DNA Replicon Research Articles

Presence of a linear plasmid-like DNA molecule in the fungal pathogen Ceratocystis fimbriata Ell. & Halst.

A plasmid-like molecule was detected in a strain of the ascomycete Ceratocystis fimbriata Ell. & Halst., a pathogenic fungus of Populus spp. The DNA replicon, designated pFQ501, was found to have a linear structure with a length of 6.0 kb (3.9 × 106 daltons) and a density of 1.685 g/cc. This molecule was found to be associated with the mitochondria and was isolated from the gel; its restriction map was deduced from single and double digestions.

Mean rate of DNA replication and replicon size in the shoot apex ofSilene coelirosa L. During the initial 120 minutes of the first day of floral induction

28-day-old plants ofSilene coeli-rosa were exposed, at 1,700 hours, to long day (LD) conditions comprising light of low fluence rate provided by tungsten bulbs, or maintained in darkness as short day (SD) controls. All plants were exposed at 1,700 hours to tritiated-(methyl-3H)-thymidine for 30, 45, 60, 90, or 120 minutes. Apical domes were isolated and prepared as fiber autoradiographs from which replicon size and rates of DNA replication, per single replication fork were recorded. In SD, replicon size was between 15–20 μm and exposure to LD conditions altered neither replicon size nor the pattern of deployment of replicons during S-phase relative to the SD controls. However, the mean rate of replication in LD was 8.7 μm h−1 compared with 5.2 μm h−1 in SD. Thus, exposure to LD resulted in a 1.7-fold increase in the rate of DNA replication relative to the SD controls. This rapid increase in replication rate, detectable within 30 minutes of the start of the LD is discussed in relation to changes known to occur to the cell cycle inSilene during the first day of floral induction.

Effect of benzo[a]pyrene-diol-epoxide-I on growth of nascent DNA in synchronized human fibroblasts.

In logarithmically growing cultures of human fibroblasts, benzo[a]pyrene-diol-epoxide-I (BPDE-I) treatment inhibits both replicon initiation and DNA chain elongation. In this study we have focused on the effect of BPDE-I treatment on the growth of nascent DNA strands in synchronized human fibroblasts. Cells were collected at the beginning of the S phase by replating confluent cultures in the presence of aphidicolin for 24 h. At 1 h after release from aphidicolin, cells were incubated with [3H]thymidine for 10-15 min and treated with BPDE-I for 10 min. Following different periods of incubation with unlabeled thymidine, cells were lysed on top of alkaline sucrose gradients for analysis of the size distribution of nascent DNA and its average molecular weight. After a brief pulse with the radiolabeled precursor, a unimodal distribution of nascent DNA strands was observed in control cells. Upon chase this distribution was displaced to higher average molecular weights at an approximate rate of 1 X 10(6) daltons/min. Treatment with low doses of BPDE-I (less than 0.2 microM) did not decrease this rate. Indeed the nascent DNA in BPDE-I-treated cells appeared to grow faster than in control cells. This higher rate of DNA strand growth may be related to the inhibition of replicon initiation. Treatment with 0.3 microM or 0.7 microM BPDE-I, which are doses that interfere with DNA synthesis in operating replicons in asynchronous cells, also inhibited the growth of nascent DNA strands in synchronized cells by 22 and 64%, respectively. Because of the simultaneous inhibition of replicon initiation, these values are probably underestimations of the total inhibition of DNA strand growth. The use of synchronized cells in this type of study should aid in the elucidation of mechanisms of replication of carcinogen-damaged DNA.

Xeroderma pigmentosum variant and normal fibroblasts show the same response to the inhibition of DNA replication by benzo[a]pyrene-diol-epoxide-I.

Xeroderma pigmentosum (XP) variant cells are characterized by an abnormal pattern of replication of DNA damaged by 254 nm radiation (u.v.). To see whether benzo[a]pyrene-diol-epoxide-I (BPDE-I) elicits the same response, we have compared the effects of u.v. and BPDE-I on DNA replication in XP variant and normal skin fibroblasts. Doses of u.v. that only affected replicon initiation in normal cells, inhibited DNA strand growth in the XP variant. These results were confirmed by measurements of the rate of growth of single-stranded nascent DNA in cells synchronized at the beginning of the S phase. Identical analyses using BPDE-I, however, indicated that the two cell types were equally sensitive to the inhibitions of both replicon initiation and DNA strand growth. These results indicate that the XP variant phenotype cannot be recognized in vitro by the pattern of response of fibroblasts to the inhibition of DNA replication by BPDE-I.

Effect of ultraviolet light on thymidine incorporation, DNA chain elongation and replicon initiation in wild-type and excision-deficient Chinese hamster ovary cells

Wild-type Chinese hamster ovary cells (AA8) and five excision-deficient clones derived from the AA8 line (UV-4, UV-5, UV-20, UV-24 and UV-41) were exposed to ultraviolet light and then analyzed for their ability to incorporate [ 3H]thymidine and to initiate as well as elongate replicon-sized DNA fragments. After exposure to ultraviolet light, all cell lines exhibited a depression in the rate of thymidine incorporation. For exposures of 4.0 J/m 2 or higher the wild-type cells recovered normal rates of thymidine incorporation within a few hours, while none of the excision-deficient lines exhibited complete recovery. For fluences below 4.0 J/m 2 all but the UV-5 line exhibited at least some recovery. The ability to elongate DNA chains appeared to correlate with the thymidine incorporation data, with the UV-5 line exhibiting the strongest blockage of DNA chain elongation, the AA8 line exhibiting the least blockage, and the UV-20 line exhibiting an intermediate response. All cell lines exhibited a decrease in the distance between replication origins, thus supporting models which propose that exposure to ultraviolet light results in the use of alternative sites for the initiation of replication.

Quantitative variation in components of the maize mitochondrial genome between tissues and between plants with different male-sterile cytoplasms

The amounts of a 1.9 kb mitochondrial plasmid relative to sequences in another mitochondrial DNA replicon and also to nuclear ribosomal DNA sequences have been compared in maize leaves and anthers. Similar comparisons have been made between plants with the same nuclear genotype but containing normal, S, or T cytoplasms. The ratio of 1.9 kb plasmid to nuclear rDNA is lower in plants with normal cytoplasm than in plants with S or T cytoplasm. It also differs between leaves and anthers. Furthermore, the relative concentration of the mitochondrial DNA sequences belonging to different replicons differs between leaves and anthers. It is concluded that components of different mitochondrial replicons are not maintained in fixed ratios during development and that the concentration of the 1.9 kb plasmid is regulated, in part, by cytoplasmically-inherited determinants. The 1.9 kb plasmid is absent from lines with the Vg cytoplasm, but related sequences are found in the maize nuclear genome.

Theophylline release of replicon initiation inhibition by nitrosoureas correlates with the synergistic killing in L1210 leukemia in vitro

This report demonstrates the synergistic killing of murine L1210 leukemia in vitro by BCNU and theophylline as has previously been reported in vivo. Synergism is also seen with the related nitrosourea CNU plus theophylline. As measured on alkaline sucrose gradients and by pH-step alkaline elution, the nitrosourea-induced inhibition of DNA replicon initiation is completely reversed in the presence of theophylline. DNA interstrand crosslinking, the damage which usually correlates with nitrosourea cytotoxicity, is not increased by the combination of nitrosourea plus theophylline. At high nitrosourea doses, this interstrand crosslinking is reduced in the presence of theophylline. At least part of the mechanism of the two-drug synergism is the theophylline release of nitrosourea-induced DNA initiation inhibition. Some of the results have been presented at the Annual Meeting of the American Association for Cancer Research.

Inhibition of mammalian cell DNA synthesis by ionizing radiation.

A semi-log plot of the inhibitory effect of ionizing radiation on the rate of DNA synthesis in normal mammalian cells yields a two-component curve. The steep component, at low doses, has a D0 of about 5 Gy and is the result of blocks to initiation of DNA replicons. The shallow component, at high doses, has a D0 of greater than or equal to 100 Gy and is the result of blocks to DNA chain elongation. The target size for the inhibition of DNA replicon initiation is about 1000 kb, and the target size for inhibition of DNA chain elongation is about 50 kb. There is evidence that the target for both components is DNA alone. Therefore, the target size for inhibition of DNA chain elongation is consistent with the idea that an effective radiation-induced lesion in front of the DNA growing point somehow blocks its advance. The target size for inhibition of DNA replicon initiation is so large that it must include many replicons, which is consistent with the concept that a single lesion anywhere within a large group (cluster) of replicons is sufficient to block the initiation of replication of all replicons within that cluster. Studies with radiosensitive human cell mutants suggest that there is an intermediary factor whose normal function is necessary for radiation-induced lesions to cause the inhibition of replicon initiation in clusters and to block chain elongation; this factor is not related to poly(ADP-ribose) synthesis. Studies with radiosensitive Chinese hamster cell mutants suggest that double-strand breaks and their repair are important in regulating the duration of radiation-induced inhibition of replicon initiation but have little to do with effects on chain elongation. There is no simple correlation between inhibition of DNA synthesis and cell killing by ionizing radiation.

Theophylline reversal of alkylator-induced replicon initiation inhibition: no correlation with DDP-induced cytotoxicity

The synergistic cytotoxic activity exhibited by bifunctional alkylating agents in the presence of methylxanthines has been associated with methylxanthine-induced reversal of alkylator-induced DNA replicon initiation inhibition. This has also beenseen with methylxanthines and ionizing irradiation. Methylxanthines do not appear exacerbate drug or ionizing radiation-induced damage. We report here a situation in which methylxanthine-induced reversal of DNA replicon initiation inhibition is not associated with increased cytotoxicity of the alkylator. Murine L1210 leukemia cells were assayed for cytotoxicity following treatment with either l-PAM or cis-DDP in the presence or absence of theophylline. Theophylline increased the cytotoxicity seen after l-PAM treatment but failed to increase the cis-DDP induced cytotoxicity. Analysis of pulse-labeled DNA on alkaline sucrose gradients revealed the expected decrease in DNA replicton initiation in L1210 cells treated with either l-PAM or cis-DDP. Theophylline had no effect on replicon initiation in untreated cells. Theophylline reversed the replicon initiation inhibition in cells treated with either l-PAM or cis-DDP. The reason for the apparent lack of added toxicity of the replicon initiation inhibition reversal in L1210 cells treated with theophylline and DDP is unknown.

Theophylline does not reverse DNA replicon initiation inhibition in human cells resistant to alkylating agent-theophylline killing synergism

The human Burkitt's lymphoma cell line BHM fails to show synergistic killing by alkylating agents in the presence of theophylline. Nitrosoureas (BCNU and CNU), a mustard agent (L-phenylalanine mustard), and a platinum coordination complex ( cis-diamminedichloroplatinum-II) did not show increased cytotoxicity when cells were treated in the presence of theophylline. Despite varying abilities of the drugs to induce DNA damage in BHM cells (no DNA interstrand cross-linking with nitrosoureas or platinum and significant interstrand cross-linking following L-PAM treatment) theophylline did not alter the pattern of DNA damage. DNA interstrand cross-linking following treatment by L-PAM with theophylline was slightly decreased from that seen with L-PAM alone. All three drugs induced DNA replicon initiation inhibition in BHM cells as measured both by alkaline sucrose gradient sedimentation and pH step alkaline elution. As opposed to cell lines where methylxanthines increase alkylating agent cytotoxicity, theophylline and caffeine failed to reverse the drug-induced replicon initiation inhibition seen in BHM cells. These findings support the hypothesis that the synergistic killing seen in some cell lines with alkylating agents and methylxanthines is due to the reversal of replicon initiation inhibition by the methylxanthines.

Inhibition of mammalian deoxyribonucleic acid synthesis by neocarzinostatin: selective effect on replicon initiation in CHO cells and resistant synthesis in ataxia telangiectasia fibroblasts.

Treatment of CHO cells with low doses of the protein antibiotic neocarzinostatin severely inhibited DNA replicon initiation but had no effect on chain elongation. The selectivity of the effect on initiation, which was greater than that seen with other chemical agents and comparable to that seen with X-rays, explains the biphasic dose response seen for DNA synthesis inhibition by this drug. Parallel experiments employing the nucleoid sedimentation technique indicated that half-maximal relaxation of domains of DNA supercoiling and half-maximal inhibition of replicon initiation required the same dose of neocarzinostatin, approximately 0.03 micrograms/mL. These results, similar results obtained with the protein antibiotic auromomycin, and previous results obtained with X-rays suggest a quantitative correlation between inhibition of replicon initiation and induction of sufficient strand breakage to relax domains of supercoiling in DNA of mammalian cells. Results in human ataxia telangiectasia fibroblasts indicated that neocarzinostatin, like X-rays, is much less effective in inhibiting DNA synthesis in these cells than in normal human fibroblasts. This finding is consistent with the hypothesis that the genetic defect in ataxia telangiectasia involves a failure to recognize the presence of strand breaks in cellular DNA.

Relationship between DNA chain growth termination and replicon sizes in γ-irradiated mouse cells

Unirradiated mouse leukemic L5178Y cells were pulse-labeled with [ 3H]thymidine continuously for up to 150 minutes. The resulting DNA fiber autoradiograms showed a continuously increasing fiber length up to 70 μm. However, in cells irradiated with 500 to 2000 rad of γ-rays, the resulting DNA fiber lengths leveled off at approximately 35 μm. Independent experiments to estimate replicon size by measuring the center-to-center distance in tandem tracks yielded a value of 48 μm. These results are consistent with a model proposing that the average replicon size is equal to √2 times the plateau value of the average length of labeled DNA measured in irradiated cells.

Bleomycin induced inhibition of dna synthesis in ataxia-telangiectasia cell lines

Summary Exposure of fibroblast and lymphoblastoid cell lines from normal subjects to bleomycin (30–300 μg/ml) results in a dose dependent biphasic inhibition of DNA synthesis when compared with untreated cells. Using alkaline sucrose density gradient sedimentation we have confirmed that bleomycin decreases both DNA replicon initiation and chain elongation in normal lymphoblastoid cells. Doses of up to 100 μ/ml which caused a marked decrease in the rate of DNA synthesis in normal lymphoblastoid cells had much less effect on the inhibition of DNA synthesis in lymphoblastoid cell lines from ataxia-telangiectasia patients. The inhibition of DNA replicon initiation and chain elongation in these cell lines occurred only at high doses of bleomycin (100 μg/ml).

Mice, men, mustard and methylated xanthines: the potential role of caffeine and related drugs in the sensitization of human tumours to alkylating agents.

The relationships between DNA damage from UV radiation, alkylating drugs and the methylated xanthines (MX) have been studied in normal and malignant rodent and human cells. A comparison of the level of DNA excision repair (repair replication and unscheduled DNA synthesis) confirms that some forms of alkylating-agent damage (probably mono-filar DNA adducts) are less completely removed by both normal and malignant rodent cells than by their human counterparts, rendering rodent cells more susceptible to the toxic potential of unexcised lesions. The toxicity of alkylating agents can be increased by the presence of several MXs during the period of DNA replication which follows infliction of the damage. Human cells appear capable of excising more DNA damage, rendering them somewhat less susceptible to enhancement of cytotoxicity by MX. This resistance of human cells is only quantitative, however, since 2 human cancer cell lines (HeLa and HT-29) could be sensitized to a variety of alkylating agents by appropriate concentrations of MX. Trimethylxanthine (caffeine) and the 2 clinically useful dimethylxanthines (theophylline and theobromine) appeared equally effective in sensitizing cells. The sensitization was dependent upon a slightly cytotoxic concentration of the MX and a suitably prolonged period of post-damage MX exposure. Of these 3 classic MXs, only theobromine might be clinically useful. The levels required for alkylating-agent sensitization exceed the clinically tolerable level of theophylline, and probably approach the tolerance of man to caffeine. The most likely mechanism by which MX sensitization is achieved is reversal of the inhibition of DNA replicon initiation which follows the infliction of significant DNA damage. Through the selection of suitable clinically useful alkylating agents (those dependent on active cellular transport for cell penetration) and appropriate MX scheduling, an enhanced therapeutic ratio might be achieved, potentially increasing the clinical usefulness of these alkylating agents. MX would thus form a useful class of agents adjuvant to conventional anti-cancer drugs.

Curing of Saccharomyces cerevisiae 2-?m DNA by transformation

A general procedure for the curing of 2-μm in Saccharomyces cerevisiae is described. The method is based on the displacement of endogenous 2-μm DNA by the recombinant plasmid pMP78-1, which carries the yeast leu2 gene and the 2 -μm DNA replicon, but cannot be maintained stably in a yeast cell without endogenous 2-μm DNA. After transformation with pMP78-1 cells are grown selectively to displace 2-μm DNA. During the non-selective growth which follows, plasmid pMP78-1 is lost and up to 100% of the cells completely lack plasmids. In conjunction with a kanamycin resistance marker, as present in plasmid pMP81, this method should be applicable to cure any wild-type yeast strain. The stability of recombinant plasmids in cir (+) and cir (0) strains has been compared.

Effects of activated aflatoxin B1 and caffeine on DNA replicon initiation in HeLa cells.

Aflatoxin B1 (AFB1) is activated by a rat microsomal extract (S-9) to form a product that inhibits DNA synthesis in HeLa cells. At 10(-7) M, AFB1 inhibited initiation of replicons, as shown in alkaline sucrose gradient profiles 30 min after incubation with the drug. Ninety minutes later, the profile of treated cells was similar to that of control, but 4 h later there was another effect on replicon initiation. At 10(-6) M, the inhibition of initiation was greater than at 10(-7) M and increased progressively. Four hours after removal of the drug, the gradient profile showed low amounts of radioactivity in all size classes of DNA. When cells were incubated in medium containing caffeine (2mM) even as late as 60 min after incubation with AFB1, the inhibition of replicon initiation was prevented. If caffeine was later removed from the medium, replicon initiation was then inhibited. At 10(-7) M or 10(-6) M, AFB1 had little immediate effect on chain elongation, but at 10(-5) M, the gradient profiles showed an accumulation of low molecular weight DNA molecules, with no radioactivity in the region of high molecular weight DNA, owing to a block to chain elongation; this was not affected by caffeine. These results suggest that AFB1 induces damage that changes the conformation of chromatin so that initiation of new replicons cannot occur; in the presence of caffeine this change does not occur and DNA replication is not inhibited.

Changes in replicon behaviour during the S period in Sorex araneus cells in culture

The parameters of DNA replicon synthesis have been examined at successive stages in the S period of synchronised Sorex araneus (S3/4) cells in culture by DNA fibre autoradiography. Both mean rate of chain growth and distance between initiation sites remain constant. There is, however, an indication that during mid-S, when cells are subjected to the maximum utilization of the DNA-elongating system, there is a slight reduction in the rate of chain elongation, particularly among the faster growing chains of DNA.

Equations for measuring the rate of DNA chain growth and replicon size by density labeling techniques

The effects of initiation, termination and clustering of replicons have been considered in the development of equations which are used to measure DNA chain elongation in mammalian cells by density gradient techniques. These equations can be used to determine the average replicon size as well as the rate of chain elongation. Experimental data from WI-38 and HeLa cells are presented which show the applicability of these methods. Several models of replication initiation and termination have been developed. Some of these models can be eliminated experimentally and the experimental results are consistent with the notion that neighboring replicons are initiated simultaneously or sequentially with short (∼-0·5 min) interinitiation time.

Evidence that x-irradiation inhibits DNA replicon initiation in Chinese hamster cells

Summary Analysis of DNA replicated 20–30 min after x-irradiation showed that the relative size distribution of single-strand DNA was deficient in DNA 4 × 107 daltons. During this time, depressed thymidine incorporation into total DNA could be accounted for by failure to replicate DNA

Families of replicating units in cultured hamster fibroblasts

An examination of the patterns of DNA replication in pseudodiploid Don C and diploid Don cell lines in culture has been made. Pulse-chase labelling experiments with 3H-thymidine in both synchronized and log-phase cells indicate that the newly replicated DNA can be divided into two and three large temporally distinct fractions in Don C and Don cells, respectively. This is shown radiochemically by fluctuations in the incorporation of 3H-thymidine into the DNA of synchronized cells and autoradiographically by fluctuations in counts of labelled metaphases and grain over mitotic figures. Pulse-chase experiments and fluorometric determinations indicate that the periodic incorporation of 3H-thymidine can be accounted for by discontinuous synthesis and turnover of DNA during the cell cycle. A survey of the literature reveals that fluctuations in DNA synthetic activity during the S phase are to be found in a large number of published graphs of cell population kinetics. The phenomenon is observable in both diploid and non-diploid cells. A change in the timing of DNA replicon synthesis during the S phase according to the developmental stage and age of the cell is proposed.