Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “replication”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,459 records · Page 81Linked to original sources
PubMed2000

Formation and stability of the bacteriophage lambda replication complexes in UV-irradiated Escherichia coli.

Bacteriophage lambda replication complex, containing the phage-encoded O initiator protein protected from proteases by other elements of this complex, is a stable structure that can be inherited by one of the two daughter lambda DNA copies after a replication round in Escherichia coli. In normal growth conditions in bacteria bearing a plasmid derived from bacteriophage lambda, such a complex may be stable for many cell generations. However, it was found that this stable structure is disassembled under certain conditions, namely, after heat shock. Therefore, we asked whether other environmental stresses may cause disassembly of the lambda replication complex. We found that UV irradiation of the host cells prevented formation of the stable lambda replication complex (though not preventing phage replication), while the same UV doses did not affect the stability of the replication complex assembled prior to the irradiation. These results indicate that the stable lambda replication complex, although sensitive to heat shock, is resistant to some other environmental stresses and that formation of at least two types of lambda replication complexes is possible. Both stable and unstable lambda replication complexes are functional because replication of lambda DNA under conditions preventing formation of the stable complex proceeds efficiently.

Bacteriolysis↗
PubMed2000

Replicative senescence and oxidant-induced premature senescence. Beyond the control of cell cycle checkpoints.

Normal human diploid fibroblasts (HDFs) undergo replicative senescence inevitably in tissue culture after a certain number of cell divisions. A number of molecular changes observed in replicative senescent cells occur in somatic cells during the process of aging. Genetic studies on replicative senescence indicate the control of tumor suppression mechanisms. Despite the significance of replicative senescence in aging and cancer, little is known about the central cause of the complex changes observed in replicative senescent cells. The interest in the phenomenon has intensified in recent years, since damaging agents, certain oncogenes and tumor suppressor genes have been found to induce features of senescence in early passage young HDFs or in immortalized tumor cells. The reported features of senescence are summarized here in order to clarify the concept of replicative senescence or premature senescence. The experimental results of extending the replicative life span by reducing ambient oxygen tension or by N-tert-butyl-alpha-phenylnitrone (PBN) argue a role of oxidative damage in replicative senescence. By inducing premature senescence with a pulse treatment of H2O2, we can study the role of the cell cycle checkpoint proteins p53, p21, p16 and Rb in gaining each feature of senescence. Although p53 and Rb control G1 arrest and Rb appears to control cell enlargement, activation of the senescent associate beta-galactosidase, loss of cell replication and multiple molecular changes observed in premature senescent or replicative senescent cells are likely controlled by mechanisms beyond the cell cycle checkpoints.

Animals↗
PubMed2001

Interleukin-10 stimulates Coxiella burnetii replication in human monocytes through tumor necrosis factor down-modulation: role in microbicidal defect of Q fever.

Coxiella burnetii, an obligate intracellular bacterium, is the agent of Q fever. The chronic form of the disease is associated with the overproduction of interleukin-10 and deficient C. burnetii killing by monocytes. We hypothesized that the replication of C. burnetii inside monocytes requires a macrophage-deactivating cytokine such as interleukin-10. In the absence of interleukin-10, C. burnetii survived but did not replicate in monocytes. C. burnetii replication (measured 15 days) was induced in interleukin-10-treated monocytes. This effect of interleukin-10 is specific since transforming growth factor beta1 had no effect on bacterial replication. C. burnetii replication involves the down-modulation of tumor necrosis factor (TNF) release. First, interleukin-10 suppressed C. burnetii-stimulated production of TNF. Second, the addition of recombinant TNF to interleukin-10-treated monocytes inhibited bacterial replication. Third, the incubation of infected monocytes with neutralizing anti-TNF antibodies favored C. burnetii replication. On the other hand, deficient C. burnetii killing by monocytes from patients with chronic Q fever involves interleukin-10. Indeed, C. burnetii replication was observed in monocytes from patients with Q fever endocarditis, but not in those from patients with acute Q fever. Bacterial replication was inhibited by neutralizing anti-interleukin-10 antibodies. As monocytes from patients with endocarditis overproduced interleukin-10, the defective bacterial killing is likely related to endogenous interleukin-10. These results suggest that interleukin-10 enables monocytes to support C. burnetii replication and to favor the development of chronic Q fever.

Antigens, CD↗
PubMed1973

Control of F'lac replication in Escherichia coli B-r.

The timing of replication of an F'lac plasmid during the division cycle of Escherichia coli B/r lac(-)/F'lac was examined in relation to the timing of initiation of chromosome replication. This was accomplished by measuring the induction of beta-galactosidase and the incorporation of radioactive thymidine into cells at different ages in cultures growing exponentially at various rates. In cells growing with interdivision times of 27, 36, and 55 min, the F'lac replicated at various stages in the division cycle but always at approximately the same time as initiation of chromosome replication. In cells growing with an interdivision time of 85 min, the F'lac episome replicated midway through the division cycle, whereas chromosome replication initiated at the start of the cycle. Measurements of absorbance at 450 nm per cell suggested that the F'lac replicated when the cells reached a mass which was a constant multiple of the number of episomes per cell at each growth rate. In contrast, the mass per cell at initiation of chromosome replication in cells with an 85-min interdivision time was significantly lower than this constant value. A possible explanation for the apparent coupling between F'lac replication and initiation of chromosome replication at the higher growth rates, and the lack of coupling at the lowest growth rate, is discussed.

Carbon Isotopes↗
PubMed2003

Multiple functional elements comprise a Mammalian chromosomal replicator.

The structure of replication origins in metazoans is only nominally similar to that in model organisms, such as Saccharomyces cerevisiae. By contrast to the compact origins of budding yeast, in metazoans multiple elements act as replication start sites or control replication efficiency. We first reported that replication forks diverge from an origin 5' to the human c-myc gene and that a 2.4-kb core fragment of the origin displays autonomous replicating sequence activity in plasmids and replicator activity at an ectopic chromosomal site. Here we have used clonal HeLa cell lines containing mutated c-myc origin constructs integrated at the same chromosomal location to identify elements important for DNA replication. Replication activity was measured before or after integration of the wild-type or mutated origins using PCR-based nascent DNA abundance assays. We find that deletions of several segments of the c-myc origin, including the DNA unwinding element and transcription factor binding sites, substantially reduced replicator activity, whereas deletion of the c-myc promoter P1 had only a modest effect. Substitution mutagenesis indicated that the sequence of the DNA unwinding element, rather than the spacing of flanking sequences, is critical. These results identify multiple functional elements essential for c-myc replicator activity.

Animals↗
PubMed2004

Ionizing radiation induces frequent translocations with delayed replication and condensation.

Certain chromosome rearrangements display a significant delay in replication timing that is associated with a delay in mitotic chromosome condensation. Chromosomes with delay in replication timing/delay in mitotic chromosome condensation participate in frequent secondary rearrangements, indicating that cells with delay in replication timing/delay in mitotic chromosome condensation display chromosomal instability. In this report, we show that exposing cell lines or primary blood lymphocytes to ionizing radiation results in chromosomes with the delay in replication timing/delay in mitotic chromosome condensation phenotype, and that the delay in replication timing/delay in mitotic chromosome condensation phenotype occurs predominantly on chromosome translocations. In addition, exposing mice to ionizing radiation also induces cells with delay in replication timing/delay in mitotic chromosome condensation chromosomes that persist for as long as 2 years. Cells containing delay in replication timing/delay in mitotic chromosome condensation chromosomes frequently display hyperdiploid karyotypes, indicating that delay in replication timing/delay in mitotic chromosome condensation is associated with aneuploidy. Finally, using a chromosome engineering strategy, we show that only a subset of chromosome translocations displays delay in replication timing/delay in mitotic chromosome condensation. Our results indicate that specific chromosome rearrangements result in the generation of the delay in replication timing/delay in mitotic chromosome condensation phenotype and that this phenotype occurs frequently in cells exposed to ionizing radiation both in vitro and in vivo.

Cell Line↗
PubMed1998

Self-replicating structures: evolution, emergence and computation.

Since von Neumann's seminal work around 1950, computer scientists and others have studied the algorithms needed to support self-replicating systems. Much of this work has focused on abstract logical machines (automata) embedded in two-dimensional cellular spaces. This research was motivated by a desire to understand the basic information-processing principles underlying self-replication, the potential long-term applications of programmable self-replicating machines, and the possibility of gaining insight into biological replication and the origins of life. We view past research as taking three main directions: early complex universal computer-constructors modeled after Turing machines, qualitatively simpler self-replicating loops, and efforts to view self-replication as an emergent phenomenon. We discuss our recent studies in the latter category showing that self-replicating structures can emerge from nonreplicating components, and that genetic algorithms can be applied to program automatically simple but arbitrary structures to replicate. We also describe recent work in which self-replicating structures are successfully programmed to do useful problem solving as they replicate. We conclude by identifying some implications and important research directions for the future.

Algorithms↗
PubMed1976

Pancreatic beta cell replication: effects of hexose sugars.

Neonatal rat pancreatic monolayer cultures were utilized to investigate the effects of various hexose sugars on insulin release and beta cell replication. Sugars tested were D-glucose, L-glucose, 3-O-methyl-D-glucose, D-mannose and D-fructose. These agents were added at varying concentrations to a control medium containing a baseline level of 5.5 mM D-glucose. Replication was estimated by incubating cultures with [3H]thymidine and determining the frequency of beta cell labelling in aldehyde-thionin stained radioautographs. Although the addition of D-glucose to the control medium resulted in a concentration-dependent increase in both insulin release and beta cell replication, the sensitivity of these two processes to glucose differed. Insulin release was stimulated by a 2.75 mM elevation in the D-glucose concentration of the control medium, while an elevation of 11 mM D-glucose was required to increase the frequency of beta cell replication. Moreover, while insulin release was maximally stimulated by an 11 mM elevation in the concentration of D-glucose, the frequency of replication continued to rise as the concentration of D-glucose was further increased. The specificity of these responses to D-glucose was demonstrated by the inability of 11 mM L-glucose or 11 mM 3-O-methyl-D-glucose to stimulate beta cell replication. D-mannose and D-fructose were less potent insulin secretagogues than D-glucose on an equimolar basis and neither compound enhanced beta cell replication at a concentration of 11 mM. However, higher concentrations of D-mannose (16.5 and 22 mM) enhanced beta cell replication, while comparable concentrations of D-fructose did not. These results indicate that the sensitivity of insulin release and beta cell replication to D-glucose differ, and that in addition to D-glucose, D-mannose is also capable of stimulating beta cell replication.

Animals↗
PubMed2004

Analysis of triplet repeat replication by two-dimensional gel electrophoresis.

Expansions of triplet repeats are responsible for more than 15 hereditary neurological disorders in humans. Triplet repeats are fairly stable when the number of elementary units is under approx 30, but become polymorphic in length with a clear bias for expansions when this threshold is exceeded. This results in the rapid addition of hundreds or even thousands of extra repeats and, ultimately, disease. The mechanisms of triplet repeat expansions are not yet understood. The role of several genetic processes, including replication, recombination, and repair, was suggested. However, given the swift accumulation of extra DNA material, DNA replication seems to be an intuitive candidate for generating expansions. Numerous data point to the aberrant replication of triplet repeats as a cause of triplet repeat expansions. Direct experimental proof of aberrant replication through triplet repeats was lacking. This encouraged us to study the mode of replication fork progression through triplet repeats in vivo. We analyzed the effects of triplet repeats on replication of bacterial or yeast plasmids using an approach called two-dimensional neutral/neutral gel electrophoresis of replication intermediates. This technique, originally developed for mapping replication origins, is also instrumental in defining replication pause sites. Using this technique, we were able to unambiguously demonstrate that expandable triplet repeats attenuate replication fork progression in vivo and get some insights into the mechanisms of repeat expansions.

Electrophoresis, Gel, Two-Dimensional↗
PubMed1979

Late replicating X chromosomes in human triploidy.

The status of X-chromosome replication was studied in twenty-seven 69,XXY and nine 69,XXX human triploids in which the parental origin of the additional haploid set was known from the study of chromosome heteromorphisms. Among the 69,XXY triploids, fourteen had no late replicating X, two had one late replicating X in all cells examined, and eleven had two populations of cells, one with late replicating X chromosome, and one without any. Among the 69,XXX triploids, four had a single late replicating X, and five had two populations of cells, one with one late replicating X, and one with two late replicating X chromosomes. There was no correlation between the parental origin of the triploidy and the type of X-chromosome inactivation. However the number of late replicating X chromosomes was significantly lower in cultures grown from fetal tissue when compared with those grown from extra-embryonic tissue. In cultures derived from extra-embryonic tissue there was a significant correlation between the gestational age of the sample and the proportion of late replicating X chromosomes. The older the specimen, the greater the number of late replicating X chromosomes.

Abortion, Spontaneous↗
PubMed1999

Eukaryotic DNA replication.

One of the fundamental characteristics of life is the ability of an entity to reproduce itself, which stems from the ability of the DNA molecule to replicate itself. The initiation step of DNA replication, where control over the timing and frequency of replication is exerted, is poorly understood in eukaryotes in general, and in mammalian cells in particular. The cis-acting DNA element defining the position and providing control over initiation is the replication origin. The activation of replication origins seems to be dependent on the presence of both a particular sequence and of structural determinants. In the past few years, the development of new methods for identification and mapping of origins of DNA replication has allowed some understanding of the fundamental elements that control the replication process. This review summarizes some of the major findings of this century, regarding the mechanism of DNA replication, emphasizing what is known about the replication of mammalian DNA. J. Cell. Biochem. Suppls. 32/33:1-14, 1999.

Animals↗
PubMed1999

Replication origins in metazoan chromosomes: fact or fiction?

The process by which eukaryotic cells decide when and where to initiate DNA replication has been illuminated in yeast, where specific DNA sequences (replication origins) bind a unique group of proteins (origin recognition complex) next to an easily unwound DNA sequence at which replication can begin. The origin recognition complex provides a platform on which additional proteins assemble to form a pre-replication complex that can be activated at S-phase by specific protein kinases. Remarkably, multicellular eukaryotes, such as frogs, flies, and mammals (metazoa), have counterparts to these yeast proteins that are required for DNA replication. Therefore, one might expect metazoan chromosomes to contain specific replication origins as well, a hypothesis that has long been controversial. In fact, recent results strongly support the view that DNA replication origins in metazoan chromosomes consist of one or more high frequency initiation sites and perhaps several low frequency ones that together can appear as a nonspecific initiation zone. Specific replication origins are established during G1-phase of each cell cycle by multiple parameters that include nuclear structure, chromatin structure, DNA sequence, and perhaps DNA modification. Such complexity endows metazoa with the flexibility to change both the number and locations of replication origins in response to the demands of animal development.

Animals↗
PubMed1993

Constitutive binding of EBNA1 protein to the Epstein-Barr virus replication origin, oriP, with distortion of DNA structure during latent infection.

Replication of the circular, 170 kb genome of Epstein-Barr virus (EBV) during latent infection is performed by the cellular replication machinery under cell-cycle control. A single viral protein, EBNA1, directs the cellular replication apparatus to initiate replication within the genetically defined replication origin, oriP, at a cluster of four EBNA1 binding sites, referred to here as the physical origin of bidirectional replication, or OBR. A second cluster of EBNA1 binding sites within oriP, the 30 bp repeats, serves an essential role as a replication enhancer and also provides a distinct episome maintenance function that is unrelated to replication. We examined the functional elements of oriP for binding by EBNA1 and possibly other proteins in proliferating Raji cells by generating in vivo footprints using two reagents, dimethylsulfate (DMS) and KMnO4. We also employed deoxyribonuclease I (DNase I) with permeabilized cells. The in vivo and permeabilized cell footprints at the EBNA1 binding sites, particularly those obtained using DMS, gave strong evidence that all of these sites are bound by EBNA1 in asynchronously dividing cells. No consistent evidence was found to suggest binding by other proteins at any other sites within the functional regions of oriP. Thymines at symmetrical positions of the OBR within oriP were oxidized when cells were treated with permanganate, suggestive of bends or other distortions of DNA structure at these positions; binding of EBNA1 in vitro to total DNA from Raji cells induced reactivity to permanganate at identical positions. The simplest interpretation of the results, which were obtained using asynchronously dividing cells, is that EBNA1 binds to its sites at oriP and holds the OBR in a distorted conformation throughout most of the cell cycle, implying that replication is initiated by a cellular mechanism and is not limited by an availability of EBNA1 for binding to oriP.

Antigens, Viral↗
PubMed1995

Chromatin assembly factor 1 (CAF-1) colocalizes with replication foci in HeLa cell nuclei.

In the S-phase of the eukaryotic cell cycle, newly replicated DNA is assembled into chromatin. I used indirect immunofluorescence microscopy to localize the sites of chromatin assembly in respect to DNA replication. Replication foci in the nuclei of permeabilized HeLa cells were labeled by incorporation of biotin-16-dUTP and detected by fluorescent streptavidin. Prelabeling of replication foci in vivo with bromodeoxyuridine showed that replication in permeabilized cells proceeds at preexisting replication forks. The localization of chromatin assembly factor 1 (CAF-1) was determined with subunit-specific monoclonal antibodies. CAF-1 is not detectable in mitotic cells and is detectable only at background levels in about 60% of all interphase nuclei. The other interphase nuclei show an intense punctate immunostaining of CAF-1. These sites of CAF-1 colocalize with replication foci during all stages of the S-phase. No other discrete sites of CAF-1 are observed. Human replication protein A (RPA) colocalizes with these replication/chromatin assembly sites. In addition, extra nuclear sites of RPA are observed that probably represent prereplication foci, poised for initiation of DNA replication.

Antibodies, Monoclonal↗
PubMed1998

In vitro replication of mitochondrial plasmid mp1 from the higher plant Chenopodium album (L.): a remnant of bacterial rolling circle and conjugative plasmids?

According to the endosymbiotic theory, mitochondrial genomes evolved from the chromosome of an alpha-proteobacterium-like ancestor and developed during evolution an extraordinary variation in size, structure and replication. We studied in vitro DNA replication of the mitochondrial circular plasmid mp1 (1309 bp) from the higher plant Chenopodium album (L.) as a model system that replicates in a manner reminiscent of bacterial rolling circle plasmids. Several mp1 subclones were tested for their ability to support DNA replication using a newly developed in vitro system. Neutral/neutral two-dimensional gel electrophoresis of the in vitro products revealed typical simple Y patterns of intermediates consistent with a rolling circle type of replication. Replication activity was very high for a BamHI-restricted total plasmid DNA clone, a 464 bp BamHI/KpnI fragment and a 363 bp BamHI/SmaI fragment. Further subcloning of a 148 bp BamHI/EcoRI fragment resulted in the strongest in vitro DNA replication activity, while a 1161 bp-template outside of this region resulted in a substantial loss of activity. Electron microscopic studies of in vitro DNA replication products from the highly active clones also revealed sigma-shaped molecules. These results support our in vivo data for the presence of a predominant replication origin between positions 628 and 776 on the plasmid map. This sequence shares homology with double-stranded rolling circle origin (dso) or transfer origin (oriT) nicking motifs from bacterial plasmids. mp1 is the first described rolling circle plasmid in eukaryotes.

Base Sequence↗
PubMed2000

Replication fork density increases during DNA synthesis in X. laevis egg extracts.

Duplication of the eukaryotic genome depends on the temporal and spatial organization of DNA replication during the cell cycle. To investigate the genomic organization of DNA replication in a higher eukaryote, multiple origins of replication must be simultaneously analyzed over large regions of the genome as DNA synthesis progresses through S phase of the cell cycle. We have employed a novel technique that allows for the quantitative analysis of DNA replication on a genome wide basis. The technique involves stretching and aligning individual DNA molecules on a glass surface. As a model system, Xenopus laevis egg extract was used to differentially label sperm chromatin at successive time points after the start of DNA synthesis. The differentially labeled DNA allows earlier and later replicating sequences to be distinguished, and hence the sites of DNA synthesis at any given time can be directly visualized. Genomic DNA was extracted, and measurements made on the linearized molecules provided a comprehensive analysis of the spatial and temporal organization of DNA replication in the X. laevis in vitro replication system. It was found that: (i) DNA synthesis initiates asynchronously at irregular intervals but continuously as DNA replication advances; and (ii) that the frequency of initiation (the number of activated origins per kilobase) increases as DNA synthesis nears completion. The implications of these findings for the regulation of DNA replication in early embryos is discussed.

Animals↗
PubMed1995

Identification and analysis of a putative origin of DNA replication in the Choristoneura fumiferana multinucleocapsid nuclear polyhedrosis virus genome.

A recombinant plasmid containing the Choristoneura fumiferana multinucleocapsid nuclear polyhedrosis virus (CfMNPV) HindIII R fragment (m.u. 2.2-3.9) was shown to undergo CfMNPV infection-dependent DNA replication in Cf-124T cells. Replication of this DNA sequence was detectable by 24 hr p.i. and did not appear to have resulted as a consequence of recombination with the virus genome. Replication was inhibited by mimosine, an inhibitor of eukaryotic DNA replication. These data suggest that HindIII R of CfMNPV DNA contains an origin of DNA replication which we call ori1. HindIII R contains five GC-rich and three AT-rich regions and a 0.9-kb homologous repeat region 1 (hr1). Two short 440- and 740-bp contiguous sequences at the right end of the HindIII R fragment separately exhibited limited ori function. HindIII R subfragments with optimal ori activity contained a cluster of repeated and inverted sequences including nine copies of a 50-bp homologous repeat sequence (hr1a to hr1i) within hr1. The CfMNPV hr1 sequence was somewhat homologous with the homologous repeat (hr) of the putative Autographa californica MNPV (AcMNPV) replication origins. HindIII Y, another CfMNPV DNA fragment containing an hr sequence, hr3, also supported infection-dependent DNA replication, suggesting that it too contains an ori. Although replication of a putative AcMNPV origin (HindIII Q) was detectable in CfMNPV-infected Cf-124T cells, replication of CfMNPV HindIII R was not detectable in AcMNPV-infected Spodoptera frugiperda cells.

Animals↗
PubMed1997

Early region 4 modulates adenovirus DNA replication by two genetically separable mechanisms.

Three viral proteins, all products of early region 2 (E2), participate directly in adenovirus DNA replication. Three products of early region 4 (E4) also affect viral DNA synthesis: the product of E4 ORF4 inhibits viral DNA accumulation, while the products of E4 ORFs 3 and 6 antagonize that effect of ORF4 expression. Because no E4 products are required for DNA synthesis, these proteins probably act indirectly. The E4 ORF3, 4, and 6 proteins all participate in aspects of the regulation of viral gene expression. To determine whether they modulate DNA replication by effects on expression of viral replication proteins, we examined E2 expression in E4 mutant-infected cells. In cells infected by ORF3-, 6- mutants, expression of ORF4 substantially depressed the steady-state levels of replication proteins and E2 mRNAs, reduced E2 transcription rates, and profoundly inhibited viral DNA replication. Thus, in the absence of E4 ORFs 3 and 6, ORF4 acts as a transcriptional regulator of E2 expression, and reduced replication protein levels largely account for the inhibition of DNA replication by ORF4. Cells infected by viruses that express ORFs 3 and 6 in addition to ORF4 accumulated much larger quantities of viral DNA than did cells infected by the ORF3-, 6-, 4+ mutant. Increased DNA accumulation was not accompanied by a comparable increase in E2 expression. Therefore, the ORF3 and 6 products counteract the ORF4-induced reduction of DNA replication by a mechanism other than reversing the inhibitory effect of ORF4 on E2 expression. The effect of ORF4 on E2 expression is consistent with its ability to regulate levels of the transcription factor AP-1 (Müller et al., 1992, J. Virol. 66, 5867-5878); the mechanism by which ORFs 3 and 6 enhance replication is unknown.

Adenovirus E2 Proteins↗