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At least 793 records · Page 44Linked to original sources
PubMed1994

DNA replication from initiation zones of mammalian cells in a model system.

We reported that DNA replication initiates from the region containing an autonomously replicating sequence from Saccharomyces cerevisiae when negatively supercoiled plasmid DNA is incubated with the proteins required for simian virus 40 DNA replication (Y. Ishimi and K. Matsumoto, Proc. Natl. Acad. Sci. USA 90:5399-5403, 1993). In this study, the DNAs containing initiation zones from mammalian cells were replicated in this model system. When negatively supercoiled DNA containing an initiation zone (2 kb) upstream of the human c-myc gene was incubated with simian virus 40 T antigen as a DNA helicase, HSSB (also called replication protein A), and DNA polymerase alpha-primase complex isolated from HeLa cells, DNA replication was specifically initiated from the center of the initiation zone, which was elongated bidirectionally in the presence of a DNA swivelase. Without HSSB, the level of DNA synthesis was significantly reduced and the localized initiation could not be detected, indicating that HSSB plays an essential role in the initiation of DNA replication. The digestion of negatively supercoiled template DNA with a single-strand-specific nuclease revealed that HSSB stimulated DNA unwinding in the center of the initiation zone where the DNA duplex is relatively unstable. In contrast, DNA replication started from a broad region of an initiation zone downstream of the dihydrofolate reductase gene from chinese hamster ovary cells, but the center of the region was mapped near the origin of bidirectional DNA replication. These results suggested that this system mimics a fundamental process of initiation of eukaryotic DNA replication. The mechanism of initiation is discussed.

Base Sequence↗
PubMed1978

[Effect of cycloheximide on DNA replication. III. Results of autoradiography of the DNA of lysed cells].

With the help of DNA-fiber autoradiography on L cells, the question of mechanism of a rapid block of DNA replication by cycloheximide, an inhibitor of protein synthesis, was examined. The presented data show that the elongation of labeled regions in replicating units is blocked. In non-treated cells the replication rate was 0.4 mcm/min; the mean size of replicon was 21 mcm. The difficulties encountered in the explanation of the data obtained are discussed.

Autoradiography↗
PubMed1992

Effect of camptothecin on mitogenic stimulation of human lymphocytes: involvement of DNA topoisomerase I in cell transition from G0 to G1 phase of the cell cycle and in DNA replication.

The possible involvement of DNA topoisomerase I in cell transition from G0 to G1 and in progression through the cell cycle was studied by estimating the ability of human peripheral blood lymphocytes to undergo mitogenic stimulation in the presence of the topoisomerase I inhibitor camptothecin (CAM). Exposure of quiescent G0 lymphocytes to up to 3 microM CAM for 24 h had no significant effect on their ability to subsequently undergo mitogenic stimulation in the presence of phytohemagglutinin (PHA); higher doses of CAM, although not immediately cytotoxic, impaired the mitogenic response. Stimulation of lymphocytes with PHA in the presence of < or = 1.5 microM CAM resulted in unperturbed transition of these cells from G0 to G1 characterized as an increase in cellular rRNA content, appearance of interleukin-2 receptor, and, after removal of CAM, response to interleukin-2 by entering S phase of the cell cycle. However, lymphocytes were prevented from entering S phase in the presence of CAM at a concentration of > or = 30 nM, and their rate of progression through S was minimal even at CAM concentration as low as 3 nM. When cycling lymphocytes (48 h after stimulation by PHA) were treated with CAM, the cell progression through S and G2 was also very sensitive to the inhibitor: the cells were "frozen" in S and G2 at > or = 6 nM CAM. These cells died within 24 h; their selective loss from the cultures (with only G0/G1 cells remaining) coincided with the appearance of cells with fractional DNA content, typical of apoptotic cells. Human lymphocytic leukemic MOLT-4 cells were arrested in S and G2 at > or = 7.5 nM CAM. Thus, progressions through S and G2 of both normal and leukemic lymphocytes were perturbed at approximately two orders of magnitude lower CAM concentration than the G0 to G1 transition. These data suggest that DNA replication and chromosomal events during G2 are more sensitive to inhibition of DNA topoisomerase I, compared with the early events of lymphocyte stimulation, which involve activation and transcription of numerous genes associated with the G0 to G1 transition. The antitumor properties of CAM may be related to its high cytostatic/cytotoxic activity toward cycling cells and relative resistance of cells in G0 or undergoing transition from G0 to G1.

Camptothecin↗
PubMed1993

Yeast pre-meiotic DNA replication utilizes mitotic origin ARS1 independently of CDC7 function.

In budding yeast, mitotic DNA replication initiates at sequence-specific replication origins, the prototype for which is ARS1. Initiation serves as the primary control point for mitotic DNA replication, and is catalyzed by the Cdc7 protein kinase. In contrast, premeiotic DNA replication apparently does not require Cdc7, and the existence and nature of specific replication origins in the meiotic division cycle have not been previously reported. We have begun to investigate the mechanism of premeiotic DNA synthesis by determining whether or not ARS1 functions as a DNA replication origin in meiosis. We have taken advantage of the fact that transcription through ARS1 disrupts its ability to function as an origin to show that ARS1 is required for premeiotic DNA replication of a plasmid bearing this element. Further, premeiotic replication from ARS1 still occurs in a cdc7 mutant strain held at conditions non-permissive for Cdc7 protein kinase activity. These findings reveal that premeiotic DNA replication can initiate from origins also used in mitosis, and is not regulated by Cdc7. Taken together with previous findings implicating Cdc7 in meiotic DNA recombination and induced mutagenesis, these findings prompt us to postulate that the Cdc7 protein kinase regulates some step common to several DNA metabolic processes such as local disassembly of chromatin or activation of a key component of the DNA metabolic machinery.

Cell Cycle Proteins↗
PubMed2001

Where it all starts: eukaryotic origins of DNA replication.

Chromosomal origins of DNA replication in eukaryotic cells not only are crucial for understanding the basic process of DNA duplication but also provide a tool to analyze how cell cycle regulators are linked to the replication machinery. During the past decade much progress has been made in identifying replication origins in eukaryotic genomes. More recently, replication initiation point (RIP) mapping has allowed us to detect start sites for DNA synthesis at the nucleotide level and thus to monitor replication initiation events at the origin very precisely. Beyond giving us the precise positions of start sites, the application of RIP mapping in yeast and human cells has revealed a single, defined start point at which replication initiates, a scenario very reminiscent of transcription initiation. More importantly, studies in yeast have shown that the binding site for the initiator, the origin recognition complex (ORC), lies immediately adjacent to the replication start point, which suggests that ORC directs the initiation machinery to a distinct site. Therefore, in our pursuit of identifying ORC-binding sites in higher eukaryotes, RIP mapping may lead the way.

Animals↗
PubMed1998

Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal.

DNA polymerases copy DNA templates with remarkably high fidelity, checking for correct base-pair formation both at nucleotide insertion and at subsequent DNA extension steps. Despite extensive biochemical, genetic and structural studies, the mechanism by which nucleotides are correctly incorporated is not known. Here we present high-resolution crystal structures of a thermostable bacterial (Bacillus stearothermophilus) DNA polymerase I large fragments with DNA primer templates bound productively at the polymerase active site. The active site retains catalytic activity, allowing direct observation of the products of several rounds of nucleotide incorporation. The polymerase also retains its ability to discriminate between correct and incorrectly paired nucleotides in the crystal. Comparison of the structures of successively translocated complexes allows the structural features for the sequence-independent molecular recognition of correctly formed base pairs to be deduced unambiguously. These include extensive interactions with the first four to five base pairs in the minor groove, location of the terminal base pair in a pocket of excellent steric complementarity favouring correct base-pair formation, and a conformational switch from B-form to underwound A-form DNA at the polymerase active site.

Binding Sites↗
PubMed1971

DNA replication and proteins that bind to DNA.

Cells of Escherichia coli 15T(-) were exposed to nalidixic acid or starved for thymine to inhibit DNA synthesis while protein synthesis was allowed to continue. These treatments are known to allow subsequent DNA synthesis to continue for many hours in the absence of protein synthesis. The proteins extracted from these cells that bind to DNA were examined by DNA-cellulose chromatography and disc-gel electrophoresis. One or two species were found to be absent, or to be present in greatly reduced amounts, under these conditions.

Amino Acids↗
PubMed1980

On the fidelity of DNA replication. The accuracy of Escherichia coli DNA polymerase I in copying natural DNA in vitro.

The accuracy with which Escherichia coli DNA polymerase I (Pol I) copies natural DNA in vitro has been determined. When phi X174 viral DNA containing an amber mutation (am3) is primed with a single restriction endonuclease fragment, copied in vitro with Pol I and then expressed in E. coli spheroplasts (Weymout, L. A., and Loeb, L. A. (1978) Proc. Natl. Acad. Sci. U. S. A. 75, 1924), the reversion frequency of this DNA is greater than that of uncopied DNA. This change in reversion frequency can be increased by selectively increasing the concentration of either dATP or dCTP relative to the other deoxyribonucleotide substrates. DNA sequence analyses of revertants obtained from substrate pool bias experiments demonstrates that the revertants contain the selectively biased nucleotide as an incorrect substitution at position 587 of the am3 codon. We have analyzed the product of the in vitro Pol I reaction using neutral and alkaline sucrose gradients. Fifty per cent of the input phi X174 DNA template molecules are copied past the am3 site. The phenotypic expression of the product (revertant) strand in the spheroplast assay was estimated using a model heteroduplex molecule similar in structure to the product of the reaction and containing a single base mismatch (A:A or A:C) at position 587. Using these data, and by extrapolation from pool bias experiments, we estimate the error rate of Pol I in Mg2+-activated reactions using equimolar concentrations of the four deoxynucleotide substrates is 1/680,000 for an A:C mispair and < 1/6,300,000 for an A:A mispair at position 587 of the am3 codon in phi X174 DNA.

Bacteriophage phi X 174↗
PubMed2004

DNA replication checkpoint control mediated by the spindle checkpoint protein Mad2p in fission yeast.

The relationship between the DNA replication and spindle checkpoints of the cell cycle is unclear, given that in most eukaryotes, spindle formation occurs only after DNA replication is complete. Fission yeast rad3 mutant cells, which are deficient in DNA replication checkpoint function, enter, progress through, and exit mitosis even when DNA replication is blocked. In contrast, the entry of cds1 mutant cells into mitosis is delayed by several hours when DNA replication is inhibited. We show here that this delay in mitotic entry in cds1 cells is due in part to activation of the spindle checkpoint protein Mad2p. In the presence of the DNA replication inhibitor hydroxyurea (HU), cds1 mad2 cells entered and progressed through mitosis earlier than did cds1 cells. Overexpression of Mad2p or inactivation of Slp1p, a regulator of the anaphase-promoting complex, also rescued the checkpoint defect of HU-treated rad3 cells. Rad3p was shown to be involved in the physical interaction between Mad2p and Slp1p in the presence of HU. These results suggested that Mad2p and Slp1p act downstream of Rad3p in the DNA replication checkpoint and that Mad2p is required for the DNA replication checkpoint when Cds1p is compromised.

Carrier Proteins↗
PubMed2005

Visualization of bidirectional initiation of chromosomal DNA replication in a human cell free system.

Initiation of DNA replication is tightly controlled during the cell cycle to maintain genome integrity. In order to directly study this control we have previously established a cell-free system from human cells that initiates semi-conservative DNA replication. Template nuclei are isolated from cells synchronized in late G1 phase by mimosine. We have now used DNA combing to investigate initiation and further progression of DNA replication forks in this human in vitro system at single molecule level. We obtained direct evidence for bidirectional initiation of divergently moving replication forks in vitro. We assessed quantitatively replication fork initiation patterns, fork movement rates and overall fork density. Individual replication forks progress at highly heterogeneous rates (304 +/- 162 bp/min) and the two forks emanating from a single origin progress independently from each other. Fork progression rates also change at the single fork level, suggesting that replication fork stalling occurs. DNA combing provides a powerful approach to analyse dynamics of human DNA replication in vitro.

Cell Line↗
PubMedDate not supplied

Effect of ultraviolet light on DNA replication in excision-deficient mammalian cells.

DNA replication after exposure to 254-nm ultraviolet light was examined in wild-type (AA8) and excision-deficient (UV-5) Chinese hamster ovary (CHO) cells. DNA replication was examined by measuring the incorporation of [3H]thymidine into acid-precipitable form and by DNA fiber autoradiography. Following exposure to UV both cell lines exhibited a fluence-dependent reduction in the rate of incorporation of thymidine. For exposures of 3.25 and 6.5 J/m2 the response was quantitatively similar in both cell lines for the first hour or two following exposure, with thymidine incorporation dropping to less than 50% of the control rate within the first 1-2 h. For the AA8 cells the depression was only temporary with the rate of thymidine incorporation eventually recovering to control levels. UV-5 cells, on the other hand, never exhibited a recovery in the rate of thymidine incorporation, even at a fluence as low as 0.8 J/m2. DNA fiber-autoradiographic analysis revealed that for both AA8 and UV-5 lines there were about a 40% reduction in the rate of chain growth in the first 40 min after exposure to 6.5 J/m2. The rate of DNA chain elongation recovered to normal rates in less than 5 h in AA8 cells while little or no recovery in the rate of DNA chain elongation was observed for up to 5 h in the UV-5 cells. From these results it appears that the steps of excision repair that are missing in the UV-5 cells are required not only for excision repair, but also for the ability of cells to recover normal rates of DNA replication following exposure to UV.

Animals↗
PubMed1993

A general protocol for evaluating the specific effects of DNA replication inhibitors.

Inhibitors of DNA replication in mammalian cells are of great interest because of their potential use in chemotherapy and in cell synchronizing protocols in the laboratory. We have used a combination of isotopic labelling protocols and a two-dimensional gel replicon mapping procedure to determine the specific effects of five different replication inhibitors in cultured cells. Utilizing this protocol, we show that hydroxyurea, aphidicolin, and cytosine arabinoside, three known chain elongation inhibitors, are rather ineffective at preventing fork progression even at relatively high concentrations. In contrast, two related compounds that have been suggested to be G1/S inhibitors (mimosine and ciclopyrox olamine [CPX]) actually appear to inhibit initiation at origins. One of these agents (CPX) appears also to inhibit replication in yeast, opening the possibility that the gene encoding the target (initiator?) protein can first be identified in yeast by genetic approaches and can then be used to isolate the mammalian homologue.

Animals↗
PubMed1990

Adeno-associated virus DNA replication is induced by genes that are essential for HSV-1 DNA synthesis.

Adeno-associated virus (AAV) DNA replication is not detectable unless cells are coinfected with a helper adenovirus (Ad) or herpesvirus or unless AAV infection is carried out in certain established cell lines that have been treated with various metabolic inhibitors or uv irradiation. In helper-dependent infections, it has been shown that AAV DNA synthesis depends on one or more early Ad genes, whereas little is known concerning any herpesvirus gene that promotes AAV DNA synthesis. In this study we tested the ability of four cloned Xbal fragments of herpes simplex virus type 1 (HSV-1) DNA to induce AAV DNA synthesis in Vero cells. Cotransfections, which were carried out with pAV1 (an infectious AAV2 plasmid), revealed that AAV DNA synthesis could be optimally induced by three of these clones (C,D, and F) plus a clone of the HSV-1 ICP4 (IE 175) gene. ICP4, an immediate early gene, was presumably required to activate expression of other HSV genes. To help identify the additionally needed HSV genes, we tested Xbal C,D, and F subclones that contain genes previously found necessary for origin-dependent HSV DNA synthesis and found that at least five of these genes (UL 5, 8, 9, 29, and 30) contributed to the induction of AAV DNA synthesis. In contrast to their absolute requirement for HSV DNA synthesis, none of these genes were strictly necessary for AAV DNA replication. Because they are all known to specify proteins that are directly involved in HSV DNA synthesis, our results suggest that some or all of their products also may directly participate in the replication of AAV DNA.

Animals↗
PubMed1990

The initiation of chromosomal DNA replication in eukaryotes.

Eukaryotic DNA replication initiates at many sites on each chromosome during the S phase of the cell cycle. Each origin of replication lies in a unique chromosomal environment and can be regulated in different cell types both at the level of utilization and the time of initiation during S phase. In this review, we examine the control and the mechanism of eukaryotic origin function.

Animals↗
PubMed2003

Heritable gene silencing in lymphocytes delays chromatid resolution without affecting the timing of DNA replication.

Temporal control of DNA replication has been implicated in epigenetic regulation of gene expression on the basis of observations that certain tissue-specific genes replicate earlier in expressing than non-expressing cells. Here, we show evidence that several leukocyte-specific genes replicate early in lymphocytes regardless of their transcription and also in fibroblasts, where these genes are never normally expressed. Instead, the heritable silencing of some genes (Rag-1, TdT, CD8alpha and lambda5) and their spatial recruitment to heterochromatin domains within the nucleus of lymphocytes resulted in a markedly delayed resolution of sister chromatids into doublet signals discernable by 3D fluorescence in situ hybridization (FISH). Integration of transgenes within heterochromatin (in cis) did, however, confer late replication and this was reversed after variegated transgene expression. These findings emphasise that chromosomal location is important for defining the replication timing of genes and show that retarded sister-chromatid resolution is a novel feature of inactive chromatin.

Animals↗
PubMed1995

The requirement for molecular chaperones in lambda DNA replication is reduced by the mutation pi in lambda P gene, which weakens the interaction between lambda P protein and DnaB helicase.

During the initiation of lambda DNA replication, the host DnaB helicase is complexed with phage lambda P protein in order to be properly positioned near the ori lambda-lambda O initiation complex. However, the lambda P-DnaB interaction inhibits the activities of DnaB. Thus, the concerted action of bacterial heat shock proteins, DnaK, DnaJ, and GrpE, is required to activate the helicase. Wild-type phage lambda cannot grow on the E. coli dnaB, dnaK, dnaJ, and grpE mutants. However, lambda phage with a mutation pi in the lambda P gene, is able to produce progeny in these mutants as well as in the wild-type bacteria. Purified mutant lambda pi protein reveals a much lower affinity to DnaB than wild-type lambda P, and the lambda pi-DnaB complex is unstable. Also, a very low concentration of DnaK protein is sufficient to activate the helicase in a replication system based on lambda dv dsDNA. In that system, the mutant DnaK756 protein, inactive in the lambda P-dependent replication, revealed its activity in the lambda pi-dependent reaction. The lambda O-lambda P-dependent replication system based on M13 ssDNA efficiently replicates DNA in the absence of any chaperone protein, unless lambda P is substituted by the lambda pi mutant protein. Data presented in this paper explain why lambda pi phage is able to grow on wild-type and dnaK756 bacteria.

Bacterial Proteins↗
PubMed1985

Effects of coordinated gold compounds on in vitro and in situ DNA replication.

Auranofin, a coordinated gold compound, inhibits in vitro DNA synthesis and displays in vivo antitumor activity. To understand the mechanisms of inhibition of DNA replication, we have examined the effects of auranofin and other gold complexes on the activities of purified cellular and herpesvirus-induced DNA polymerases, and on in situ DNA replication in permeabilized S phase KB cells. Evaluation of the data suggests the following conclusions. (1) The gold compounds varied in their abilities to inhibit DNA polymerase activities. DNA polymerase alpha was more sensitive to inhibition by gold compounds than DNA polymerase beta; (2) Inhibition of purified DNA polymerases by gold (I) compounds was noncompetitive with both DNA template and triphosphate substrates. Inhibition by SKF 101675, a gold (III) complex was competitive with DNA. (3) None of the gold compounds tested preferentially inhibited herpesvirus-induced DNA polymerases. (4) The gold complexes that inhibited in vitro DNA replication also inhibited in situ DNA synthesis. However, the potency and order of potency of the compounds varied between the in vitro and in situ systems. (5) Auranofin and other gold compounds inhibited the clonogenic capacity of KB cells in a concentration-dependent manner. The IC50 values measured in the clonogenic assay were significantly lower than those obtained from the in vitro and in situ DNA replication assays.

Anti-Inflammatory Agents↗