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At least 649 records · Page 36Linked to original sources
PubMed1983

Maintenance and incompatibility of plasmids carrying the replication origin of the Escherichia coli chromosome: evidence for a control region of replication between oriC and asnA.

Plasmids that replicate only by means of the cloned Escherichia coli replication origin (oriC) are called minichromosomes or oriC-plasmids. In this paper it is shown that sequences located between oriC and asnA are involved in maintenance and incompatibility of minichromosomes. These sequences include part of the 16kD and 17kD genes, previously allocated within this region (1,2). Transcription towards oriC that is initiated at the 16kD promoter, specifically enhances the stability and copy-number of minichromosomes. Three regions are involved in minichromosome incompatibility. One region, incA, includes the minimal oriC sequence. A second, incB, maps within a 210 base pairs fragment that overlaps the 16kD promoter. The third, incC, encompasses the 17kD gene. Neither one of the regions expresses incompatibility on its own, but the additional presence of one of the others is required. The data presented indicate that sequences of the 16kD and 17kD genes are part of the replication control system of oriC-plasmids.

Base Sequence↗
PubMed1985

Individual Xenopus histone genes are replication-independent in oocytes and replication-dependent in Xenopus or mouse somatic cells.

We have assessed the response of many histone H3 mRNAs and an H1C mRNA in Xenopus tissue culture cells after treatment with the DNA synthesis inhibitor hydroxyurea. The amount of the histone mRNAs falls rapidly in response to the inhibitor. This response is prevented by cycloheximide. Cloned Xenopus histone genes were transfected into mouse cells and a cell line was obtained in which the Xenopus genes were actively expressed giving rise to mRNA with correct 5'-termini. The Xenopus genes were correctly regulated at the level of mRNA amounts in the mouse cell line. Nuclear microinjection experiments with Xenopus oocytes and S1 nuclease analysis of normal ovary RNA showed that the H1C gene, and probably also two H3 genes, which are replication-dependent in somatic cells are expressed in oocytes and are therefore replication-independent in this cell type. The same promoters are used in both replication-dependent and independent expression.

Amino Acid Sequence↗
PubMed2001

hMYH cell cycle-dependent expression, subcellular localization and association with replication foci: evidence suggesting replication-coupled repair of adenine:8-oxoguanine mispairs.

The human MutY homolog, hMYH, is an adenine-specific DNA glycosylase that removes adenines or 2-hydroxyadenines mispaired with guanines or 8-oxoguanines. In order to prevent mutations, this activity must be directed to the newly synthesized strand and not the template strand during DNA synthesis. The subcellular localization and expression of hMYH has been studied in serum-stimulated, proliferating MRC5 cells. Using specific antibodies, we demonstrate that endogenous hMYH protein localized both to nuclei and mitochondria. hMYH in the nuclei is distinctly distributed and co-localized with BrdU at replication foci and with proliferating cell nuclear antigen (PCNA). The levels of hMYH in the nucleus increased 3- to 4-fold during progression of the cell cycle and reached maximum levels in S phase compared to early G(1). Similar results were obtained for PCNA, while there were no notable changes in expression of 8-oxoguanine glycosylase or the human MutT homolog, MTH1, throughout the cell cycle. The cell cycle-dependent expression and localization of hMYH at sites of DNA replication suggest a role for this glycosylase in immediate post-replication DNA base excision repair.

Adenine↗
PubMed1980

Replication of human cytomegalovirus at supra-optimal temperatures is dependent on the virus strain, multiplicity of infection and phase of virus replication.

The kinetics of replication of five strains of human cytomegalovirus (CMV) were studied to determine the influence of (i) temperature, (ii) virus strain, (iii) m.o.i. and (iv) cell type. Relative to growth at 37 degrees C (m.o.i. = 3 to 9) eclipse periods were extended from 24 to 48 h at 33 degrees C and to 72 h at 40.5 degrees C. Yields were reduced at 33 degrees C and almost eliminated at 40.5 degrees C. No replication occurred in most instances at 40.5 degrees C and with 0.05 p.f.u./cell. Temperature shift studies (40.5 to 37 degrees C) indicated that the block to replication at 40.5 degrees occurred about 12 to 16 h p.i. resulting in little synthesis of CMV DNA or late antigens. The degree of inhibition of late functions at 40.5 degrees C is virus strain and m.o.i. dependent, but is not dependent on the type of fibroblastic cell used. These data suggest that persistent CMV infections are favoured at 40.5 degrees C.

Antigens, Viral↗
PubMed1982

Replication of lactate dehydrogenase-elevating virus in macrophages. 1. Evidence for cytocidal replication.

Cultures of starch-elicited peritoneal mouse macrophages in medium containing macrophage growth factor (MGF) were infected with lactate dehydrogenase-elevating virus (LDV) and, after various times in culture, LDV production was monitored as a function of time by infectivity titrations in mice, by measuring [3H]uridine incorporation into LDV RNA and extracellular LDV, by autoradiographic analysis of the proportion of productively infected cells and by electron microscopy. Regardless of the age of the cultures when infected with LDV, only a small proportion of the macrophages (generally between 3 and 20% of the total) became productively infected after a primary infection; maximum virus RNA synthesis and virus production occurred during the first 24 h after infection and then decreased precipitously. Productively infected macrophages could be readily recognized in electron micrographs of 24-h infected macrophage cultures and in sections of spleens from 24-h infected mice by characteristic morphological alterations. These consisted of formation of clusters of double-membrane vesicles with a diameter of 100 to 300 mumol, budding of nucleocapsids into vesicles with single membranes and accumulation of mature virions in these vesicles. One to 4 days later, however, such cells were no longer found in infected cultures or spleens of infected mice and superinfection did not restimulate LDV replication. Cultures established with macrophages from 1-day LDV-infected mice also did not support LDV replication. We conclude that LDV replication in cultures or mice is limited to a single cycle in a subpopulation of macrophages and that infection leads to cell death and rapid phagocytosis of the dead cells by the resistant, uninfected macrophages.

Animals↗
PubMed1992

Lack of human immunodeficiency virus type 1 (HIV-1) replication and accumulation of viral DNA in HIV-1-infected T cells blocked in cell replication.

Human immunodeficiency virus type 1 (HIV-1) infection of the CD4+ SupT and CEM cell lines, blocked in cell replication by the polymerase alpha inhibitor aphidicolin (APC), was studied. The APC-treated cells showed a lack of viral production, but the presence of single cell killing. High levels of unintegrated viral DNA forms were found in the infected APC-treated cells as compared with untreated cells. Moreover, an increased rate of viral replication occurred in the remaining viable cells following removal of APC. The results indicate that HIV-1 entry and reverse transcription can take place in cells blocked in the S phase of the cell cycle. Replication of infectious progeny virions appears to require de novo cell division. Finally, accumulation of viral DNA in cells during APC treatment can result in cytopathological effects and subsequent enhancement of virus production.

Aphidicolin↗
PubMed1978

Properties of a temperature-sensitive mutant of Staphylococcus aureus defective in DNA replication and cell division and replication of plasmids in the mutant.

The properties of a temperature-sensitive mutant (ts39) of Staphylococcus aureus NCTC 8235 are described. After transfer to the restrictive temperature (42 degrees C), absorbance increased 10-to 20-fold but DNA content did not increase beyond 150 to 200% and cell division continued at a greatly reduced rate. On transfer back to the permissive temperature, both cell division and DNA synthesis resumed if the transfer occurred after less than 120 min at 42 degrees C. Resumption of DNA replication was blocked by chloramphenicol (100 microgram ml-1). The results are discussed with reference to possible defects in DNA replication. Replication of the plasmids pI258 and pT10501 and the chromosome were affected to a similar extent in ts39. Growth at 42 degrees C resulted in the appearance of an increased amount of pI258 DNA in a form that sedimented slowly in a sucrose gradient.

Chromosomes, Bacterial↗
PubMed1991

Cooperativity at a distance promoted by the combined action of two replication initiator proteins and a DNA bending protein at the replication origin of pSC101.

We have investigated the interaction of the host-encoded DNA bending protein IHF, the host-encoded initiator DnaA, and the plasmid-encoded initiator RepA with the replication origin of pSC101. We have discovered that DNA bending induced by IHF in vitro promoted the interaction of DnaA protein with two physically separated binding sites called dnaAs and dnaAw. This cooperative interaction at a distance, most probably, caused looping out of the ihf site. We have also discovered that RepA protein binding to its cognate sites promoted enhanced binding of DnaA protein to the physically distant dnaAs site, probably also by DNA looping. The addition of RepA to a binding reaction containing IHF and DnaA further enhanced the binding of DnaA protein to the dnaAs site. Thus, the three DNA-binding proteins interacted with the origin, generating a higher order structure in vitro. On the basis of the results of the known requirement of all three proteins for replication initiation, we have proposed a model for the structure of a preinitiation complex at the replication origin.

Bacterial Proteins↗
PubMed2019

Replication timing networks reveal a link between transcription regulatory circuits and replication timing control.

DNA replication occurs in a defined temporal order known as the replication timing (RT) program and is regulated during development, coordinated with 3D genome organization and transcriptional activity. However, transcription and RT are not sufficiently coordinated to predict each other, suggesting an indirect relationship. Here, we exploit genome-wide RT profiles from 15 human cell types and intermediate differentiation stages derived from human embryonic stem cells to construct different types of RT regulatory networks. First, we constructed networks based on the coordinated RT changes during cell fate commitment to create highly complex RT networks composed of thousands of interactions that form specific functional subnetwork communities. We also constructed directional regulatory networks based on the order of RT changes within cell lineages, and identified master regulators of differentiation pathways. Finally, we explored relationships between RT networks and transcriptional regulatory networks (TRNs) by combining them into more complex circuitries of composite and bipartite networks. Results identified novel trans interactions linking transcription factors that are core to the regulatory circuitry of each cell type to RT changes occurring in those cell types. These core transcription factors were found to bind cooperatively to sites in the affected replication domains, providing provocative evidence that they constitute biologically significant directional interactions. Our findings suggest a regulatory link between the establishment of cell-type-specific TRNs and RT control during lineage specification.

Cell Differentiation↗
PubMed2004

A NAC domain protein interacts with tomato leaf curl virus replication accessory protein and enhances viral replication.

Geminivirus replication enhancer (REn) proteins dramatically increase the accumulation of viral DNA species by an unknown mechanism. In this study, we present evidence implicating SlNAC1, a new member of the NAC domain protein family from tomato (Solanum lycopersicum), in Tomato leaf curl virus (TLCV) REn function. We isolated SlNAC1 using yeast (Saccharomyces cerevisiae) two-hybrid technology and TLCV REn as bait, and confirmed the interaction between these proteins in vitro. TLCV induces SlNAC1 expression specifically in infected cells, and this upregulation requires REn. In a transient TLCV replication system, overexpression of SlNAC1 resulted in a substantial increase in viral DNA accumulation. SlNAC1 colocalized with REn to the nucleus and activated transcription of a reporter gene in yeast, suggesting that in healthy cells it functions as a transcription factor. Together, these results imply that SlNAC1 plays an important role in the process by which REn enhances TLCV replication.

Amino Acid Sequence↗
PubMed1983

Replication and inactivation of an isodicentric X: presence of an inactive centromere influences the replication patterns.

An isodicentric X-chromosome (idic(X)(pter leads to q23::q23 leads to pter)) was found in a phenotypically normal 30-year-old female with symptoms of premature menopause. A study of DNA replication revealed that in a proportion of cells there was an asymmetric pattern of replication. The region with the inactive centromere had a tendency to replicate later than the portion with the functioning centromere.

Adult↗
PubMed1978

Replication of M-13 DNA in plasmolysed Escherichia coli cells. Structure of a replicative intermediate with restricted binding of intercalating dyes.

DNA molecules with restricted binding of intercalating dyes are observed as replicative intermediates during the replication of bacteriophage M-13 duplex DNA in a cellular system in vitro prepared by plasmolysis of M-13-am5-infected Escherichia coli cells. Restriction of dye binding is abolished by heating the DNA to 80 degrees C, but can be recovered by slow cooling of the heat-treated DNA. Radioactive pulse-label incorporated by these molecules is found exclusively in elongated viral strands of more than one genome length. In the electron microscope this DNA fraction is seen to contain a significant number of duplex DNA rings with two single-stranded tails protruding from the same region of the ring. It is proposed that these structures arise by branch migration during the isolation of replicating molecules containing only one single-stranded tail. The topological constraint in these molecules is most likely caused by base-pairing between partially complementary regions of the two single-stranded tails.

Binding Sites↗
PubMed2002

The bacterial replication initiator DnaA. DnaA and oriC, the bacterial mode to initiate DNA replication.

The initiation of replication is the central event in the bacterial cell cycle. Cells control the rate of DNA synthesis by modulating the frequency with which new chains are initiated, like all macromolecular synthesis. The end of the replication cycle provides a checkpoint that must be executed for cell division to occur. This review summarizes recent insight into the biochemistry, genetics and control of the initiation of replication in bacteria, and the central role of the initiator protein DnaA.

Bacteria↗
PubMed1977

Initiation and termination of deoxyribonucleic acid replication in bacteria after a stepwise increase in the velocity of replication.

The theoretical relations between replication, initiation, termination, and deoxyribonucleic acid (DNA) accumulation were derived for experiments in which the length of the time required for the replication of the bacterial chromosome (C period) can be varied. This theory enables one to determine absolute values of the C period from kinetics of DNA accumulation after a "stepup" with thymine-requiring bacteria that are subjected to a sudden increase in the exogenous thymine concentration. Application of this method of data evaluation to an observed step-up experiment with a thy-derivative of Escherichia coli B/r (ATCC 12407) indicated that the theory describes the observed post-step accumulation of DNA accurately within experimental errors. It is also concluded that changes in the replication velocity (C) do not measurably affect the timing of initiation events in a culture.

DNA Replication↗
PubMed1983

Overproduction of Escherichia coli replication proteins by the use of runaway-replication plasmids.

A derivative of the runaway-replication plasmid was constructed. This plasmid, pSY343, has the gene for kanamycin resistance and single sites for EcoRI, BamHI, HindIII, KpnI, and XhoI that can be used as cloning sites without inactivating the kanamycin resistance gene or the replication genes. Three replication genes of Escherichia coli were cloned on the plasmid. The activity of dnaA, dnaZ, and ssb gene products were 200-, 90-, and 60-fold greater, respectively, in the cells containing these plasmids than in normal cells.

Bacterial Proteins↗
PubMed1990

Replication of the broad-host-range plasmid RK2: direct measurement of intracellular concentrations of the essential TrfA replication proteins and their effect on plasmid copy number.

The trfA gene of the broad-host-range plasmid RK2 is essential for initiation of plasmid replication. Two related TrfA proteins of 43 and 32 kilodaltons (kDa) are produced by independent translation initiation at two start codons within the trfA open reading frame. These proteins were o overproduced in Escherichia coli and partially purified. Rabbit antisera raised against the 32-kDa TrfA protein (TrfA-32) and cross-reacting with the 43-kDa protein (TrfA-43) were used in Western blotting (immunoblotting) assays to measure intracellular TrfA levels. In logarithmically growing E. coli HB101, RK2 produced 4.6 +/- 0.6 ng of TrfA-32 and 1.8 +/- 0.2 ng of TrfA-43 per unit of optical density at 600 nm (mean +/- standard deviation). On the basis of determinations of the number of cells per unit of optical density at 600 nm, this corresponds to about 220 molecules of TrfA-32 and 80 molecules of TrfA-43 per cell. Dot blot hybridizations showed that plasmid RK2 is present in about 15 copies per E. coli cell under these conditions. Using plasmid constructs that produce different levels of TrfA proteins, the effect of excess TrfA on RK2 replication was tested. A two- to threefold excess of total TrfA increased the copy number of RK2 by about 30%. Additional increases in TrfA protein concentration had no further effect on copy number, even at levels 170-fold above normal. An RK2 minimal origin plasmid showed a similar response to intracellular TrfA concentration. These results demonstrate that TrfA protein concentration is not strictly rate limiting for RK2 replication and that a mechanism that is independent of TrfA concentration functions to limit RK2 copy number in the presence of excess TrfA.

Bacterial Proteins↗
PubMed1995

Transcriptional analysis of rolling circle replicating plasmid pVT736-1: evidence for replication control by antisense RNA.

Several plasmids have been described in Actinobacillus actinomycetemcomitans, a gram-negative coccobacillus. Recently, the nucleotide sequence of pVT736-1, a cryptic plasmid of A. actinomycetemcomitans VT736, was determined. This plasmid possesses all the features necessary for rolling circle replication. The present study involved a transcriptional analysis of pVT736-1. Results of Northern (RNA) blot analyses and primer extension studies indicated that the two open reading frames identified in pVT736-1 are each preceded by at least one promoter. Expression of these promoters varied with growth phase. In addition, an antisense RNA (Cop RNA) appeared to control the synthesis of the putative replication protein. To our knowledge, this is the first rolling circle replicating plasmid isolated from a gram-negative organism that has been subjected to such detailed analysis.

Aggregatibacter actinomycetemcomitans↗
PubMed1998

Replication terminator protein-based replication fork-arrest systems in various Bacillus species.

The replication terminator protein (RTP) of Bacillus subtilis interacts with its cognate DNA terminators to cause replication fork arrest, thereby ensuring that the forks approaching one another at the conclusion of a round of replication meet within a restricted terminus region. A similar situation exists in Escherichia coli, but it appears that the fork-arrest systems in these two organisms have evolved independently of one another. In the present work, RTP homologs in four species closely related to B. subtilis (B. atrophaeus, B. amyloliquefaciens, B. mojavensis, and B. vallismortis) have been identified and characterized. An RTP homolog could not be identified in another closely related species, B. licheniformis. The nucleotide and amino acid changes from B. subtilis among the four homologs are consistent with the recently established phylogenetic tree for these species. The GC contents of the rtp genes raise the possibility that these organisms arose within this branch of the tree by horizontal transfer into a common ancestor after their divergence from B. licheniformis. Only 5 amino acid residue positions were changed among the four homologs, despite an up to 17.2% change in the nucleotide sequence, a finding that highlights the importance of the precise folded structure to the functioning of RTP. The absence of any significant change in the proposed DNA-binding region of RTP emphasizes the importance of its high affinity for the DNA terminator in its functioning. By coincidence, the single change (E30K) found in the B. mojavensis RTP corresponds exactly to that purposefully introduced by others into B. subtilis RTP to implicate a crucial role for E30 in the fork-arrest mechanism. The natural occurrence of this variant is difficult to reconcile with such an implication, and it was shown directly that RTP.E30K functions normally in fork arrest in B. subtilis in vivo. Additional DNA terminators were identified in the new RTP homolog-containing strains, allowing the definition of a Bacillus terminator consensus and identification of two more terminators in the B. subtilis 168 genome sequence to bring the total to nine.

Bacillus↗