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At least 289 records · Page 16Linked to original sources
PubMed1992

The simian virus 40 T antigen double hexamer assembles around the DNA at the replication origin.

An initial step in the replication of simian virus (SV40) DNA is the ATP-dependent formation of a double hexamer of the SV40 large tumor (T) antigen at the SV40 DNA replication origin. In the absence of DNA, T antigen assembled into hexamers in the presence of magnesium and ATP. Hexameric T antigen was stable and could be isolated by glycerol gradient centrifugation. The ATPase activities of hexameric and monomeric T antigen isolated from parallel glycerol gradients were identical. However, while monomeric T antigen was active in the ATP-dependent binding, untwisting, unwinding, and replication of SV40 origin-containing DNA, hexameric T antigen was inactive in these reactions. Isolated hexamers incubated at 37 degrees C in the presence of ATP remained intact, but dissociated into monomers when incubated at 37 degrees C in the absence of ATP. This dissociation restored the activity of these preparations in the DNA replication reaction, indicating that hexameric T antigen is not permanently inactivated but merely assembled into a nonproductive structure. We propose that the two hexamers of T antigen at the SV40 origin assemble around the DNA from monomer T antigen in solution. This complex untwists the DNA at the origin, melting specific DNA sequences. The resulting single-stranded regions may be utilized by the T antigen helicase activity to initiate DNA unwinding bidirectionally from the origin.

Adenosine Triphosphate↗
PubMed2003

Cell line-specific accumulation of the baculovirus non-hr origin of DNA replication in infected insect cells.

Successive viral passage of Spodoptera exigua multicapsid nucleopolyhedrovirus (SeMNPV) in the S. exigua cell line Se301 leads to the rapid accumulation of the non-hr origin of DNA replication (ori) as large concatemers. Passage of SeMNPV in two other S. exigua cell lines, SeUCR1 and SeIZD2109, did not show the accumulation of such concatemers. When introduced into SeUCR1 and SeIZD2109 cells, the non-hr ori concatemers generated in Se301 cells were maintained but did not increase. This suggests that the non-hr ori confers a strong selective advantage in Se301 cells, but not or to a lesser extent in the other cell lines. The cell line-specific accumulation of non-hr ori concatemers might be due to a higher intrinsic recombination frequency in Se301 cells and may reflect tissue related differences involving some host cell factor(s). Since non-hr ori concatemers in Se301 cells were more abundant in intracellular than in extracellular viral DNA preparations, episomal replication and the requirement of a minimal DNA size for packaging into nucleocapsids is hypothesized.

Animals↗
PubMed1997

Identification and analysis of a lytic-phase origin of DNA replication in human herpesvirus 7.

Human herpesvirus 7 (HHV-7) DNA sequences colinear with the HHV-6 lytic-phase origin of DNA replication (oriLyt) were amplified by PCR. Plasmid constructs containing these sequences were replicated in HHV-7-infected cord blood mononuclear cells but not in HHV-6-infected cells. In contrast, plasmids bearing HHV-6 oriLyt were replicated in both HHV-6- and HHV-7-infected cells. Finally, the minimal HHV-7 DNA element necessary for replicator activity was mapped to a 600-bp region which contains two sites with high homology to the consensus binding site for the HHV-6 origin binding protein. At least one of these binding sites was shown to be essential for replicator function of HHV-7 oriLyt.

Base Sequence↗
PubMed1998

A Mec1- and Rad53-dependent checkpoint controls late-firing origins of DNA replication.

DNA replication in eukaryotic cells initiates from many replication origins which fire throughout the S phase of the cell cycle in a predictable pattern: some origins fire early, others late. Little is known about how the initiation of DNA replication and the elongation of newly synthesized DNA strands are coordinated during S phase. Here we show that, in budding yeast, hydroxyurea, which blocks the progression of replication forks from early-firing origins, also inhibits the firing of late origins. These late origins are maintained in the initiation-competent prereplicative state for extended periods. The block to late origin firing is an active process and is defective in yeast with mutations in the rad53 and mec1 checkpoint genes, indicating that regulation of late origin firing may also be an important component of the 'intra-S-phase' checkpoint and may aid cell survival under adverse conditions.

Cell Cycle↗
PubMed1978

Origin of DNA replication in papovavirus chromatin is recognized by endogenous endonuclease.

Isolated simian virus 40 (SV40) and polyoma nucleoprotein complexes contain endonuclease that, under in vitro conditions, converts part (up to 30%) of the covalently closed superhelical DNA to full-length linear rods. The positions of the cleavage sites within the genomes of SV40 and polyoma were determined by digestion with various single-cut restriction endonucleases and subsequent agarose gel electrophoresis of the cleavage products. Both SV40 and polyoma covalently closed superhelical DNA were cleaved open at their respective origins of DNA replication (+/- 75 base pairs). The full-length linear DNA rods whose ends map adjacent to the origin of DNA replication could also be isolated by sodium dodecyl sulfate/phenol extraction both from SV40-infected permissive cells and from purified SV40 virions. These data reveal the presence of a unique structure of the papovavirus chromatin close to the initiation site of DNA replication.

Chromatin↗
PubMed1989

Cellular proteins specifically bind single- and double-stranded DNA and RNA from the initiation site of a transcript that crosses the origin of DNA replication of herpes simplex virus 1.

The small-component origins of herpes simplex virus 1 DNA synthesis are transcribed late in infection by an RNA with heterogeneous initiation sites approximately 290-360 base pairs from the origins. We report that cellular proteins react with a labeled RNA probe representing the 5' terminus of a subset of this RNA but not with the complementary strand of this RNA. The proteins form two complexes. Complex 2 was formed by all nuclear extracts tested, whereas complex 1 was invariably formed by proteins present only in nuclear extracts of mock-infected cells. Complex 1 protects a contiguous stretch of 40 nucleotides of the labeled RNA probe from nuclease degradation. Formation of complex 1 was competitively inhibited in a sequence-specific fashion by single-stranded RNA and DNA and by double-stranded RNA and DNA. The protein(s) forming complex 1 is, thus, quite distinct from known nucleic acid-binding proteins in that they recognize a specific nucleotide sequence, irrespective of the nature (single- and double-stranded RNA and DNA) of the nucleic acid. We conclude the following: (i) the proteins forming complex 1 and 2 are probably different, (ii) complex 1 is neither required throughout infection for viral replication nor able to hinder viral replication in cells in culture, and (iii) cells susceptible to infection encode one or more proteins that recognize specific sequences in single-stranded nucleic acids; either these proteins impart a compatible conformation on single-stranded nucleic acids with the conformation of the same strand in the double-stranded nucleic acid, or these proteins confer a specific, distinct conformation to both single-stranded and double-stranded nucleic acids.

Animals↗
PubMed2001

An alternative mode of translation permits production of a variant NBS1 protein from the common Nijmegen breakage syndrome allele.

Nijmegen breakage syndrome (NBS) is a rare chromosomal-instability syndrome associated with cancer predisposition, radiosensitivity and radioresistant DNA synthesis-S phase checkpoint deficiency, which results in the failure to suppress DNA replication origins following DNA damage. Approximately 90% of NBS patients are homozygous for the 657del5 allele, a truncating mutation of NBS1 that causes premature termination at codon 219. Because null mutations in MRE11 and RAD50, which encode binding partners of NBS1, are lethal in vertebrates, and mouse Nbs1-null mutants are inviable, we tested the hypothesis that the NBS1 657del5 mutation was a hypomorphic defect. We showed that NBS cells contain the predicted 26-kD amino-terminal protein fragment, NBS1p26, and a 70-kD NBS1 protein (NBS1p70) lacking the native N terminus. The NBSp26 protein is not physically associated with the MRE11 complex, whereas the p70 species is physically associated with it. NBS1p70 is produced by internal translation initiation within the NBS1 mRNA using an open reading frame generated by the 657del5 frameshift. We propose that the common NBS1 allele encodes a partially functional protein that diminishes the severity of the NBS phenotype.

Alleles↗
PubMed1983

DNA-protein interaction at the origin of DNA replication of the plasmid pSC101.

The initiation of DNA replication of the low copy number plasmid pSC101 is dependent on the dnaA initiator protein encoded by Escherichia coli. We have previously reported that the minimum essential replicon of the plasmid encodes a approximately 37.5 kd protein and that the protein is necessary along with host-encoded proteins for the replication of the plasmid chromosome. In this communication we show that the plasmid-encoded protein has sequence-specific DNA-binding activity. The protein binds cooperatively to the replication origin of pSC101. Using chemical and enzymatic probes we have determined the contact points of the protein with the DNA and the precise domain of the replication origin recognized by the 37.5 kd protein. The specificity of the DNA-protein interaction would suggest that the 37.5 kd protein may possibly function by guiding the replisome to the correct DNA sequence on the chromosome of pSC101.

Bacterial Proteins↗
PubMed1994

A putative non-hr origin of DNA replication in the HindIII-K fragment of Autographa californica multiple nucleocapsid nuclear polyhedrosis virus.

In addition to the seven known homologous regions (hrs) of Autographa californica multiple nucleocapsid polyhedrosis virus (AcMNPV) the HindIII-K fragment was also found to carry a putative ori, although this fragment does not contain an hr. Deletion analysis showed that this ori contains several segments essential for its activity and other 'auxiliary' sequences that enhance the ori activity. Sequence analysis identified several structures often found in other viral replication oris, such as palindromes and other repeated motifs. Although most of the auxiliary sequences of this ori were found to be deleted in the Bombyx mori nucleocapsid polyhedrosis virus genome, the essential part of this ori, containing the palindromes and the A/T-rich region, was retained. This and the fact that after prolonged serial passage of AcMNPV large replicating DNA molecules are found in which repeated sequences derived from the HindIII-K fragment accumulate are consistent with this region being a putative origin of AcMNPV DNA replication.

Animals↗
PubMed1997

Identification and functional analysis of a non-hr origin of DNA replication in the genome of Spodoptera exigua multicapsid nucleopolyhedrovirus.

The genome of Spodoptera exigua multicapsid nucleopolyhedrovirus (SeMNPV) was screened for the presence of putative origins of DNA replication (oris). Using a transient DNA replication assay, several fragments were identified that underwent SeMNPV-dependent DNA replication in Spodoptera frugiperda cells (Sf-AE-21). Preliminary sequence data revealed the presence of multiple copies of homologous repeats (hrs). Restriction fragment Xbal-F2 showed a distinct sequence reminiscent of Autographa californica and Orgyla pseudotsugata MNPV (AcMNPV and OpMNPV) non-hr oris. Deletion analysis of this fragment indicated that the essential sequences of this putative non-hr ori mapped within a region of 800 bp. Sequence analysis of this region showed a unique distribution of six different (im)-perfect palindromes, several polyadenylation motifs and the occurrence of multiple direct repeats. No sequence homology or similarities to other reported baculovirus oris were detected. The spatial and modular distribution of these motifs are similar to those of the non-hr oris of AcMNPV and OpMNPV. Comparison of baculovirus non-hr and consensus eukaryotic oris revealed no consensus ori but indicated that each of the non-hrs studied so far is unique. From the structural similarity, however, it was concluded that the SeMNPV Xbal-F2 ori represents a baculovirus non-hr type ori. In addition, evidence is provided that SeMNPV renders more specificity to baculovirus DNA replication than AcMNPV.

Animals↗
PubMed1985

Mutagenesis of a herpes simplex virus origin of DNA replication and its effect on viral interference.

Supercoiled plasmid molecules containing cloned copies of a DNA fragment which includes a functional herpes simplex virus type 1 origin of DNA replication were cleaved preferentially at two positions within the viral insert by nuclease S1. Plasmids with molecular linker insertions at these sites were constructed, and analysis of two representative plasmids demonstrated the presence of palindromic DNA sequences at the preferred cleavage positions. One of these palindromic sequences occurred within a 90 bp region in which the cis-acting sequences essential for viral origin function had previously been located. Insertion of a linker at this position abolished origin activity, demonstrating an essential role for sequences within the palindrome in the initiation of DNA synthesis. In transfection assays, plasmids containing a functional viral origin of DNA replication markedly interfered with the infectivity of non-defective viral DNA even in the absence of viral encapsidation signals. Inactivation of the origin greatly reduced this effect on DNA infectivity, suggesting that viral interference may be mediated by a mechanism involving the replicative machinery.

Base Sequence↗
PubMed1995

E1 recognition sequences in the bovine papillomavirus type 1 origin of DNA replication: interaction between half sites of the inverted repeats.

The E1 protein encoded by bovine papillomavirus type 1 (BPV-1) is required for viral DNA replication, and it binds site specifically to an A/T-rich palindromic sequence within the viral origin of replication. The protein is targeted to this site through cooperative interactions and binding with the virus-encoded E2 protein. To explore the nature of the E1 binding site, we inserted a series of homologous DNA linkers at the center of dyad symmetry within the E1 recognition palindrome. The effects of these modifications indicated that the E1 recognition palindrome can be separated into functional half sites. The series of insertions manifest a phasing relationship with respect to the wild-type BPV-1 genome in that greater biological activity was measured when full integral turns of the DNA helix separated the palindrome than when the separations were half-turns. This phasing pattern of activity was observed to occur in a variety of biological phenotypes, including transformation efficiency, stable plasmid copy number in cell lines established from pooled foci, and transient replication of full-length viral genomes. For replication reporter constructs where E1 and E2 are supplied in trans by the respective expression vectors, distance between the half sites seems to play a major role, yet the phasing relationships are measurable. DNase I protection studies showed that E1 bound very poorly to the construct containing a 5-bp linker, and binding was close to the wild-type level for the 10-bp insertion, consistent with a requirement for a phasing function between half sites with a modulus of 10 bp. Binding to the 15- and 20-bp insertion mutants was weak, but only for the 20-bp insertions was protection over both halves of the palindrome measurable. As it had been previously reported that the 18-bp palindrome contains sufficient nucleotide sequence information for E1 binding, we speculate that a minimal E1 recognition motif is presented in each half site. A comparison between this sequence and that of an upstream region that also binds E1 (the E2RE1 region) revealed a common pentanucleotide motif of APyAAPy. Mutants with substitutions of the ATAAT elements within E2RE1 failed to bind E1 protein. We present models for how repeats of the pentanucleotide sequence may coordinate E1 binding at the dyad symmetry axis of the origin and compare the DNA sequence organization of BPV-1 with those of the simian virus 40 and polyomaviruses at their origins of DNA replication.

Base Sequence↗
PubMedDate not supplied

Sequence-induced DNA curvature at the bacteriophage lambda origin of replication.

DNA replication in bacteriophage lambda begins at a unique origin between residues 39,000 and 39,200 of the lambda genome. This segment of DNA serves a dual function since it also lies within the coding sequence of the lambda replication initiator protein O which binds origin DNA. The lambda origin sequence contains four 19-base-pair (bp) segments (iterons) which have dyad symmetry, followed by a 40-bp A + T-rich zone of highly asymmetrical base composition. It was noted earlier that lambda origin DNA exhibits an anomalous electrophoretic mobility on gels; that is, the length of DNA as determined by DNA sequencing is approximately 20% less than is predicted from electrophoretic mobility. Recent studies of kinetoplast minicircle DNA (K-DNA) from the protozoan Leishmania tarentolae have led to the proposal that sequence-induced DNA curvature could account for such electrophoretic anomalies by alteration of the shape of the DNA molecule. We now present evidence that the lambda origin contains a static curve.

Bacteriophage lambda↗
PubMed2005

Mutational analysis of the direct tandem repeat sequences at the origin of DNA replication of porcine circovirus type 1.

Mutational analysis was conducted to investigate the role of the nucleotide sequences flanking the stem-loop palindromic structure at the origin of DNA replication of porcine circovirus type 1 (PCV1) with respect to self-DNA replication and progeny virus generation. The results demonstrated that the A-rich sequence to the left of the palindrome is non-essential for virus replication. Although a set of four hexanucleotide (H) sequences to the right of the palindrome (organized in two tandem repeats: the proximal H1/H2 and the distal H3/H4) are binding sites for the viral Rep-associated proteins in vitro, only a proximal tandem (H/H or h-like/H) is essential for PCV1 DNA replication. In the presence of H1/H2, mutations engineered into H3/H4 were preserved in the progeny viruses. Mutations engineered into H1/H2 were invariably deleted so that the downstream H3/H4 was placed next to the palindrome. Viral genome with mutations engineered into both H1/H2 and H3/H4 underwent extensive nucleotide reorganization to yield progeny viruses containing either H3/H4, h-like/H4, or h-like/H3/H4 sequences.

Animals↗
PubMed1992

DNA damage-inducible origins of DNA replication in Escherichia coli.

Upon induction of the SOS response in Escherichia coli, the mode of initiation of DNA replication is altered such that it can occur in the absence of normally required protein synthesis. This type of DNA replication has been termed induced stable DNA replication (iSDR). We examined the origin usage during iSDR and found that the initiation of iSDR occurs primarily in the oriC and terC regions of the chromosome in a manner completely independent of transcription, translation and DnaA protein. Minichromosomes (oriC plasmids) pOC23 and pOC81 were induced to replicate in the absence of DnaA protein and transcription after SOS induction. The results localized one of the iSDR origin activities in a 596 bp region which includes the minimal oriC.

Bacterial Proteins↗
PubMed1999

The interaction of herpes simplex type 1 virus origin-binding protein (UL9 protein) with Box I, the high affinity element of the viral origin of DNA replication.

The herpes simplex type 1 (HSV-1) origin binding protein, the UL9 protein, exists in solution as a homodimer of 94-kDa monomers. It binds to Box I, the high affinity element of the HSV-1 origin, Oris, as a dimer. The UL9 protein also binds the HSV-1 single strand DNA-binding protein, ICP8. Photocross-linking studies have shown that although the UL9 protein binds Box I as a dimer, only one of the two monomers contacts Box I. It is this form of the UL9 homodimer that upon interaction with ICP8, promotes the unwinding of Box I coupled to the hydrolysis of ATP to ADP and Pi. Photocross-linking studies have also shown that the amount of UL9 protein that interacts with Box I is reduced by its interaction with ICP8. Antibody directed against the C-terminal ten amino acids of the UL9 protein inhibits its Box I unwinding activity, consistent with the requirement for interaction of the C terminus of the UL9 protein with ICP8. Inhibition by the antibody is enhanced when the UL9 protein is first bound to Box I, suggesting that the C terminus of the UL9 protein undergoes a conformational change upon binding Box I.

Animals↗
PubMed1990

Identification of an origin of bidirectional DNA replication in mammalian chromosomes.

Mechanistically, an origin of bidirectional DNA replication (OBR) can be defined by the transition from discontinuous to continuous DNA synthesis that must occur on each template strand at the site where replication forks originate. This results from synthesis of Okazaki fragments predominantly on the retrograde arms of forks. We have identified these transitions at a specific site within a 0.45 kb sequence approximately 17 kb downstream from the 3' end of the dihydrofolate reductase gene in Chinese hamster ovary chromosomes. At least 80% of the replication forks in a 27 kb region emanated from this OBR. Thus, initiation of DNA replication in mammalian chromosomes uses the same replication fork mechanism previously described in a variety of prokaryotic and eukaryotic genomes, suggesting that mammalian chromosomes also utilize specific cis-acting sequences as origins of DNA replication.

Animals↗
PubMed1983

DNA sequences which support activities of the bacteriophage phi X174 gene A protein.

The DNA sequence of 30 nucleotides which surrounds the origin of viral strand DNA replication is highly conserved amongst the icosahedral single-stranded DNA bacteriophages. The A gene of these phages encodes a protein which is required for initiation and termination of viral strand DNA synthesis and acts as a nicking-closing activity specifically within this 30-nucleotide sequence. A system of purified Escherichia coli host proteins and phi X174 gene A protein has been developed which specifically replicates in vitro the viral strand of phi X174 from RF (replicative form) I template DNA and yields single-stranded circular DNA products (RF leads to SS(c) DNA replication system). Recombinant plasmids carrying inserts derived from phage phi X174 or G4 DNA which range in length from 49 to 1175 base pairs and contain the 30-nucleotide conserved sequence have been shown to support phi X A protein-dependent DNA synthesis in vitro in this replication system. We report here that insertion of the 30-nucleotide sequence alone into pBR322 allows the resulting recombinant plasmids to support phi X A protein-dependent in vitro DNA synthesis as efficiently as phi X174 template DNA in the RF leads to SS(c) replication system. The 30-nucleotide sequence functions as a fully wild type DNA replication origin as determined by the rate of DNA synthesis and the structure of resulting DNA products. Furthermore, the DNA sequence requirements for nicking of RF I DNA by the phi X A protein and for supporting replication origin function have been partially separated. Homology to positions 1, 29, and 30 of the 30-nucleotide conserved sequence are not required for cleavage of RF I DNA by the A protein; homology to position 1 but not 29 or 30 is required for efficient DNA replication.

Bacteriophage phi X 174↗