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PubMed2000

On the relationship of matrix association and DNA replication.

The nuclear matrix is believed to contain sites of assembly of protein complexes that catalyze the initiation of DNA replication as well as DNA elongation. To explore this relationship, DNA replicated by human fibroblasts at the beginning of the S phase was purified and used to construct a cosmid library. Hybridization studies with a subgroup of clones (about one-sixth of the total clones in this library) showed that many of them were highlighted by probes prepared from early replicating DNA, as well as from nuclear matrix-associated DNA. Statistical analysis showed a positive correlation between these hybridization results. We seek to identify origins of replication that are activated early in the S phase of the cell cycle in human cells. Therefore, clones isolated from this library are being analyzed for the presence of structural motifs that have been found in other origins of replication and for potential sites of attachment to the nuclear matrix. This method of analysis is illustrated here using the published sequences for the origins of replication reported for the human lamin B2 and HPRT genes.

DNA Replication↗
PubMed1981

DNA replication of bacteriophage T5. 3. Studies on the structure of concatemeric T5 DNA.

The replication of bacteriophage T5 DNA has been shown to proceed via branched concatemeric intermediates. The structures of this concatemeric DNA was studied with respect to single-stranded regions and single-strand interruptions by digestion with S1 nuclease and agarose gel electrophoresis after alkali denaturation. The results were compared with the pattern of 'nicks' in the mature virion DNA, and the possible origins of these nicks are discussed. The structure of T5 concatemeric DNA was also studied by electron microscopy. Replication forks, loops and rare circular structures were observed, all of which were similar to those seen in replicating DNA of other large phages. Phage capsid structures were detected in association with both concatemeric and mature phage length DNA. These observations are discussed in relation to the replication, maturation and packaging of T5 DNA.

Capsid↗
PubMed1985

Flow cytometric analysis of DNA replication during the differentiation of 3T3-L1 preadipocytes.

We have employed a flow cytometric method of monitoring DNA synthesis in order to study the stimulation of DNA replication during the induction of adipocyte differentiation in the preadipocyte cell line 3T3-L1. When confluent monolayers of this cell line are treated with a mixture of methyl isobutyl xanthine, dexamethasone, and insulin (MDI), they undergo at least one round of cell division, which is followed by the de novo synthesis of many enzymes that are involved in the formation of lipid. If the MDI-treated cells are incubated in iododeoxyuridine (IdUrd)- or bromodeoxyuridine (BrdUrd)-containing medium and subsequently stained with antibodies specific for these base analogues and with propidium iodide (PI), the kinetics of the induction of replication can be monitored. No differences in the patterns of IdUrd incorporation versus PI staining were observed between exponentially growing 3T3-L1 cells and those that had been stimulated to replicate DNA with MDI. In addition, we developed a flow cytometric (FCM) method for staining fatty acid synthetase and localizing the antigen in the G1 phase. We have thus demonstrated the feasibility of this methodology for correlating by FCM the production of enzymes such as fatty acid synthetase with IdUrd and BrUrd incorporation. The technique should permit studies of the inhibition of differentiation of adipocytes by halogenated pyrimidines.

Adipose Tissue↗
PubMed1988

Analysis of the chromosomal DNA replication pattern using the bromodeoxyuridine labeling method.

The DNA replication of human lymphocytes was studied using the labeling pattern on chromosomes after pulse labeling with bromodeoxyuridine and immunostaining with the monoclonal antibody to bromodeoxyuridine. The sites of bromodeoxyuridine incorporation were defined by comparison with the same karyotype treated G-banding, and a more precise analysis was performed using the image analyzer, Maziscan III. Early phase DNA synthesis roughly coincided with R-bands and late phase DNA synthesis with G-bands. One case of acute myeloid leukemia which developed from myelodysplastic syndrome, had a 46,XY, t(4;11) (p12;p15) karyotype, and revealed an altered DNA replication time at the translocated site, 4p15, from the late to the early phase. The present method was useful in detecting an alteration of DNA replication timing according to chromosomal translocation.

Bromodeoxyuridine↗
PubMed1976

Effects of ultraviolet irradiation on the rate and sequence of DNA replication in synchronized Chinese hamster cells.

The effects of ultraviolet light (UV) irradiation on the rate of DNA replication in synchronized Chinese hamster ovary (CHO) cells were investigated. A technique for measuring semiconservative DNA replication was employed that involved growing the cells in medium containing 5-bromodeoxyuridine and subsequently determining the amount of DNA that acquired hybrid buoyant density in CsCl density gradients. One of the advantages of this technique was that it allowed a characterization of the extent of DNA replication as well as rate after irradiation. It was found that while there was a dose-dependent reduction in the rate of DNA replication following UV-irradiation, doses of up to 10 J/m2 (which produce many dimers per replication) did not prevent the ultimate replication of the entire genome. Hence, we conclude that dimers cannot be absolute blocks to DNA replication. In order to account for the total genome replication observed, a mechanism must exist that allows genome replication between dimers. The degree of reduction in the rate of replication by UV was the same whether the cells were irradiated at the G1-S boundary or 1 h into S-phase. Previous work had shown that cells in early S-phase are considerably more sensitive to UV than cells at the G1-S boundary. Experiments specifically designed to test for reiterative replication showed that UV does not induce a second round of DNA replication within the same S-phase.

Base Sequence↗
PubMed1977

Ficellomycin and feldamycin; inhibitors of bacterial semiconservative DNA replication.

The two peptide-like antibiotics ficellomycin and feldamycin impair semiconservative DNA replication but not DNA repair synthesis in bacteria. Specifically both antibiotics cause the accumulation of a 34S DNA species in toluenized Escherichia coli cells which lacks the capability of being integrated into larger DNA pieces and eventually the complete bacterial chromosome. Novobiocin, a known inhibitor of replicative DNA synthesis, was investigated for comparative purposes. The action of this latter antibiotic differs from the ones exerted by ficellomycin and feldamycin in the novobiocin appears to block an event associated with the initiation of Okazaki fragments. The fact that novobiocin impairs DNA gyrase suggests that this enzyme plays an essential role during the initiation of Okazaki pieces.

Anti-Bacterial Agents↗
PubMed1999

Protein kinase A is required for chromosomal DNA replication.

Passage through mitosis resets cells for a new round of chromosomal DNA replication [1]. In late mitosis, the pre-replication complex - which includes the origin recognition complex (ORC), Cdc6 and the minichromosome maintenance (MCM) proteins - binds chromatin as a pre-requisite for DNA replication. S-phase-promoting cyclin-dependent kinases (Cdks) and the kinase Dbf4-Cdc7 then act to initiate replication. Before the onset of replication Cdc6 dissociates from chromatin. S-phase and M-phase Cdks block the formation of a new pre-replication complex, preventing DNA over-replication during the S, G2 and M phases of the cell cycle [1]. The nuclear membrane also contributes to limit genome replication to once per cell cycle [2]. Thus, at the end of M phase, nuclear membrane breakdown and the collapse of Cdk activity reset cells for a new round of chromosomal replication. We showed previously that protein kinase A (PKA) activity oscillates during the cell cycle in Xenopus egg extracts, peaking in late mitosis. The oscillations are induced by the M-phase-promoting Cdk [3] [4]. Here, we found that PKA oscillation was required for the following phase of DNA replication. PKA activity was needed from mitosis exit to the formation of the nuclear envelope. PKA was not required for the assembly of ORC2, Cdc6 and MCM3 onto chromatin. Inhibition of PKA activity, however, blocked the release of Cdc6 from chromatin and subsequent DNA replication. These data suggest that PKA activation in late M phase is required for the following S phase.

8-Bromo Cyclic Adenosine Monophosphate↗
PubMed1997

DnaJ/hsp40 chaperone domain of SV40 large T antigen promotes efficient viral DNA replication.

The amino-terminal domain of SV40 large tumor antigen (TAg) is required for efficient viral DNA replication. However, the biochemical activity associated with this domain has remained obscure. We show here that the amino-terminal domain of TAg shares functional homology with the J-domain of DnaJ/hsp40 molecular chaperones. DnaJ proteins function as cofactors by regulating the activity of a member of the 70-kD heat shock protein family. Genetic analyses demonstrated that amino-terminal sequences of TAg comprise a novel J-domain that mediates a specific interaction with the constitutively expressed hsc70 and show that the J-domain is also required for efficient viral DNA replication in vivo. Furthermore, we demonstrated that the J-domain of two human DnaJ homologs, HSJ1 or DNAJ2, could substitute functionally for the amino-terminus of TAg in promoting viral DNA replication. Together, our findings suggest that TAg uses its J-domain to support SV40 DNA replication in a manner that is strikingly similar to the use of Escherichia coli DnaJ by bacteriophage lambda in DNA replication. However, TAg has evolved a more efficient strategy of DNA replication through an intrinsic J-domain to associate directly with a partner chaperone protein. Our observations provide evidence of a role for chaperone proteins in the process of eukaryotic DNA replication.

Amino Acid Sequence↗
PubMed2001

A moving DNA replication factory in Caulobacter crescentus.

The in vivo intracellular location of components of the Caulobacter replication apparatus was visualized during the cell cycle. Replisome assembly occurs at the chromosomal origin located at the stalked cell pole, coincident with the initiation of DNA replication. The replisome gradually moves to midcell as DNA replication proceeds and disassembles upon completion of DNA replication. Although the newly replicated origin regions of the chromosome are rapidly moved to opposite cell poles by an active process, the replisome appears to be an untethered replication factory that is passively displaced towards the center of the cell by the newly replicated DNA. These results are consistent with a model in which unreplicated DNA is pulled into the replication factory and newly replicated DNA is bidirectionally extruded from the complex, perhaps contributing to chromosome segregation.

Bacterial Proteins↗
PubMed1975

Adenovirus type 2 DNA replication. I. Evidence for discontinuous DNA synthesis.

Isolated nuclei from adenovirus type 2-infected HeLa cells catalyze the incorporation of all four deoxyribonucleoside triphosphates into viral DNA. The observed DNA synthesis occurs via a transient formation of DNA fragments with a sedimentation coefficient of 10S. The fragments are precursors to unit-length viral DNA, they are self-complementary to an extent of at least 70%, and they are distributed along most of the viral chromosome. In addition, accumulation of 10S DNA fragments is observed either in intact, virus-infected HeLa cells under conditions where viral DNA synthesis is inhibited by hydroxyurea or in isolated nuclei from virus-infected HeLa cells at low concentrations of deoxyribonucleotides. Under these suboptimal conditions for DNA synthesis in isolated nuclei, ribonucleoside triphosphates determine the size distribution of DNA intermediates. The evidence presented suggests that a ribonucleoside-dependent initiation step as well at two DNA polymerase catalyzed reactions are involved in the discontinuous replication of adenovirus type 2 DNA.

Adenosine Triphosphate↗
PubMed1983

Regulation of transcription and DNA replication of bacteriophage phi 80.

Transcriptional mapping and DNA replication measurements have been used to characterize a series of phi 80 suppressor-sensitive mutants which are defective in genes 15, 14, 16, and 17. These genes are localized within the inner right arm of the vegetative phi 80 DNA genome. The sus326 mutation in gene 15 leads to a decrease in major leftward (pL-att80) RNA levels and to a marked pleiotropic reduction in major rightward RNA synthesis; however, phi 80 DNA synthesis is reduced only moderately (about two-fold). These findings are consistent with the gene 15 product being a positive control regulator that is essential for normal transcriptional development, in particular, beyond a termination signal(s) (tR) located between genes 16 and 17. The sus8 and sus258 mutations (in genes 14 and 16, respectively) lead to severe blockage of both major rightward RNA transcription and phi 80 DNA synthesis. The products of genes 14 and 16 appear to be required for both autonomous phi 80 DNA replication and the "late" transcriptional development. The sus121 mutation in gene 17 reduces the level of "late" major rightward transcription (gene 17-1-13-att'80 segment) by about 10-fold but does not have any apparent effect on the levels of phi 80 DNA synthesis. These profiles identify the product of gene 17 as a "Q-type" positive control regulator for the "late" major rightward RNA. These studies reveal the functional characterization of four genes, the products of which are necessary for the efficient expression of the "early" RNA transcribed segments, autonomous DNA replication, and the production of normal levels of "late" (17-1-13-att'80) RNA synthesis.

Coliphages↗
PubMed1986

Characterization of DNA replication at a restrictive temperature in a mouse DNA temperature-sensitive mutant, tsFT20 strain, containing heat-labile DNA polymerase alpha activity.

tsFT20 cells derived from a mouse mammary carcinoma cell line FM3A have temperature-sensitive DNA polymerase alpha activity (Murakami, Y., Yasuda, H., Miyazawa, H., Hanaoka, F., and Yamada, M. (1985) Proc. Natl. Acad. Sci. U. S. A. 82, 1761-1765). DNA replication in tsFT20 cells at the restrictive temperature (39 degrees C) has been characterized in detail. DNA-synthesizing ability of these cells was measured by [3H] thymidine incorporation and autoradiography. The incorporation of [3H]thymidine decreased rapidly after temperature shift-up, and the incorporation was less than 20% of the initial level after 4 h at 39 degrees C. The rapid decrease correlated well with the decrease in the grain number in the individual nucleus but not with the number of cells with labeled nuclei. Alkaline sucrose gradient sedimentation analysis and DNA fiber autoradiography revealed that DNA chain elongation proceeded normally within a replicon in the temperature-sensitive cells incubated at the restrictive temperature and the DNA elongation rate did not change during the incubation at the restrictive temperature up to at least 6 h. On the other hand, the maturation of replicon-sized DNA to higher molecular weight DNA was retarded or inhibited in the temperature-sensitive cells at the restrictive temperature. The analysis of the center to center distance between replicons by DNA fiber autoradiography revealed that the frequency of replicon initiation decreased in tsFT20 cells at 39 degrees C.

Animals↗
PubMed1989

DNA replication and cell cycle control in Xenopus egg extracts.

Aspects of the regulation of DNA replication and mitosis have been studied using a cell-free extract of Xenopus eggs. The extract is characterized by repeated cycles of DNA replication and mitosis, which are accompanied by periodic synthesis and degradation of cyclins as well as fluctuations in the level of Histone H1 kinase activity. DNA replication in this system is dependent upon the formation of a nucleus. However, while nuclear structures are clearly required for initiation, a complete nuclear membrane does not appear to be necessary. Indirect immunofluorescence and DIC microscopy indicate that nuclear reformation from chromosomes occurs asynchronously around individual chromatids. Lamin polymerization, biotin-11-dUTP incorporation and association of polymerases with chromatin occur before membrane formation is complete. S phase nuclei are typified by the co-distribution of both anti-DNA polymerase alpha and anti-PCNA antibodies as discrete spots of fluorescence which align the chromatin. However, as DNA replication is terminated, PCNA fluorescence fades and DNA polymerase alpha dissociates from the chromatin and is redistributed throughout the nucleoplasm. By inhibiting DNA replication with aphidicolin, both DNA polymerase alpha and PCNA remain associated with the chromatin throughout prolonged incubation. Under these conditions mitosis is delayed by up to 70 min, although both the general rate of protein synthesis and more importantly the rate of cyclin synthesis and histone kinase activation are unaffected. Upon nuclear envelope breakdown and lamin dispersal, cyclins degrade; however, no chromosomes are formed, and both PCNA and DNA polymerase alpha remain associated with the chromatin. Also, histone kinase activity is maintained at elevated levels.

Animals↗
PubMed1980

Isopentenyladenine as a mediator of mevalonate-regulated DNA replication.

The mechanism by which the cholesterol precursor, mevalonate, regulates S-phase DNA replication was examined in synchronized BHK cells. As previously demonstrated by this laboratory, blocking 3-hydroxy-3-methylglutaryl-CoA reductase [mevalonate:NADP+ oxidoreductase (CoA-acylating), EC 1.1.1.34] with the competitive inhibitor compactin suppresses DNA synthesis specifically during the S phase of the cell cycle. In the present study, known mevalonate derivatives were examined as possible mediators by which mevalonate controls DNA replication. Of the compounds studied, only isopentenyladenine and its 4'-hydroxylated analogue, zeatin, could substitute for mevalonate in restoring DNA replication in compactin-blocked cells. Moreover, these two derivatives proved to be at least 100 times more active than mevalonate, and both restored DNA relication to normal within 15 min of their being added to the medium. In addition, isopentenyladenine, like mevalonate, stimulated DNA synthesis specifically during the S phase of the cell cycle. Isopentenyladenine also reversed the inhibition of DNA synthesis caused by nalidixic acid, an antibiotic that does not inhibit cholesterol synthesis. These findings indicate that isopentenyladenine or a closely related derivative may mediate the regulatory role of mevalonate in DNA replication and suggest that such isoprenes may act upon DNA replication at a site common to that inhibited by nalidixic acid.

Adenine↗
PubMed2005

Inhibition of human Chk1 causes increased initiation of DNA replication, phosphorylation of ATR targets, and DNA breakage.

Human checkpoint kinase 1 (Chk1) is an essential kinase required to preserve genome stability. Here, we show that Chk1 inhibition by two distinct drugs, UCN-01 and CEP-3891, or by Chk1 small interfering RNA (siRNA) leads to phosphorylation of ATR targets. Chk1-inhibition triggered rapid, pan-nuclear phosphorylation of histone H2AX, p53, Smc1, replication protein A, and Chk1 itself in human S-phase cells. These phosphorylations were inhibited by ATR siRNA and caffeine, but they occurred independently of ATM. Chk1 inhibition also caused an increased initiation of DNA replication, which was accompanied by increased amounts of nonextractable RPA protein, formation of single-stranded DNA, and induction of DNA strand breaks. Moreover, these responses were prevented by siRNA-mediated downregulation of Cdk2 or the replication initiation protein Cdc45, or by addition of the CDK inhibitor roscovitine. We propose that Chk1 is required during normal S phase to avoid aberrantly increased initiation of DNA replication, thereby protecting against DNA breakage. These results may help explain why Chk1 is an essential kinase and should be taken into account when drugs to inhibit this kinase are considered for use in cancer treatment.

Ataxia Telangiectasia Mutated Proteins↗
PubMed1996

Stockpiling of Cdc25 during a DNA replication checkpoint arrest in Schizosaccharomyces pombe.

The DNA replication checkpoint couples the onset of mitosis with the completion of S phase. It is clear that in the fission yeast Schizosaccharomyces pombe, operation of this checkpoint requires maintenance of the inhibitory tyrosyl phosphorylation of Cdc2. Cdc25 phosphatase induces mitosis by dephosphorylating tyrosine 15 of Cdc2. In this report, Cdc25 is shown to accumulate to a very high level in cells arrested in S. This shows that mechanisms which modulate the abundance of Cdc25 are unconnected to the DNA replication checkpoint. Using a Cdc2/cyclin B activation assay, we found that Cdc25 activity increased approximately 10-fold during transit through M phase. Cdc25 was activated by phosphorylations that were dependent on Cdc2 activity in vivo. Cdc25 activation was suppressed in cells arrested in G1 and S. However, Cdc25 was more highly modified and appeared to be somewhat more active in S than in G1. This finding might be connected to the fact that progression from G1 to S increases the likelihood that constitutive Cdc25 overproduction will cause inappropriate mitosis.

CDC2 Protein Kinase↗
PubMed2003

Xenopus Cut5 is essential for a CDK-dependent process in the initiation of DNA replication.

Fission yeast Cut5/Rad4 and its budding yeast homolog Dpb11 are required for both DNA replication and the S-phase checkpoint. Here, we have investigated the role of the Xenopus homolog of Cut5 in the initiation of DNA replication using Xenopus egg extracts. Xenopus Cut5, which shows sequence similarity to DmMus101 and HsTopBP1, is essential for DNA replication in the egg extracts. It is required for the chromatin binding of Cdc45 and DNA polymerases, but not for the formation of pre-replicative complexes or the elongation stage of DNA replication. The chromatin binding of Cut5 consists of two distinct modes. S-phase cyclin-dependent kinase (S-CDK)-independent binding is sufficient for DNA replication while S-CDK-dependent binding is dispensable. Further, S-CDK acts after the chromatin binding of Cut5 and before the binding of Cdc45. These results demonstrate that the chromatin binding of Cut5 is required for the action of S-CDK, which in turn triggers the formation of pre-initiation complexes of DNA replication.

Animals↗
PubMed1990

Amino-terminal domain of NF1 binds to DNA as a dimer and activates adenovirus DNA replication.

NF1 is a DNA-binding protein involved in initiation of adenovirus DNA replication as well as in modulating the rate of transcription initiation of genes containing the sequence TGGCA. We show here that recombinant NF1 expressed via vaccinia virus is transported into the nucleus and binds to its cognate sequences with the same specificity as NF1 purified from HeLa cells. Furthermore, the recombinant NF1 forms oligomers in solution and binds as a dimer to palindromic as well as half-site sequences. NF1 expressed via vaccinia virus stimulates the initiation of adenovirus replication in vitro. The N-terminal 240 amino acids of the protein are sufficient for full DNA-binding activity as well as stimulation of adenovirus replication. By analysis of several NF1 mutants translated in vitro, we also define the minimal DNA-binding domain and localize the region responsible for DNA binding on the N-terminal and for oligomerization on the C-terminal side of this domain.

Adenoviruses, Human↗