Altered nuclear deoxyribonucleic acid alpha-polymerases in senescent cultured chick embryo fibroblasts

Replicative enzymes, DNA polymerase alpha (pol alpha), and in vitro ageing

Normal cells in culture are used to investigate the underlying mechanisms of DNA synthesis because they retain regulatory characteristics of the in vivo replication machinery. During the last few years new studies have identified a number of genetic changes that occur during in vitro ageing, providing insight into the progressive decline in biological function that occurs during ageing. Maintaining genomic integrity in eukaryotic organisms requires precisely coordinated replication of the genome during mitosis, which is the most fundamental aspect of living cells. To achieve this coordinated replication, eukaryotic cells employ an ordered series of steps to form several key protein assemblies at origins of replication. Major progress has recently been made in identifying the enzymes, and other proteins, of DNA replication that are recruited to origin sites and the order in which they are recruited during the process of replication. More than 20 proteins, including DNA polymerases, have been identified as essential components that must be preassembled at replication origins for the initiation of DNA synthesis. Of the polymerases, DNA polymerase alpha-primase (pol alpha) is of particular importance since its function is fundamental to understanding the initiation mechanism of eukaryotic DNA replication. DNA must be replicated with high fidelity to ensure the accurate transfer of genetic information to progeny cells, and decreases in DNA pol alpha activity and fidelity, which are coordinated with cell cycle progression, have been shown to be important facets of a probable intrinsic cause of genetic alterations during in vitro ageing. This has led to the proposal that pol alpha activity and function is one of the crucial determinants in ageing. In this review we summarize the current state of knowledge of DNA pol alpha function in the regulation of DNA replication and focus in particular on its interactive tasks with other proteins during in vitro ageing.

Age-dependent changes in DNA polymerase fidelity and proofreading activity during cellular aging

DNA polymerase alpha and the 3'-->5' exonuclease involved in the proofreading of DNA synthesis were isolated from human diploid fetal lung fibroblast (TIG-1) cells at various population doubling levels (PDL). The final PDL of the TIG-1 cells used in these experiments was 70. The fidelity of DNA polymerase alpha remained high until late passage and fell suddenly just before the end of the life span between 65 and 69 PDL. The activities of the 3'-->5' exonuclease related to proofreading remained unchanged from 21 to 61 PDL, but the activity decreased rapidly in more aged cells. The 3'-->5' exonuclease activity at 69 PDL was about 50% of that in TIG cells at 21 PDL. In vitro DNA synthesis by DNA polymerase alpha from TIG-1 cells harvested at 69 PDL showed the amount of non-complementary nucleotides incorporated to be decreased by the addition of the 3'-->5' exonuclease from the same cells. However, not all errors were edited out since the ratio of DNA polymerase activity to 3'-->5' exonuclease activity was adjusted to reflect that in vivo and the infidelity of DNA synthesis by error-prone DNA polymerase alpha from aged cells was improved by the addition of the highly active 3'-->5' exonuclease from cells at 41 PDL. These results suggested that the mutation frequency rises just before the end of the life span of TIG-1 cells.

Fidelity levels of DNA polymerases in tumorigenic state cells and serially transplantable tumor cells

It is well known that point mutations exist in oncogenes and tumor suppressor genes of tumor cells, and one of the causes of these mutations may be misincorporation by error-prone DNA polymerases. This hypothesis is supported by the observation of decreased fidelity levels of DNA polymerases in mouse spleen containing tumorigenic cells after infection with Friend virus, and in aged animals that suffer high rates of tumorigenesis. However, this decrease in fidelity is disadvantageous for tumor cells maintained by serial transplantation. Therefore, we measured the fidelity levels of DNA polymerases in tumor cells transplanted through many passages. The fidelity levels of DNA polymerases from Yoshida ascites hepatoma, Rhodamine sarcoma, mouse ascites hepatoma-134, and Ehrlich ascites carcinoma cells derived from rats and mice are very high for in-vitro DNA synthesis on synthetic polynucleotides. These results suggest that many kinds of mutant cells arise during tumorigenesis. Among these mutant cells, cells showing decreased DNA polymerase(s) fidelities are present and these cells may undergo cell death. On the other hand, cells with mutations in various oncogenes and tumor suppressor genes and without mutations in DNA polymerase genes may survive as serially transplantable tumor cells.

Changes in fidelity levels of DNA polymerases alpha-1, alpha-2, and beta during ageing in rats

DNA polymerases (deoxynucleoside-triphosphate:DNA deoxynucleotidyltransferase EC 2.7.7.7.) were extracted from the regenerating livers of rats of various ages. The extracts were separated into three DNA polymerase fractions (alpha-1, alpha-2, and beta) by phosphocellulose column chromatography, and their fidelity levels were then monitored with the synthetic template-primer, poly (dA-dT), poly dA-dT10, or poly dC-poly dG. The fidelity levels of the three DNA polymerases from regenerating liver of rats younger than 20 months were high, while those of DNA polymerases from rats older than 20 months were significantly lower with similar profiles on all three template-primers. On the other hand, the fidelity levels of enzymes from 23- and 26-month-old rats were similar. These results indicate that the levels of error-prone DNA polymerases increase rapidly in the regenerating liver of rats from ages 20 to 23 months. This may due to the amplification of DNA polymerase gene mutations by an error-prone enzyme itself. However, the cells in which mutations in the functional gene occur may undergo cell death because the fidelity levels of the DNA polymerases in the older animals did not increase.

Age-associated changes in the template-reading fidelity of DNA polymerase alpha from regenerating rat liver

DNA polymerases (deoxynucleosidetriphosphate: DNA deoxynucleotidyltransferase EC 2.7.7.7.) were extracted from regenerating livers from young and aged rats. DNA polymerase alpha was separated and partially purified by DEAE-cellulose column chromatography, polyethyleneglycol precipitation, and phosphocellulose column chromatography, and fidelity levels were then monitored with the synthetic template-primer poly (dG-dC). The fidelity level of the DNA polymerase from regenerating liver a 4-month-old rat was very high, while that of the DNA polymerase from a 24-month-old rat was significantly decreased. To confirm this result, DNA was synthesized on poly (dG-dC) in a reaction mixture containing [32P]dTTP, and the synthetic polynucleotide was purified and digested with HhaI restriction endonuclease. After hydrolysis, the oligonucleotides were developed by two dimensional thin layer chromatography on PEI cellulose plates. Spots containing [32P]dTMP were observed when DNA polymerase from a 24 month-old rat was used, but none was found in polynucleotides synthesized using DNA polymerase from a 4 month-old rat. Nearest neighbor analysis suggested that dG-dT and dC-dT pairs were constructed by mis-incorporation due to DNA polymerase alpha.

Age-related changes in expression and activity of DNA polymerase alpha: some effects of dietary restriction

DNA polymerase alpha (pol alpha) purified from human diploid fibroblasts (HDF) and from livers of C57BL/6N mice showed age-related decreases in: (1) mRNA levels; (2) the amount of enzyme isolated per cell; and (3) enzyme activity (HDF); as well as: a) the amount of enzyme isolated; b) the specific activity; and c) the enzyme fidelity (liver). Hepatic pol alpha from dietary restricted (DR) mice exhibited less of a decline in specific activity and copied synthetic DNA templates with relatively higher fidelity than did enzymes from animals fed ad libitum (AL). Pol alpha from fetal-derived HDF exhibited increased expression compared with aged donor-derived HDF, with both fetal and old cell pol alpha in normal cells being expressed at lower levels than in their transformed cell corollaries. Treatment of human pol alpha from aged donor-derived HDF with a pol alpha accessory protein isolated from log phase murine cells resulted in increased pol alpha binding of DNA and increased pol alpha activity. However, highly active pol alpha isolated from fetal-derived or transformed HDF, or from transformed murine cells, showed little or no activity enhancement in the presence of accessory protein. These data indicate that, as a function of increased age, there is a decrease in pol alpha expression and specific activity in HDF, as well as decreases in specific activity and fidelity of pol alpha in essentially amitotic murine hepatic tissues. Dietary restriction impedes the age-related declines in both activity and fidelity of hepatic pol alpha in mice. The data further indicate that transformation of slowly dividing HDF is associated with increased expression of pol alpha, but suggest that increased expression alone is not sufficient to explain the difference in polymerase activity levels between parental and transformed HDF. Lastly, the data suggest that interaction of pol alpha with an essential accessory protein may be altered as a function of age, an alteration that appears to be correlated with the decline in pol alpha DNA binding and specific activity.

Effects of aging and dietary restriction on DNA polymerases: gene expression, enzyme fidelity, and DNA excision repair

Hepatic DNA polymerases isolated from young and old C57BL/6N mice fed ad libitum or calorically restricted differed in chromatographic characteristics, binding affinity for DNA template-primer, specific activity, and fidelity of synthesis. DNA polymerase alpha total and specific activity declined slightly, while the nucleotide misincorporation frequency increased dramatically, with increased age of the donor animals. A positive correlation was observed between polymerase alpha specific activity and the affinity of enzyme binding to activated DNA template-primer. Both the age-associated decline in enzyme activity and the decrease in fidelity of synthesis were modified by dietary restriction, with higher specific activity levels and lower misincorporation frequencies for DNA polymerases from dietarily restricted animals compared with ad libitum animals of all ages. Fidelity of both DNA polymerase alpha and beta increased following treatment with the phosphoinositide hydrolysis product inositol-1,4-bisphosphate. The data suggest that dietary restriction could play an important role in decreasing the age-associated decline in function of physiological systems sensitive to decreased or defective DNA synthesis.

Effect of dietary restriction on the fidelity of DNA polymerases in aging mice

DNA polymerases purified from hepatic tissues of C57BL/6 mice showed an age-related decrease in both specific activity and fidelity of the various enzyme forms. Polymerases from dietary restricted mice exhibited less of a decline in specific activity and copied synthetic DNA templates with relatively higher fidelity than did enzymes from animals fed ad libitum. Polymerases treated with inositol-1,4-bisphosphate [I(1,4)P2] showed varying levels of increased activity, with fidelity increases up to 3-fold. These data indicate that aging is associated with decreases in both specific activity and fidelity of DNA polymerases isolated from a nondividing tissue, and that dietary restriction impedes the age-related decline in both specific activity and fidelity of these polymerases. The data further indicate that DNA polymerases may interact with phosphoinositide hydrolysis products resulting in increased specific activity and fidelity of the enzymes. Phosphoinositide interactions with polymerases could constitute an important mechanism moderating the age-related decrease in function and accuracy of DNA polymerases.

Size difference in catalytic polypeptides of two active forms of mouse DNA polymerase alpha and separation of the primase subunit from one form, DNA replicase

There are two active forms of DNA polymerase alpha in mouse cells. One form (DNA replicase) is a DNA polymerase associated with primase activity and the other form (7.3 S polymerase) has no primase activity (Yaugar, T., Kozu, T. and Seno, T. (1982) J. Biol. Chem. 257, 11121-11127). The primase activity was dissociated from partially purified DNA replicase by hydroxyapatite column chromatography in buffer containing dimethyl sulfoxide and ethylene glycol. Nearly homogeneous primase, consisting of a 58 kDa polypeptide was obtained by glycerol gradient sedimentation and DEAE-cellulose column chromatography. Experiments on the effect of proteinase treatment and measurement of the molecular weight of the catalytic polypeptide of DNA replicase after its dissociation from the primase polypeptide indicated that the primase is not part of the DNA polymerase molecule, but an independent protein associated with DNA polymerase alpha, and that the latter is a 115 kDa catalytic polypeptide. The other form of DNA polymerase alpha, 7.3 S polymerase, consists of a 72 kDa catalytic polypeptide. Thus, the two forms of mouse DNA polymerase alpha have partially, if not completely, different catalytic polypeptide structures, suggesting that the 7.3 S polymerase is not simply formed from DNA replicase by dissociation of the primase subunit.

Increased DNA topoisomerase I activity in aging human cell chromatin

Chromatin-associated DNA topoisomerase I activity was measured in human diploid fibroblasts during in vitro aging. No difference was detected as a function of cell age in the nicking and the closing activities of the DNA-unwinding enzyme. The capacity of type-I topoisomerase to relax superhelical DNA molecules was, however, increased in aged cells. An age-related increase in nucleoprotein content was also observed.

Synthesis of early vaccinia-virus-specific enzymes under conditions of immediate early gene expression

Cycloheximide reversal experiments in chick embryo fibroblasts and mouse L-929 cells indicate that the poxvirus-induced enzymes DNA polymerase and 'alkaline' DNase are immediate early gene products of the virus. In contrast to the vaccinia-WR-coded enzyme under conditions of immediate early gene expression the cowpox-virus-induced DNA polymerase is made only in very small amounts. The studies are consistent with the notion that all poxvirus-specific early proteins may be immediate early viral gene products.

S-phase transit times as a function of age in human diploid fibroblasts

The minimum time it takes a cell to pass completely through the S phase (MIN S) was examined in human diploid fibroblasts using a sequential [14C]thymidine, [3H]thymidine, [14C]thymidine labeling protocol. MIN S appeared to be around 6-8 h for both WI-38 and MRC-5 cells. In addition, MIN S did not increase in senescent cultures. Since damage to either DNA, its polymerases, or both would result in a reduction in the rate of DNA synthesis and a corresponding increase in MIN S, this suggests that in senescent cultures at least a portion of the cells contain DNA that is relatively undamaged and DNA polymerases that exhibit normal replicative kinetics.

Changes in DNA polymerases alpha, beta and gamma in mouse liver as a function of age

The activities of DNA polymerases alpha, beta and gamma were determined in mouse liver as a function of age by a combination of glycerol density gradient centrifugation with polymerase specific assays. Although alpha polymerase was preserved throughout the life span, the activity dropped sharply from a high level at the fetal and neonatal stages to a level one order lower after maturation through adjustment of the amount of protein administered. beta polymerase showed similar but less drastic changes than alpha. DNA polymerase gamma activity increased about two-fold in going from newborn to adult stages and remained constant after maturation. According to the amount of DNA, DNA polymerase alpha decreased after birth, but the change was less drastic compared to that through adjustment of the amount of protein. DNA polymerase beta increased the activity 2-3-fold within a period of 3 months following birth. gamma polymerase underwent more than a 10-fold increase in activity through adjustment of the amount of DNA within the same period.

Macrophage-mediated cytostatic activity blocks lymphoblast cell cycle progression independently in both G1 phase and S phase

Recent work has shown that macrophage-mediated cytostatic activity inhibits cell cycle traverse in G1 and/or S phase of the cell cycle without affecting late S, G2, or M phases. The present report is directed at distinguishing between such cytostatic effects on G1 phase or S phase using the accumulation of DNA polymerase alpha as a marker of G1 to S phase transition. Quiescent lymphocytes stimulated with concanavalin A undergo a semisynchronous progression from G0 to G1 to S phase with a dramatic increase in DNA polymerase alpha activity between 20 and 30 hr after stimulation. This increase in enzyme activity was inhibited, as was the accumulation of DNA, when such cells were cocultured with activated murine peritoneal macrophages during this time interval. However, if mitogen-stimulated lymphocytes were enriched for S-phase cells by centrifugal elutriation and cocultured with activated macrophages for 4-6 hr, DNA synthesis was inhibited but the already elevated DNA-polymerase activity was unaffected. Similar results were obtained when a virally transformed lymphoma cell line was substituted as the target cell in this assay. These results show that both G1 and S phase of the cycle are inhibited and suggest that inhibition of progression through the different phases may be accomplished by at least two distinct mechanisms.

Evidence that a critical threshold of DNA polymerase-alpha activity may be required for the initiation of DNA synthesis in mammalian cell heterokaryons

The specific activity of DNA polymerase (90% alpha) was determined in nine "neoplastoid" cell lines (Martin and Sprague, 1973) and in three different strains of HDF (human diploid fibroblast-like cells), all examined in logarithmic phases of growth. This was compared to the ability of each cell type to "rescue" (reinitiate DNA synthesis in) senescent HDF cells subsequent to polyethylene glycol-mediated cell fusions. A sharp "threshold" value of DNA polymerase activity was observed below which reinitiation of DNA synthesis in heterokaryons with senescent HDF does not occur. This threshold was especially obvious when the specific activity of DNA polymerase (p moles dTTP incorporated per mg protein or per cell) was divided by the percent of S-phase cells present in each culture as determined by flow microfluorometry. Our results indicate that the specific activity of DNA polymerase-alpha (or some other factor tightly coregulated with it) in "recessive" cell types (those unable to rescue senescent cells) is only about two times this theoretical "threshold" value, and that fusion of recessive cell types to senescent HDF cells reduces the specific activity in the heterokaryon to below this minimum, thus preventing the cells from entering S phase.

On the activity and fidelity of chromatin-associated hepatic DNA polymerase-beta in aging murine species of different life spans

Activity and accuracy of chromatin-directed DNA replication have been compared in young and aged Mus musculus and Peromyscus leucopus, two murine species with contrasting maximum lifespans. Chromatin isolated from livers of mature adults of both species copied efficiently exogenous DNA templates using predominantly DNA polymerase-beta. The DNA synthetic activity of liver chromatin remained constant in both species throughout their lifetimes. The fidelity of chromatin-directed poly [d(A-T)] synthesis was similar for the comparatively short-lived M. musculus and the relatively long-lived P. leucopus and remained unaltered in old animals. The fidelity of poly [d(A-T)] copying catalyzed by DNA polymerase-beta-dissociated from liver chromatin was comparable to that of the chromatin-directed synthesis. The dissociation enzymes did not exhibit diminished fidelity of poly [d(A-T)] synthesis with age. In all ages of both species examined, the murine liver DNA polymerase-beta, both chromatin-associated and solubilized, exhibited high error frequencies; approximately one dGMP was incorporated for every 500-1,000 complementary nucleotides polymerized. The relationship of these results to the accuracy of DNA replication and repair as a determinant of aging is considered.

Replicative activity of isolated chromatin from proliferating and quiescent early passage and aging cultured mouse cells

Replicative activity of isolated chromatin from late passage cultured mouse cells has been compared to the activities of chromatin preparaions from dividing and quiescent early passage cells. Rates of endogenous DNA synthesis are similar for chromatin from growing or resting cells but this activity is stimulated 2.5-fold in senescent cell chromatin. Chromatin from growing young cells copies exogenously added single stranded DNA at the highest efficiency. Chromatin of senescent cells copies this template at a lower rate and resting young cell chromatin replicates single stranded DNA at the lowest efficiency. Similar relative rates are obtained when activated DNA is copied by the various chromatin preparations. Total activity of DNA polymerase extracted by salt from chromatin is similar for dividing and quiescent young cells but the proportion of DNA polymerase beta is higher in the latter. Elevated activities of DNA polymerases are extracted from chromatin of old cells. It is concluded, therefore, that chromatin-directed replication is differently arrested in non-dividing senescent cells and in quiescent early passage cells. The possible regulatory mechanisms of DNA replication in quiescence and aging are discussed.

Conservation of ribosomal fidelity during ageing

The function of ribosomes prepared from the liver of young (2--5 months old) and senescent (15--26 months old) mice were compared in vitro. The conclusions that can be drawn from the liver of senescent mice is 10 to 40% lower than that of young mice; (2) the fidelity of translation does not change grossly with age; (3) the thermosensitivity of translational activity of ribosomes and the activity of ribosome-associated ribonuclease do not change with age; (4) there is an age-dependent accumulation of free 40S ribosomal subunits in the cytoplasm of mouse liver. The relation of age-dependent changes in the structure and function of ribosomes is discussed.

Increase in the ratio of 18S RNA to 28S RNA in the cytoplasm of mouse tissues during aging

The possibility of alterations in cytoplasmic RNA in mouse liver, kidney and brain during aging was investigated. The cytoplasmic RNAs in these organs gave similar profiles of optical density at 260 nm with three major peaks at 28S, 18S and 4S on sucrose gradient centrifugation. However, the ratio of the amounts of 18S and 28S RNA increased significantly with age in the brain and liver. The polyacrylamide gel electrophoretic patterns of extracts of the three tissues under both native and denaturing conditions were nearly identical regardless of the age of the animals. Since most of the minor components separated on gels were probably in vivo degradation products of ribosomal RNA, these results suggest that the extent of apparent and hidden breaks in ribosomal RNA does not change during aging.

DNA replication in human lymphocytes during aging

An analysis of the accuracy of protein and DNA synthesis in human lymphocytes with respect to aging has been carried out. The response of human peripheral lymphocytes, from young and old adults, to phytohemagglutinin was measured at varying temperatures. This should provide a sensitive test for the accumulation of altered thermolabile proteins that are rate limiting in the response to phytohemagglutinin. At 37 degrees C the rate of thymidine incorporation as well as the induction of DNA polymerase in phytohemagglutinin-stimulated lymphocytes from old and young adults were similar. Also at elevated temperatures, the thermosensitivity of DNA replication in lymphocytes from young and old adults was the same. DNA polymerase was purified from PHA-stimulated lymphocytes from young and old adults. The fidelity of DNA synthesis using poly (dC) as a template was similar with both enzymes. However, DNA polymerase-alpha purified from old adults was thermolabile compared to the enzyme from young adults. Thus, while the lymphocytes from old individuals may have heat labile proteins, they do not limit their proliferative capacity.

Highly efficient copying of single-stranded DNA by eukaryotic cell chromatin

Chromatin prepared from S phase hepatoma tissue culture (HTC) cell incorporates in vitro about 11-14 pmoles [3H]dTMP into DNA in 30 min. Single-stranded DNA added to this chromatin stimulates DNA synthesis more than 40-fold whereas activated DNA enhances it about 60-fold. By contrast, stimulation of DNA synthesis by activated DNA in a crude nuclear extract exceeds the stimulation exerted by denatured DNA by a factor of 7. Stimulation of DNA synthesis by denatured DNA is not due to stabilization of either the chromatin or the product of the endogenous reaction. On the other hand, we find that poly(dC) and poly (dT) enhance DNA synthesis by serving as templates which are copied by chromatin in a true complementary fashion. It seems therefore, that eukaryotic cell chromatin is able to copy single-stranded DNA at a high efficiency. Chromatin of G1 arrested cell copies exogenous templates at a considerably reduced rate. The enzyme responsible for the copying of denatured DNA is tentatively identified as DNA polymerase alpha on the basis of its sensitivity to sulfhydril group blocking, its requirements for ions and failure to copy the ribo strand of oligo(dT) poly(A).

Protein turnover in senescent cultured chick embryo fibroblasts

The over-all rates of protein synthesis, degradation and net accumulation were estimated in rapidly growing young and slowly doubling old cultures of chick fibroblasts. We find that not only the rate of protein synthesis is reduced in senescent cultures, but the average rate of protein degradation is also slowed down considerably. This decrease in the rate of protein breakdown in aging cells stands in contrast with the previously observed acceleration of this process by other conditions (such as serum deprivation or overcrowding) that lead to the cessation of cellular growth. Though the retarded protein degradation may contribute to the acculation of abnormal proteins in senescent cells we find that the breakdown of grossly abnormal puromycin peptides proceeds equally rapidly in young and old cultures. The protein content of senescent cells increases by 1.8-fold as compared to young cells, while the average cell volume is increased even more (almost 5-fold). By contrast, consideration of the over-all balance of protein metabolism in these cells indicates that the average concentration of metabolically turning-over proteins is somewhat higher in senescent than in young fibroblasts.

HeLa cell DNA polymerases: the effect of cycloheximide in vivo and detection of a new form of DNA polymerase alpha

Blockage of protein synthesis in HeLa cells by cycloheximide leads to selective effects on the levels of DNA polymerases alpha, beta, and gamma in the cell. The total activity of DNA polymerase alpha remains unchanged after 7 h exposure of cells to cycloheximide but drops to 50% of its original level after 24 h. The level of the beta-polymerase falls rapidly in the cell and is reduced to less than 30% of its initial value by 7 h after treatment of the cells with cycloheximide. The gamma-polymerase level is diminished by 30--40% during the 7 h cycloheximide treatment and reaches 50% of its original level after 24 h. Cells which have been exposed to cycloheximide for 7 h will regain normal levels of the beta- and gamma-polymerases within 90 min after removal of the drug. The cycloheximide-treated cells also show the presence of a new form of the alpha-polymerase, designated alpha1, which can be clearly detected as a separate entity in column chromatography. The level of alpha1 in the nucleus increases during the period that the cells are treated and cycloheximide so that after 24 h it represents almost 50% of the nuclear DNA polymerase activity. The presence of alpha1 in the cytoplasmic fraction can also be demonstrated in both cycloheximide-treated and normal, growing cells.