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At least 19 recordsLinked to original sources

Quantitative replicon analysis of DNA synthesis in cancer-prone conditions and the defects in Bloom's syndrome.

A quantitative method of replicon analysis of DNA fibre autoradiographs has been used to study the relationship between mean rate of DNA chain growth (R) and distance between adjacent replicons (ID) in fibroblasts from cancer-prone conditions. Results are expressed in terms of the mean linear regression R = delta +(K.ID)10-2. When replicon behaviour was examined in cells from patients with ataxia telangiectasia, basal cell naevus and Bloom's syndromes grown at high density after 48 h in culture, no significant differences could be found in replicon behaviour between these syndromes and normal cultures. However when Bloom's cells were grown at low density and examined 24 h earlier, the mean rate of chain growth R was reduced compared to normal cells at the same density. Both cell types at high densities at 24 h showed equal but lower R values than at 48 h after plating the cultures. The lower rate of chain growth in Bloom's was accompanied by a longer S-period and cell cycle. Studies of cell proliferation kinetics using consecutive mitoses after bromodeoxyuridine (BUdR) incorporation and harlequin banding showed that Bloom's cells at low cell density require a longer period to recover a normal cell cycle length after plating than do normal cells at the same density. Plating densities and using conditioned media shorten the recovery period in Bloom's cells, and when foetal calf serum/MEM is replaced by human AB serum/McCoy 5a medium as the growth media, cell cycle behaviour of low density Bloom's and normal cells are equal at a much earlier time. It is concluded that the slow rate of DNA chain growth in Bloom's cells is an artefact introduced by culture conditions and also may be present in normal cells at an earlier period. The behaviour of replicons during this recovery period appears to be similar in Bloom's and normal cells except for the time lag. As recovery proceeds, the DNA chain growth in the associated replicon pairs recover progressively. This alters both the mean R value from 0.4 to 0.8 micron/min, the slope of the regression K from less than 1.0 to approximately 1.0 while the distance between initiation sites (ID) remains constant throughout. Pretreatment of all cultures with fluorodeoxyuridine (FUdR) produced the same differential effect on release from DNA synthesis inhibition, that is a similar increase in the activation of normally inactive replicons and a slightly slower rate of chain growth over all replicons. No evidence of a substance released by Bloom's cells in culture capable of increasing the sister-chromatid frequency in normal cells could be found. Since SCE frequencies were found to increase with fixation time after BUdR introduction it is concluded that some of the reported changes could be due to differences in cell cycle kinetics brought about by the different media conditions.

Autoradiography

[Nature of the compatible inheritance of hybrid plasmid pAS8 and its deletion mutants with replicon ColE1].

Hybrid plasmid pAS8, that consists of RP4 and ColE1 replicons, is incompatible with RP4 but co-exists with ColE1 replicon. The deletion mutants of pAS8, that replicates under the control of ColE1 replicon only, are incompatible with ColE1 derivatives, although the copy number of pAS8 and its deletion mutants in the cell is the same (1-3 per the chromosome). Incompatibility effect of plasmids is expressed in a sharp decrease in transformant's yield during selection of incoming and resident plasmids markers. In this case incompatibility is a very fast process, that leads to the elimination of resident or incoming plasmid just before plating on the selective medium. On the base of negative control theory, the repressors yield, synthesized in the presence of 1-3 copies of the deletion mutant is enough for the expression of ColE1-specific incompatibility. This ColE1 incompatibility is probably connected with the functional activity of ColE1 replicon. When ColE1 factor replicates under the control of RP4 replicon the expression of ColE1-specific incompatibility does not occur. Possibly, the incompatibility effect takes place when pAS8 deletion mutants cause the synthesis of ColE1-specific repressor. Also, the replicons of ColE1 may competein the membrane attachment site.

Bacteriocin Plasmids

Inhibition of DNA replicon initiation by 4-nitroquinoline 1-oxide, adriamycin, and ethyleneimine.

The effects of three widely differing chemical carcinogens, 4-nitroquinoline 1-oxide, Adriamycin, and ethyleneimine, on DNA replication were studied by pulse labeling of DNA with [3H]thymidine and sedimentation analysis with alkaline sucrose gradients. At doses that reduced the rate of DNA synthesis to 30 to 60% of control values, only ethyleneimine produced damage that resulted in lower molecular weights of parental DNA. All three chemicals inhibited replicon initiation, but to differing extents. Inhibition of replicon initiation was the first clearly identified effect of 4-nitroquinoline 1-oxide and was the main cause of inhibition of DNA synthesis. Ethyleneimine caused severe inhibition of replicon initiation, but blocks to chain elongation also contributed significantly to the inhibition of overall DNA synthesis. Adriamycin affected replicon initiation to a small but significant extent; the primary cause of inhibition of DNA synthesis by this drug was a slowing of the rate of chain elongation. These results indicate that inhibition of replicon initiation is an important mechanism for the action of DNA-damaging agents in mammalian cells and strengthen the concept that control of DNA replication depends on the structural integrity of a chromosomal subunit that consists of several replicons.

4-Nitroquinoline-1-oxide

Replicon sizes in mammalian cells as estimated by an x-ray plus bromodeoxyuridine photolysis method.

A new method is described for estimating replicon sizes in mammalian cells. Cultures were pulse labeled with [3H]thymidine ([3H]TdR) and bromodeoxyuridine (BrdUrd) for up to 1 h. The lengths of the resulting labeled regions of DNA, Lobs, were estimated by a technique wherein the change in molecular weight of nascent DNA strands, induced by 313 nm light, is measured by velocity sedimentation in alkaline sucrose gradients. If cells are exposed to 1,000 rads of X-rays immediately before pulse labeling, initiation of replicon operation is blocked, although chain elongation proceeds almost normally. Under these conditions Lobs continues to increase only until operating replicons have completed their replication. This value for Lobs then remains constant as long as the block to initiation remains and represents an estimate for the average size of replicons operating in the cells before X-irradiation. For human diploid fibroblasts and human HeLa cells this estimated average size is approximately 17 micron, whereas for Chinese hamster ovary cells, the average replicon size is about 42 micron.

Animals

The organization of repeated nucleotide sequences in the replicons of mammalian DNA.

Chinese hamster ovary cells were irradiated with 100-5,000 rads of X-rays and inhibition of the initiation of replicons after irradiation was demonstrated by analyzing nascent DNA sedimented in alkaline sucrose gradients. The renaturation kinetics of DNA synthesized during 60 min of incubation after irradiation was compared with that of DNA synthesized during the 60 min after sham irradiation and with that of parental DNA. Nascent DNA from cells whose replicon initiation was inhibited renatured faster than nascent DNA from control cells in the COt range of repeated nucleotide sequences, suggesting that regions of the replicon not close to origins are enriched in repeated sequences and that regions close to origins are enriched in unique sequences. A class of repeated nucleotide sequences may be involved in the regulation of replicon initiation.

Base Sequence

DNA replication in Physarum polycephalum: bidirectional replication of DNA within replicons.

The direction of replication of DNA within replicons of Physarum polycephalum was studied by pulse-labelling with 5-bromouracil-deoxyriboside (BrdUrd) and 3H-adenosine deoxyriboside (dAdo), followed by ultraviolet- (UV) -photolysis and analysis of molecular weights of single strand DNA fragments on alkaline sucrose gradients. Newly made DNA within replicons at all stages of completion is split in two equal halves upon UV irradiation when BrdUrd was given at the time of initiation of DNA synthesis. This shows that replication within replicons of Physarum polycephalum starts at an origin located in the center of each unit, proceeding bidirectionally from this origin.

Bromodeoxyuridine

Isolation and characterization of the minimal fragment required for autonomous replication ("basic replicon") of a copy mutant (pKN102) of the antibiotic resistance factor R1.

The mini plasmids deriving from pKN102, a copy mutant of the antibiotic resistance factor R1drd-19 of E. coli, share a common DNA sequence of 2.6 kb, which carries the minimal functions for autonomous replication. By cloning of two PstI fragments of this region it could be demonstrated that the "basic replicon" is a DNA segment not larger than 1.8 kb, which carries the orgin of replication and the genetic information for at least two proteins. Protein F (NW=11.000 dalton) seems to be synthesed in larger amounts in minicells of E. coli than protein C (20.000). Plasmids containing this isolated replicon of R1 are completely compatible with the parental plasmid R1drd-19.

Anti-Bacterial Agents

Replication control in a composite plasmid constructed by in vitro linkage of two distinct replicons.

Although it carries two competent replication systems, a composite plasmid formed in vitro by linkage of the complete ColE1 and pSC101 plasmid replicons at their unique EcoRI endonuclease cleavage sites normally uses only the replication origin and functions of the ColE1 component. Restriction of ColE1 replication functions by DNA polymerase I deprivation results, however, in exclusive use of the pSC101 replication origin. When using the ColE1 replication system the composite plasmid is nevertheless incompatible with both the parent replicons. This suggests that a trans-dominant gene product is involved in plasmid incompatibility and supports negative control rather than positive control models for regulation of the initiation of DNA replication.

DNA Replication

Transition of Staphylococcus aureus tetracycline resistance plasmid pT181 from independent multicopy replicon to predominantly integrated chromosomal element over 65 years.

Mobile genetic elements (MGEs), including plasmids, phages and genome islands, are major sources of bacterial genetic diversity. The small plasmid pT181 confers tetracycline resistance in bacterial pathogen Staphylococcus aureus via an efflux pump, TetK. pT181 was one of the earliest sequenced S. aureus plasmids, and has been isolated in both clinical and livestock-associated strains for decades, both as an independent replicon and integrated in the chromosome as part of staphylococcal cassette chromosome mec (SCCmec). Bacterial genome analysis tools and high-quality sequences with metadata are publicly available, but these resources remain underleveraged for examining historical data, especially when studying the spread of MGEs across a species and over time. Using publicly available reads and metadata, we explored the evolution of pT181 over almost seven decades of samples to identify temporal trends in sequence evolution, copy number changes, and spread across S. aureus and beyond. pT181 was prevalent across S. aureus (found in 9.5% of 83,366 genomes tested), with a conserved sequence outside of three hypervariable regions. The history of pT181 since 1954 is characterized by spread across strains, significant variation in plasmid copy number of the independent replicon, and increasing frequency of integration of the plasmid into the S. aureus chromosome. We have identified multiple chromosomal integration locations of the plasmid, including outside of the previously characterized SCCmec. We find that pT181 has been transferred across staphylococcaceae and into a Gram-negative species. The repeated integration of pT181 into the chromosome may indicate co-evolution of the plasmid and the host, potentially to facilitate increased antibiotic resistance.

Journal Article

Transposition of a deoxyribonucleic acid sequence encoding trimethoprim and streptomycin resistances from R483 to other replicons.

R483, a plasmid of the Ialpha incompatibility group, contained a deoxyribonucleic acid (DNA) sequence encoding resistance to trimethoprim (TpR) and streptomycin (SmR) that could be transposed to other replicons, i.e., to the Escherichia coli chromosome and to related and unrelated plasmids. Each transposition resulted in the acquisition by the recipient replicon of a segment of DNA of about 9 X 10(6) daltons, both resistance genes, but never the colicin Ia or pilus genes of R483. Transposition took place at a single chromosomal site between dnaA and ilv and did not suppress the DnaA phenotype, in contrast to integration of the whole R483 plasmid. The chromosome, having received the transposition, could secondarily act as a transposition donor to another plasmid. Such a plasmid was indistinguishable from one having received a direct transposition from R483. TpR SmR transposition was very site specific and did not require a functional recA+ gene. We postulate that the TpR SmR segment of R483 is a transposon (TnC) with specific boundary sequences.

Base Sequence

[Replicon size and rate of DNA replication in the macronucleus of Tetrahymena pyriformis].

The size of replication units (or replicons) measured in Tetrahymena pyriformis GL macronuclear DNA reaches 20--30 microns, according to the two independent methods: DNA fiber autoradiography, and alkaline isokinetic sucrose gradient centrifugation. The synthesis of new DNA fragments--replicons and their subsequent assembly are separated by time intervals (30 min). The rate of DNA synthesis for one fork averaged 0.6--0.7 microns/min. These data were obtained for cells of cultures being both in the expotential phase of growth, and those synchronized by starvation-refeeding. The generation time of T. pyriformis cells, calculated by the increase of the part of labeled nuclei, is almost 2 hours; the synthesis lasts 1 hour. Total amount of replication units in polyploid (polygenomic) Tetrahymena macronucleus is about 3000. Their initiation during S-period is presumably asynchronous.

Animals

Inhibition of DNA synthesis in mammalian cells by daunomycin. Preferential inhibition of replicon initiation at low concentrations.

The effect of the intercalating agent daunomycin on DNA synthesis was studied in cultured bovine liver cells. At low daunomycin concentrations (1 and 2 muM) the rate of [3H]thymidine incorporation decreased progressively with the duration of exposure to the inhibitor. This was accompanied by a shift of nascent DNA intermediates of replicon size to higher sedimentation values on sucrose gradients, indicating that daunomycin preferentially affects the initiation of replicating units, both in asynchronous and synchronized cells. At high daunomycin concentrations (12 muM) the rate of chain growth was also markedly reduced. This was indicated by a rapid and nearly complete cessation of the [3H]thymidine incorporation and an accumulation of nascent DNA intermediates of low molecular weight. These observations are discussed in relation to a pre-fork mode of DNA synthesis.

Animals

The stable carriage of two TnA units on a single replicon.

Bacterial plasmids which contain a copy on TnA are refactory to the uptake of a second by transposition. However plasmids containing two such copies can be constructed by in vitro recombination techniques. Some plasmids containing two copies of TnA have been obtained by conventional transposition, but in all cases they arose by the virtually simultaneous insertion of both units into a replicon that carried no TnA. All stable plamids containing two copies of TnA carried the transposons in opposite orientation.

DNA Replication

Inhibition of initiation of HeLa cell replicons by methyl methanesulfonate.

Methyl methanesulfonate (MMS) in the culture medium inhibits the rate of DNA synthesis in HeLa cells in a dose-dependent manner. By using short (5 min) incubations with [3H]thymidine and analyzing the newly made DNA by velocity sedimentation on alkaline sucrose gradients, we found that the first affect of MMS on DNA replication, at 0.5 h after treatment, was inhibition of initiation of replicons. Recovery from this effect seemed to have begun by 2 3/4 h after treatment. The second effect of MMS, which was evident at 2 h after treatment, was to slow or block chain elongation.

Centrifugation, Density Gradient

Mutational analysis of the simian virus 40 replicon: pseudorevertants of mutants with a defective replication origin.

The circular genome of simian virus 40 is a model mammalian replicon, containing a unique origin of replication (ori) and coding for a protein (SV40 T antigen) known to be involved in initiation of viral DNA replication and to bind in vitro to the origin region. Mutations within the ori sequence lead to defective viral DNA replication and the formation of small viral plaques after infection of a cell monolayer. Second-site revertants (pseudorevertants) of ori mutants were isolated by random local mutagenesis of mutant DNA followed by transfection of cultured cells and the selection of large plaques. In each case, reversion of the plaque phenotype was associated with an increased rate of viral DNA replication. The second-site mutations that suppressed the replication defects were localized by in vitro recombination or marker rescue experiments to the gene for T antigen. Their map positions differ from those of previously described T antigen mutants, possibly reflecting a specific ori-binding domain of T antigen. From these results we infer that T antigen interacts with the ori signal during virus development as it does in vitro and that this interaction regulates the rate of viral DNA replication.

Antigens, Neoplasm

Method for the isolation of the replication region of a bacterial replicon: construction of a mini-F'kn plasmid.

A purified fragment of deoxyribonucleic acid (DNA) that determines resistance to kanamycin and is incapable of self-replication was used to select a self-replicating fragment from an EcoRI endonuclease digest of the sex factor F'lac. This F'lac fragment, exhibiting a molecular weight of 6 X 10(6), carries the genes essential for maintenance of the F replicon in Escherichia coli cells. The constructed mini-F'km plasmid also retains the incompatibility properties of the parent F'lac plasmid. Large amounts of the kanamycin resistance fragment of a molecular weight of 4.5 X 10(6) with an EcoRI-cleaved, self-replicating derivative of colicinogenic plasmid E1 that has a molecular weight of 2.2 X 10(6), The recombinant plasmid is able to replicate extensively in E. coli in medium containing chloramphenicol, and, therefore, large quantities of this plasmid DNA can be obtained. The substantial difference in size between the two fragments in the recombinant plasmid greatly facilitates their separation by preparative agarose gel electrophoresis.

Chloramphenicol