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PubMed1986

Replication timing: histone genes replicate during early S phase in cleavage-stage embryos of sea urchin.

Newly synthesized DNA was separated from the bulk of the DNA by pulse-labeling with BUdR and centrifugation in an alkaline CsCl buoyant density gradient. The content of histone gene in the newly synthesized DNA was determined by DNA dot hybridization. The gene contents in DNA replicated during the early half of S phase and during the whole S phase were compared. Results showed that histone genes were replicated during the first half of the S phase in embryos in the early cleavage stage.

Animals↗
PubMed1990

A microplate version of the DNA-synthesis inhibition test for rapid detection of DNA-alteration potentials.

A microplate version of the DNA-synthesis inhibition test (DIT) for fast detection of DNA-alteration potentials has been developed. The DIT is based on the concept that DNA damage causes inhibition of DNA synthesis that becomes detectable some time after replicating cells have been in contact with genotoxic agents. In this test procedure human tissue culture cells (HeLa S3), prelabeled with [14C]thymidine, arfe exposed for 90 min to the substances in question. After the cells are rinsed, they are allowed to recover for 2 1/2 h in fresh culture medium, thereby unspecific interactions interfering with DNA replication are practically eliminated. Next, [3H]thymidine is added for 30 min, and then the cells are harvested and thoroughly rinsed. Finally, incorporated radioactivity is determined by liquid scintillation counting for measurement of the 3H/14C ratio. This allows for the evaluation of DNA synthesis during the 3H-labeling period and of the extent of genotoxic damage. This microplate version of the DIT can be carried out fully automated in a laboratory workstation. The test is compared to other tests for genotoxicity. Its advantages are discussed.

Autoanalysis↗
PubMed2006

Heterogeneous genomic molecular clocks in primates.

Using data from primates, we show that molecular clocks in sites that have been part of a CpG dinucleotide in recent past (CpG sites) and non-CpG sites are of markedly different nature, reflecting differences in their molecular origins. Notably, single nucleotide substitutions at non-CpG sites show clear generation-time dependency, indicating that most of these substitutions occur by errors during DNA replication. On the other hand, substitutions at CpG sites occur relatively constantly over time, as expected from their primary origin due to methylation. Therefore, molecular clocks are heterogeneous even within a genome. Furthermore, we propose that varying frequencies of CpG dinucleotides in different genomic regions may have contributed significantly to conflicting earlier results on rate constancy of mammalian molecular clock. Our conclusion that different regions of genomes follow different molecular clocks should be considered when inferring divergence times using molecular data and in phylogenetic analysis.

Animals↗
PubMed1981

Replication of simian virus 40 DNA in normal human fibroblasts and in fibroblasts from xeroderma pigmentosum.

Simian virus 40 infection of semipermissive human diploid fibroblasts (HF), at early passage in cell culture, was compared with that of permissive established monkey cell lines. Viral DNA can be readily detected at 24 to 48 h postinfection at 37 degrees C with a high multiplicity of infection, approaching 10% of that of monkey cells (TC7). The length of time necessary for replication of an average molecule of viral DNA was found to be indistinguishable in HF and TC7 cells. Strand elongation plus termination were assessed by following the accumulation of DNA I at 40 degrees C from replicative intermediates of tsA30 prelabeled at 33 degrees C, obviating isotope pool problems. Combined initiation and elongation of wild-type viral DNA was measured by density shift experiments involving a 5-bromodeoxyuridine chase of prelabeled [3H]thymidine-labeled viral DNA. Determination of accumulation of viral T and V antigens supports the conclusion that the most likely basis for the reduced virus yield in HF cells results from the inefficiency of an early stage in virus infection, before or during uncoating. Similar results were obtained in fibroblasts derived from patients with xeroderma pigmentosum, suggesting that enzymes of UV repair are not required in unirradiated simian virus 40 DNA synthesis.

Animals↗
PubMed1979

Enhancement of excision-repair efficiency by conditioned medium from density-inhibited cultures in V79 Chinese hamster cells: evidence for excision repair as an error-free repair process.

Conditioned medium from density-inhibited V79 Chinese hamster cell cultures, given as a post-treatment to UV-irradiated homologous cells, was demonstrated to reduce the lethal action of ultraviolet light by temporarily blocking DNA replication. Since the increased survival was not affected by various non-toxic concentrations of caffeine, such protective effect would be attributable to the prolonged intervention of excision repair before DNA replication during the post-treatment period. The influence of conditioned medium on the UV-induced mutation at the ouabain-resistance locus was also examined and a significant decrease in mutation frequency was noted. The observed reduction in killing and mutation as a result of post-incubation in conditioned medium, which delays DNA replication, would be interpreted as evidence that conditioned medium provides a longer period of time for an error-free excision-repair process, leaving lesion in DNA available for error-prone post-replication repair.

Animals↗
PubMed1980

Characterization of the defects in bacteriophage T7 DNA synthesis during growth in the Escherichia coli mutant tsnB.

The Escherichia coli mutant tsnB (M. Chamberlin, J. Virol. 14:509-516, 1974) is unable to support the growth of bacteriophage T7, although all classes of phage proteins are produced and the host is killed by the infection. During growth in this mutant host, the rate of phage DNA synthesis is reduced and the DNA is not packaged into stable, phagelike particles. The replicating DNA forms concatemers but the very large replicative intermediates (approximately 440S) identified by Paetkau et al. (J. Virol. 22:130-141, 1977) are not detected in T7+-infected tsnB cells. These large structures are formed in tsnB cells infected with a T7 gene 3 (endonuclease) mutant, where normal processing of the large intermediates into shorter concatemers is blocked. At later times during infection of tsnB cells, the replicating DNA accumulates in molecules about 30% shorter than unit length. Analysis of this DNA with a restriction endonuclease indicates that it is missing sequences from the ends (particularly the left end) of the genome. The loss of these specific sequences does not occur during infections with T7 gene 10 (head protein) or gene 19 (maturation protein) mutants. This suggests that the processing of concatemers into unit-length DNA molecules may occur normally in T7 -infected tsnB cells and that the shortened DNA arises from exonucleolytic degradation of the mature DNA molecules. These results are discussed in relation to our recent observation (M. A. DeWyngaert and D. C. Hinkle, J. Biol. Chem. 254:11247-11253, 1979) that E. coli tsnB produces an altered RNA polymerase which is resistance to inhibition by the T7 gene 2 protein.

DNA, Viral↗
PubMed1985

Vaccinia virus proteins on the plasma membrane of infected cells. III. Infection of peritoneal macrophages.

Primary macrophage cultures were prepared from the peritoneal exudate cell population harvested from mice challenged intraperitoneally with saline, thioglycollate, or vaccinia virus. Vaccinia virus was adsorbed and penetrated into primary macrophages and L-cells with similar kinetics. As evidenced by the expression of some "early" virus-specified proteins, partial uncoating and activation of the virion-associated DNA-dependent RNA polymerase occurred in the infected macrophages. Subsequently, the viral replication cycle in macrophages was aborted; with time after infection, viral DNA and virion proteins initially associated with infected cells could be detected in an acid-soluble form in the medium harvested from infected macrophage cultures. The results suggest that at the time that the final stages of virus uncoating should have occurred, intracellular subviral particles were, instead, degraded in the infected, primary macrophages. Viral DNA synthesis could not be measured in vaccinia virus-infected macrophages, no "late" virus functions were expressed, and progeny virions were not assembled. As measured by the binding of antiviral-antibody-125I-protein A complexes to the surface of vaccinia virus-infected cells, the expression of virus-specified antigens on the surfaces of infected macrophages was significantly reduced and never exceeded that measured at 2 hr after infection on the surfaces of infected L-cells. The expression of virus-specified polypeptides with mol mass of 48-50, 45-46, 36-37, and 25 kDa on the plasma membranes of vaccinia virus-infected, thioglycollate-elicited macrophages, rendered the infected macrophages susceptible to lysis by vaccinia virus-specific cytotoxic T-cells.

Adsorption↗
PubMed2003

Quantitative analysis of human mitochondrial DNA using a real-time PCR assay.

OBJECTIVES: Known for their ability to inhibit the human DNA polymerase-gamma, nucleoside analogues induce toxic effects on mitochondria ranging from increased serum lactate levels to fatal lactic acidosis. DNA polymerase-gamma ensures the mitochondrial DNA (mtDNA) replication and, thus, its inhibition leads to the decrease of the mtDNA. We describe a real-time PCR assay for mtDNA quantification associating DNA extraction procedures applied on peripheral blood mononuclear cells (PBMCs) and subcutaneous adipose tissues and to study the antiretroviral effect on mitochondria. METHODS: Total DNA was extracted from PBMCs and subcutaneous adipose tissues. Nuclear and mitochondrial genes were amplified to determine the number of copies of mtDNA per cell using a cyt-b recombinant plasmid as standard control. We analysed eight HIV-infected asymptomatic patients never treated, four patients who had been treated for 6 months with highly active antiretroviral therapy (HAART) and six non-infected donors. RESULTS: The mtDNA quantification gave rise to reproducible results as the mean coefficients of variation were 1.09% for replicates of samples undertaken 10 times within the same run, and 5.78% and 3.7% for replicates tested in five different runs at 1:100 and 1:1000 dilutions, respectively. Median levels of mtDNA in PBMCs of healthy donors, naive and treated HIV-infected patients were 2.94, 2.78 and 1.93 log HIV-1 RNA copies/mL, respectively. Whereas DNA from PBMCs was shown to be devoid of inhibitors, subcutaneous adipose tissues needed an extra treatment as they were found to be highly inhibited. CONCLUSIONS: The method generated consistent and reproducible results and was successfully applied to DNAs extracted from PBMCs and subcutaneous adipose tissues with adapted extraction. The mtDNA changes in PBMCs were found to be fast as they fall off after 6 months' therapy, decreasing from 2.78 to 1.93 log copies/mL.

Adipose Tissue↗
PubMed1994

Requirements for DNA transcription and replication at the beginning of mouse development.

In mice, the first round of DNA replication occurs in fertilized eggs (1-cell embryos), while the onset of zygotic gene transcription begins approximately 20 hours after fertilization, a time that normally coincides with formation of a 2-cell embryo. One approach to investigating the mechanisms that control these developmentally regulated events has been to microinject plasmid DNA into the nuclei of mouse oocytes and embryos in order to determine the requirements for unique DNA sequences that regulate transcription and replication. The results from these and other studies have revealed two important mechanisms that regulate the beginning of animal development. The first is a time dependent "zygotic clock" of unknown detail that delays the onset of transcription, regardless of whether or not a 2-cell embryo is formed. The second is a mechanism that represses the activity of promoters and origins of replication specifically in maternal pronuclei of oocytes and 1-cell embryos, and in all nuclei of 2-cell embryos, regardless of their parental origin or ploidy. This repression is linked to chromatin, but the striking ability to relieve this repression with specific embryo-responsive enhancers first appears with formation of a 2-cell embryo. The need for a TATA-box to mediate enhancer stimulation of promoter activity appears even later when cell differentiation becomes evident. Thus, a biological clock delays transcription until both paternal and maternal genomes are replicated and remodeled from a post-meiotic state to one in which transcription is repressed by chromatin structure in a manner that can be relieved by cell-specific enhancers at appropriate times during development.

Animals↗
PubMed1990

Transcriptional analysis of the eight-kilobase mRNA encoding the major capsid protein of human cytomegalovirus.

The 8-kilobase mRNA coding for the major capsid protein (MCP) of human cytomegalovirus was precisely mapped. Two 5' ends of the transcript were located within HindIII fragment a, 29 and 34 base pairs, respectively, downstream of the sequence TATTAGA. The 3' end was localized within HindIII fragment b of the viral genome. The MCP transcript was synthesized at late times after infection and was not detected before viral DNA replication. In addition, the MCP promoter region could be identified, which strongly responded to viral trans activation at early and late times after infection in a transient expression assay.

Base Sequence↗
PubMed1975

Probable synchronous replication of mitochondrial DNA in cultures of chick embryo fibroblasts.

Cultures of chick embryo fibroblasts were synchronized using a procedure previously described. The profile of incorporation of tritiated thymidine showed a main peak of nuclear DNA replication followed by a small peak between 18 and 24 hr after induction of the cell division, and representing 10 to 25% of the main peak. To identify this small peak, cells were treated with ethidium bromide(EB) chloramphenicol (CAP) or 9-B-D arabinofuranosyl adenine (Ara-A). When EB (1 mug ml-1) and CAP(25mug ml-1) were added at time of induction of mitosis (T0) or 14 hr later (T14) the small peak was suppressed whereas the main peak was not decreased. On the contrary, only the main peak was suppressed when Ara-A was added at T0 or T14. These results suggest that the peak might correspond to the synchronous replication of the mitochondrial DNA during the G2 and M phases of the cell division cycle.

Animals↗
PubMed2002

Chaperone proteins abrogate inhibition of the human papillomavirus (HPV) E1 replicative helicase by the HPV E2 protein.

Human papillomavirus (HPV) DNA replication requires the viral origin recognition protein E2 and the presumptive viral replicative helicase E1. We now report for the first time efficient DNA unwinding by a purified HPV E1 protein. Unwinding depends on a supercoiled DNA substrate, topoisomerase I, single-stranded-DNA-binding protein, and ATP, but not an origin. Electron microscopy revealed completely unwound molecules. Intermediates contained two single-stranded loops emanating from a single protein complex, suggesting a bidirectional E1 helicase which translocated the flanking DNA in an inward direction. We showed that E2 protein partially inhibited DNA unwinding and that Hsp70 or Hsp40, which we reported previously to stimulate HPV-11 E1 binding to the origin and promote dihexameric E1 formation, apparently displaced E2 and abolished inhibition. Neither E2 nor chaperone proteins were detected in unwinding complexes. These results suggest that chaperones play important roles in the assembly and activation of a replicative helicase in higher eukaryotes. An E1 mutation in the ATP binding site caused deficient binding and unwinding of origin DNA, indicating the importance of ATP binding in efficient helicase assembly on the origin.

Adenosine Triphosphatases↗
PubMed1997

The ability to organize sperm DNA into functional chromatin is acquired during meiotic maturation in murine oocytes.

Following fertilization of meiotically mature eggs, the chromatin of the sperm becomes biochemically and structurally remodeled within the egg cytoplasm. Despite the essential role of the paternal genome during embryogenesis, little is known of when the activities that regulate this chromatin remodeling appear during oogenesis. To determine whether these activities were acquired during meiotic maturation, we inseminated maturing oocytes of mice shortly after germinal vesicle breakdown. As previously shown, insemination at this stage did not activate the maturing oocytes, which became arrested at metaphase II. Immunofluorescent analysis revealed that at 1 hr postinsemination the sperm chromatin was dispersed and contained protamines but was devoid of core histones H2B and H3. At 4 hr postinsemination, both protamine and core histones were detectable on the sperm chromatin. By 8 hr postinsemination protamines were absent, and histones stained maximally. The appearance of immunoreactive histones was correlated with a morphological transition of the sperm chromatin from the dispersed to a condensed state, which suggests that the assembly of the histones reflected modification of the chromatin to a somatic-like state in which it was competent to respond to the metaphase-promoting factor activity of the oocyte. Both the assembly of histones and chromatin condensation were reversibly blocked when protein synthesis was inhibited, indicating that the remodeling process required proteins synthesized during maturation. Injection of core histones into protein synthesis-inhibited oocytes failed to induce condensation of the sperm chromatin, which implies that correct remodeling requires synthesis during maturation of nonhistone proteins. To test the functional capacity of remodeled sperm chromatin, maturing oocytes were inseminated, allowed to continue maturation for 17 hr and then parthenogenetically activated. Following activation, the sperm-derived chromatin as well as that of the oocyte became decondensed within pronuclei and underwent DNA replication, indicating that sperm chromatin remodeled in maturing oocyte cytoplasm was functionally normal. When the postinsemination incubation time was reduced to 11 hr; however, neither the female nor the male pronuclei underwent DNA replication, implying that factors synthesized late during maturation are required for DNA replication after activation. Taken together, these results indicate that the ability to organize sperm DNA into functional somatic-like chromatin develops in oocytes during meiotic maturation, requires proteins synthesized during maturation, and can be expressed independently of activation.

Animals↗
PubMed1981

DNA polymerases in replication and repair of DNA during carcinogenesis induced by feeding N-acetylaminofluorene.

To study the roles of DNA polymerases alpha and beta during replication and repair of damaged DNA, use was made of the fact that during chronic treatment with carcinogens, replication and repair do not necessarily follow the same time sequence. Early cell damage and restorative hyperplasia cause a transient wave of DNA synthesis, while repair replication might be expected to continue throughout the period of treatment with the carcinogen. N-acetylaminofluorene (AAF) was fed in the diet for periods of up to 35 weeks, and at intervals during the feeding period measurements were made of DNA synthesis in vivo, and of DNA polymerases alpha and beta as assayed in vitro after fractionation. The activity of polymerase alpha increased and decreased with the transient early wave of DNA synthesis. Polymerase beta showed an initial rapid increase in activity which peaked before the increase in DNA synthesis, and then decreased. The decrease in activity may be due to the fact that, although AAF continues to be fed in the diet, the foci and nodules which develop no longer metabolise the carcinogen to a form which damages DNA. Thus replication occurs in the nodules while DNA damage and repair occur in the surrounding non-neoplastic liver. With the rapid growth of nodules there is overall an increase in neoplastic tissue, a relative decrease in nonneoplastic tissue, and thus a relative decrease in DNA damage, repair, and induction of polymerase beta. Histological examination showed that by 35 weeks the conversion to neoplasia was virtually complete. These results support the concept that polymerase alpha functions in de novo replication of DNA, and is induced during cell replication, while polymerase beta functions in repair replication, and increases in activity during chronic damage to DNA. Whether it is induced by treatment with carcinogens depends on the duration of treatment, and on other processes (e.g. metabolism of the carcinogen) which take place during the development of malignancy.

2-Acetylaminofluorene↗
PubMed1999

Detection of chromatin-bound PCNA in mammalian cells and its use to study DNA excision repair.

Compelling evidence indicates that proliferating cell nuclear antigen (PCNA) is an indispensable factor not only in DNA replication but in nucleotide excision repair (NER), alternative pathway of base excision repair (BER), and mismatch repair. The common function of PCNA in each of these is to assist in the initiation of DNA synthesis by providing a scaffolding clamp as a trimer catalyzed by RF-C at the 3'-OH terminus of a nascent DNA strand, to which DNA polymerase delta or epsilon can bind. Interestingly, DNA synthesis is reported to be ingeniously inhibited in replication, but not in NER owing to the interaction with CDKN1A (formerly known as p21/WAF1/CIP1). Furthermore, several proteins, XPG, FEN1, and DNA ligase I, recently were shown to competitively bind to the same region of PCNA, the interdomain connector loop, to which DNA polymerase delta or epsilon also binds. PCNA therefore seems to have a regulatory role in these DNA transactions. The in vitro reconstituted experimental system has been a powerful tool to obtain these lines of evidence, but another approach, immunofluorescence studies, also has been a contributor. In fact, the involvement of PCNA in DNA replication, NER, and BER has for the first time been indicated by a unique method that makes visible only in vivo chromatin-bound PCNA. The usefulness of this method and the importance of cooperative studies done with in vitro and in vivo experimental systems is discussed in terms of DNA excision repair.

Animals↗
PubMed2001

Regulation of DNA replication fork progression through damaged DNA by the Mec1/Rad53 checkpoint.

The checkpoint kinase proteins Mec1 and Rad53 are required in the budding yeast, Saccharomyces cerevisiae, to maintain cell viability in the presence of drugs causing damage to DNA or arrest of DNA replication forks. It is thought that they act by inhibiting cell cycle progression, allowing time for DNA repair to take place. Mec1 and Rad53 also slow S phase progression in response to DNA alkylation, although the mechanism for this and its relative importance in protecting cells from DNA damage have not been determined. Here we show that the DNA-alkylating agent methyl methanesulphonate (MMS) profoundly reduces the rate of DNA replication fork progression; however, this moderation does not require Rad53 or Mec1. The accelerated S phase in checkpoint mutants, therefore, is primarily a consequence of inappropriate initiation events. Wild-type cells ultimately complete DNA replication in the presence of MMS. In contrast, replication forks in checkpoint mutants collapse irreversibly at high rates. Moreover, the cytotoxicity of MMS in checkpoint mutants occurs specifically when cells are allowed to enter S phase with DNA damage. Thus, preventing damage-induced DNA replication fork catastrophe seems to be a primary mechanism by which checkpoints preserve viability in the face of DNA alkylation.

Alkylating Agents↗
PubMed2000

The complex of DNA gyrase and quinolone drugs on DNA forms a barrier to the T7 DNA polymerase replication complex.

Quinolone drugs can inhibit bacterial DNA replication, via interaction with the type II topoisomerase DNA gyrase. Using a DNA template containing a preferred site for quinolone-induced gyrase cleavage, we have demonstrated that the passage of the bacteriophage T7 replication complex is blocked in vitro by the formation of a gyrase-drug-DNA complex. The majority of the polymerase is arrested approximately 10 bp upstream of this preferred site, although other minor sites of blocking have been observed. The ability of mutant gyrase proteins to arrest DNA replication in vitro has been investigated. Gyrase containing mutations in the A subunit at either the active-site tyrosine (Tyr122) or Ser83 (a residue known to be involved in quinolone interaction) failed to halt the progress of the polymerase. A low-level, quinolone-resistant mutation in the B subunit of gyrase showed reduced blocking compared to wild-type. We have demonstrated that DNA cleavage and replication blocking occur on similar time-scales and we conclude that formation of the cleavable complex is a prerequisite for polymerase blocking. Additionally, we have shown that collision of the replication proteins with the gyrase-drug-DNA complex is not sufficient to render this complex irreversible and that further factors must be involved in processing this stalled complex.

Anti-Infective Agents↗
PubMed1976

Replication of bacteriophage T4 DNA in vitro. I. Basic properties of the system.

A new in vitro system for T4 DNA replication was developed by concentrating cell lysates on cellophane disks. The time course of [3H]dTTP incorporation into DNA by the system was separated into two phases: one was a very rapid incorporation which was terminated within 2 min (phase I reaction), and the other was a slow but continuous incorporation thereafter (phase II reaction). More than half of the phase I reaction product was Escherichia coli DNA, but the phase II reaction was mostly T4 DNA. Phase II reaction required four deoxyribonucleoside triphosphates, ATP, Mg2+, and KCl. 5-Hydroxymethyldeoxycytidine triphosphate was essential for the reaction and not substitutable by dCTP. The presence of KCN or NaN3 in the reaction mixture did not interfere with [3H]dTTP incorporation, but the addition of deoxyribonuclease completely degraded the system. Alkaline sucrose sedimentation analysis of phage II reaction product revealed that phase II reaction proceeded by the discontinuous mode of DNA replication as in vivo. After T4 infection, the activity for phase II reaction appeared in parallel with the activity of T4 phage DNA replication in vivo.

Adenosine Triphosphate↗