protein of A31-3T3 cell cultures undergoes turnover. 2. First-order exponential kinetics were used to provide a crude approximation of averaged protein synthesis, Ks, degradation, Kd, and net accumulation, Ka, as cells ceased growth at near-confluent density in unchanged Dulbecco's medium containing 10% serum. The values of the relationship Ka = Ks - Kd were : 5%/h = 6%/h - 1%/h in growing cells, and 0%/h = 3%/h - 3%/h in steady-state resting cells. 3. As determined by comparison of the progress of protein synthesis and net protein accumulation, the time course of increase in protein degradation coincided with the onset of an increase in lysosomal proteinase activity and decrease in thymidine incorporation after approx. 2 days of exponential growth. 4. After acute serum deprivation, rapid increases in protein degradation of less than 1%/h could be superimposed on the prevailing degradation rate in either growing or resting cells. The results indicate that two proteolytic mechanisms can be distinguished on the basis of the kinetics of their alterations. A slow mechanism changes in relation to proliferative status and lysosomal enzyme elevation. A prompt mechanism, previously described by others, changes before changes in cell-cycle distribution or lysosomal proteinase activity. 5. When the serum concentration of growing cultures was decreased to 1% or 0.25%, then cessation of growth was accompanied by a lower steady-state protein turnover rate of 2.0%/h or 1.5%/h respectively. When growth ceased under conditions of overcrowded cultures, or severe nutrient insufficiency, protein turnover did not attain a final steady state, but declined continually into the death of the culture.

Phenotypic expression time of mutagen-induced 6-thioguanine resistance in Chinese hamster ovary cells (CHO/HGPRT system): expression in division-arrested cell cultures

The phenotypic expression time of ethyl methanesulfonate (EMS) induced 6-thioguanine-resistant mutants was studied with Chinese hamster ovary cells in culture (CHO/HGPRT system). After mutagen treatment of exponential phase cultures, the cells were maintained either in the exponential phase through subculture in medium containing 5% dialyzed fetal bovine serum (FBS) or in a nondividing viable state by use of medium containing 0-1% dialyzed FBS. The time course of expression of the 6-thioguanine-resistant phenotype was similar with both exponential phase and division-arrested cultures showing maximum expression by 9 days after mutagen treatment, and both methods of expression also yielded similar mutant frequencies over a range of EMS concentrations. This study shows that once the mutagenic event is fixed, the expression of the mutant phenotype does not require continued cell division since it occurs in division-arrested cultures. These results also suggest that both dilution of pre-existing hypoxanthine-guanine phosphoribosyl transferase (HGPRT) enzyme by cell division and turnover by protein degradation are involved in the phenotypic expression. Both processes occur in exponential cultures, but only protein turnover in arrested cultures. Consistent with this was the demonstration that the rates of total cell protein turnover increased in division-arrested cultures maintained in serum-free medium. These results separate genetic damage and phenotypic expression in a temporal sense, and point out the need to consider the mechanisms responsible for each process involved in the induction and expression of mutations.

Hydrocortisone effects on nucleic acid and nuclear protein content and protein metabolism in aging WI-38 cells

Confluent late passage WI-38 human diploid fibroblast cultures grown in the presence or absence of hydrocortisone for fifteen population doublings were measured cytochemically for DNA, nuclear RNA, basic nuclear protein and acidic nuclear protein content during a 12-hour interval following a medium-change stimulation. Radioisotope tracer studies were utilized to assess the effects of prolonged hydrocortisone treatment on protein synthesis and degradation in aging confluent and logarithmically growing cultures. Hydrocortisone-treated cultures exhibited an increased Feulgen--DNA stainability, no difference in basic nuclear protein content, a significantly larger initial decrease followed by an increase in acidic nuclear protein content, and elevated levels of nuclear RNA as compared to untreated controls. Hydrocortisone treatment also resulted in increased incorporation of leucine into protein and decreased breakdown of pre-labeled protein in both confluent and logarithmically growing cultures. These results indicate that many of the metabolic changes associated with proliferation are stimulated by prolonged hydrocortisone treatment of late passage WI-38 fibroblast cells.

The selective degradation of injected proteins occurs principally in the cytosol rather than in lysosomes

These studies use microinjection to determine whether the selective degradation of cytosolic proteins involves selective transfer of proteins to lysosomes or selective proteolysis within the cytosol. 14C-Sucrose-labeled bovine serum albumin (14C-sucBSA) was conjugated to polylysine, and monolayers of L929 cells were exposed to the conjugate. The 14C-sucrose-labeled peptides that arose upon degradation of the added 14C-sucBSA polylysine accumulated exclusively within lysosomes. In contrast, when 14C-sucBSA or 14C-sucrose-labeled pyruvate kinase (14C-sucPK) was microinjected into L929 cells, over half the 14C-sucrose-labeled peptides derived form the injected proteins were present in the postlysosomal supernatant. Control experiments demonstrated that the microinjection procedure did not cause 14C-sucrose peptides to leak from lysosomes. Therefore, the presence in the cytosol of substantial amounts of the degradation products from injected 14C-sucBSA and 14C-sucPK confirms the existence of a major proteolytic system(s) within or readily accessible to the cytosol of animal cells.

Cumulative population doublings as the determinant of chick cell lifespan in vitro

Chick embryo fibroblasts were maintained at confluency for up to 35 days in medium containing 0.5% or 0.75% fetal bovine serum or 2.5% or 5.0% horse serum. At weekly intervals cells were subcultured and serially propagated in medium containing 10% FBS until their replicative lifespans were completed. The results showed that the replicative lifespan of embryonic chick fibroblasts was dependent on the cumulative number of population doublings undergone by the culture and was not related to the calendar time cells were in culture. Further characterization of 0.75% FBS maintained chick cells returned to 10% FBS medium showed that cells had protein contents and incorporated 3H-thymidine into DNA at a rate that resembled that of young cells, despite an advanced chronological age.

Dual pathways for ribonucleic acid turnover in WI-38 but not in I-cell human diploid fibroblasts

The turnover rates of 3H-labeled 18S ribosomal ribonucleic acid (RNA), 28S ribosomal RNA, transfer RNA, and total cytoplasmic RNA were very similar in growing WI-38 diploid fibroblasts. The rate of turnover was at least twofold greater when cell growth stopped due to cell confluence, 3H irradiation, or treatment with 20 mM NaN3 or 2 mM NaF. In contrast, the rate of total 3H-protein turnover was the same in growing and nongrowing cells. Both RNA and protein turnovers were accelerated at least twofold in WI-38 cells deprived of serum, and this increase in turnover was inhibited by NH4Cl. These results are consistent with two pathways for RNA turnover, one of them being nonlysosomal and the other being lysosome mediated (NH4Cl sensitive), as has been suggested for protein turnover. Also consistent with the notion of two pathways for RNA turnover were findings with I-cells, which are deficient for many lysosomal enzymes, and in which all RNA turnover was nonlysosomal (NH4Cl resistant).

Protein degradation in skin fibroblasts from patients with Duchenne muscular dystrophy

The rates of degradation of [3H]leucine-labelled proteins have been measured in cultures of skin fibroblasts obtained from normal controls (five subjects) and patients with Duchenne muscular dystrophy (six subjects). Cultures were incubated with [3H]leucine (10 microCi/ml) for 60 min to label "short-lived" proteins, and with [3H]leucine (5 microCi/ml) for 60 h to label "long-lived" proteins. Optimal wash procedures were devised for removal of [3H]leucine from the extracellular space and from cell pools before beginning degradation measurements. Re-utilization of [3H]leucine released from degraded labelled proteins was prevented by supplementing the medium with 4mM-leucine. Rates of degradation did not depend on the growth state of the cells or on cell age over the range used (passages eight-20). Degradation of long-lived proteins was approximately linear over a 24h period, at a rate of 1.0% per h. 30% of short-lived protein was degraded within 6h. No differences were observed between protein degradation in normal fibroblasts and in those from patients with Duchenne muscular dystrophy.

Cultured animal cells exposed to amino acid analogues or puromycin rapidly synthesize several polypeptides

Four major acidic polypeptides, with molecular weights of 88, 72, 71, and 23 thousand, and minor polypeptides with molecular weights of 110, 50, 38, and 30 thousand rapidly accumulated in cultured chick embryo (CE) cells which were exposed for three hours to the arginine analogue canavanine. P110, P88, P71,72, and P23 had unique peptide maps. Evidence of a 27,000 dalton precursor to P23 was obtained. The analogue-stimulated proteins were not related to another set of inducible avian polypeptides known as the glucose-regulated proteins. In mammalian cells, the rate of accumulation of several polypeptides, which were similar in size to the avian proteins, sharply increased after canavanine treatment. Proteins with the same electrophoretic mobilities, isoelectric points, and peptide maps as the analogue-stimulated proteins were expressed at low levels in untreated cultures. To determine the time courses of the canavanine-mediated increases in protein accumulation and the recovery of protein metabolism after analogue treatment, radioactively labeled proteins were extracted from CE cells and analyzed on SDS-polyacrylamide gels. In cultures exposed to canavanine, the rates of accumulation of P88 and P71,72 increased from basal to new plateau levels in about 1.5 hours, while P23 required about 2.5 hours. When added with the analogue, actinomycin D and cordycepin blocked the increases in protein accumulation. These inhibitors also blocked the rapid decline in the rates of accumulation of the enhanced proteins which occurred after removal of canavanine. Studies of the matabolic stability of the enhanced proteins indicated that the changes in their accumulation were caused by alterations in their rates of synthesis. Thus, the analogue-mediated response fulfilled several of the criteria for inducible eucaryotic gene expression. The amino acid analogue p-fluorophenylalanine and the chain-terminating analogue of amino acyl-tRNA puromycin stimulated the synthesis of the same set of proteins induced by canavanine. The enhanced synthesis of these proteins appeared to be a cellular response to either the presence or catabolism of abnormal proteins and puromycyl peptides.