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PubMed1983

Evolution of antibiotic resistance plasmids in Neisseria gonorrhoeae and Haemophilus species.

The emergence of beta-lactamase producing strains of Haemophilus influenzae and Neisseria gonorrhoeae has required fundamental changes in the antimicrobial therapy of disease caused by these organisms. Ampicillin resistance in both organisms is caused by plasmid mediated production of TEM beta-lactamase. This enzyme is specified by a sequence of mol. wt 3.2 X 10(6) which is capable of inserting itself at multiple sites in DNA replicons without the requirement for significant base sequence homology between donor and recipient replicon. Further, it does so without requirement for conventional recombination enzymes. Analysis of beta-lactamase specifying plasmids of H. influenzae show that they generally have a molecular mass in the order of 30 X 10(6) and contain the complete TnA sequence. They are conjugative but are incapable of mobilizing smaller beta-lactamase plasmids. Previous studies have presented evidence suggesting that these plasmids may have evolved by insertion of the TnA sequence (perhaps introduced from enteric bacteria) into a phenotypically cryptic plasmid of mol. wt 27 X 10(6) resident in rare strains of H. influenzae. In this study, we review data showing a high degree of homology between the small (3--7 X 10(6) mol. wt), nonconjugative beta-lactamase specifying plasmids of N. gonorrhoeae, H. parainfluenzae and H. ducreyl and present new evidence that cryptic plasmids highly homologous to the beta-lactamase plasmids are present in many strains of H. parainfluenzae. This suggests that the small beta-lactamase specifying plasmids of H. parainfluenzae, H. ducreyi and N. gonorrhoeae may have arisen by insertion of TnA into phenotypically cryptic plasmids present in H. parainfluenzae.

Ampicillin↗
PubMed1984

Inhibition of semiconservative DNA synthesis in ICR 2A frog cells by pyrimidine dimers and nondimer photoproducts induced by ultraviolet radiation.

DNA synthesis was examined in ultraviolet (uv)-irradiated ICR 2A frog cells in which either pyrimidine dimers or nondimer photoproducts represented the major class of DNA lesions. Dimers were induced by exposure of cells to 254 nm uv, while nondimer photoproducts were induced by irradiation of cells with uv produced by a fluorescent sunlamp (FSL) that was filtered through 48A Mylar (removes wavelengths less than 310 nm). The FSL-irradiated cultures were also treated with photoreactivating light (PRL) which removed most of the small number of dimers induced by the irradiation, leaving a relatively pure population of nondimer photoproducts. In addition, cells were exposed to 60Co gamma rays. The cultures were pulse-labeled and the size distribution of the DNA synthesized was estimated using both sucrose gradient sedimentation and alkaline step elution. Using either of these techniques, it was found that the presence of dimers resulted in a reduction principally in the synthesis of high molecular weight (MW) DNA. In contrast, nondimer photoproducts caused a strong inhibition in the synthesis of low MW DNA, as was also observed in gamma-irradiated cells. Hence the induction of pyrimidine dimers in DNA mainly affected the elongation of replicons, whereas nondimer lesions primarily caused an inhibition of replicon initiation.

Animals↗
PubMed1983

[Autonomous replication of plasmid pBR322 containing a mitochondrial DNA fragment of animal origin in the cells of bacteria mutant for DNA-polymerase I].

Escherichia coli K-12 p108(polA6), p3478(polA1) and KS55(polA12 ts) strains were transformed by recombinant DNA consisting of pBR322 plasmid and BamHI fragment A of rat liver mtDNA containing the origin. For all the strains tested, it was shown that the cells containing hybrid molecules were able to grow on the selective medium under the conditions when pBR322 replicon is not functional. The existence of mtDNA insertion in hybrid molecules was confirmed by electrophoresis and colony hybridization with the 125I-mtDNA. Thus, the ability of a vector containing plasmid replicon and the mitochondrial origin to replicate under the conditions nonpermissive for stable replication of plasmid DNA alone, was demonstrated for the first time.

Animals↗
PubMed1982

[Plasmid DNA of Salmonella derby].

S. derby K 89 isolated from sick children have been found to contain plasmids which determine the resistance of these organisms to penicillin and chloramphenicol. 3 types of plasmid DNA with molecular weights of 40. 12 and 8 megadaltons (Md) have been detected by electrophoretic analysis. The dissociation of the large plasmid (40 Md) into 3 independent replicons has been observed. The circular, covalently closed forms of the DNA cointegrate and its constituent replicons have been identified by electron microscopy. In S. derby K 89 grown in broth prepared from dried meat concentrate the loss of these plasmids is observed, and the culture thus becomes sensitive to penicillin and chloramphenicol. This suggests that dried meat concentrate contains some factor capable of eliminating the plasmids.

Chloramphenicol↗
PubMed1980

DNA replication in Physarum polycephalum. Analysis of replicating nuclear DNA using the electron microscope.

DNA has been isolated from Physarum polycephalum nuclei obtained from macroplasmodia at different stages in the mitotic cycle, and examined using the electron microscope. Putative replicating structures were identified, the majority of which contained clusters of 2--37 'microbubbles', each microbubble corresponding to a segment of DNA 100--5000 nucleotides long. The microbubble-containing structures are unstable in the formamide hyperphase used to prepare specimens for electron microscopy, possibly due to dissociation of newly replicated nascent DNA fragments from the parental DNA template during manipulation. The microbubble clusters present in early S-phase DNA extent over segments averaging 16400 nucleotide residues, and are separated by non-replicated regions of DNA varying in length from 10000 to 50000 nucleotides. It is suggested that each microbubble cluster may represent a 'replicon', and that many 'replicons' in Physarum DNA may contain several sites for the initiation of DNA synthesis that are active during S-phase.

Cell Nucleus↗
PubMed1976

Structural evolution of bacterial plasmids: role of translocating genetic elements and DNA sequence insertions.

Recent evidence suggests that plasmids have evolved by site-specific recombinational events involving translocation and insertion of discretely defined DNA segments. The role of translocating genetic elements and repeated DNA sequences in the formation and structural evolution of bacterial plasmids, and in the control of plasmid gene expression, is the subject of this brief review. Insertion sequence (IS) regions are discrete segments of DNA that are known to cause strongly polar mutations in the genes of Escherichia coli and several bacteriophages as a consequence of their insertion into bacterial or phage genomes. Recent investigations have identified three separate kinds of IS segments on plasmids, and have indicated that such regions may have a role in 1) site-specific reversible dissociation of antibiotic resistance plasmids into their component segments, 2) recombination of certain plasmids with the bacterial chromosome, and 3) translocation of segments of plasmid DNA onto other replicons, or onto different sites of the same replicon. In addition, such DNA sequences, which may be repeated on plasmid genomes in either direct or reverse orientation, are involved in the control of plasmid gene expression. Inverted repeats other than the genetically characterized IS segments also appear to be involved in recA-independent, recombination and translocation of plasmid DNA segments. These inverted repeats contain palindromic nucleotide sequences on each strand of DNA and are detectable as hairpin-loop structures by electron microscope heteroduplex analysis. Such palindromes resemble the recognition sites for restriction endonucleases, some of which are encoded by plasmids, suggesting that similar endonucleolytic enzymes may be involved in the translocation of plasmid DNA segments.

Base Sequence↗
PubMed1976

Transformation of Escherichia coli by R404 factor DNA and properties of the transformants.

Three r-determinants (Cb Cm Cf) out of eight present in R404 factor were transferred in transformation of Escherichia coli by the plasmid DNA isolated from minicells. The r-determinants acquired in this way formed the replicon tr404-1 and were untransferable by conjugation unless another self-transmissible plasmid was present in recipient. The evidences are presented in support of hypothesis that the transfer events consist in infection of transformant cells with sex factor, recombination between tr404-1 replicon and the sex factor and finally transfer of the new formed structure to the host cells of the sex factor.

Anti-Bacterial Agents↗
PubMed1994

Megabase pair deletions in mutant mammalian cells following exposure to amsacrine, an inhibitor of DNA topoisomerase II.

Amsacrine, [4'-(9-acridinylamino)-methanesulfon-m-auisidide], belongs to the class of cancer chemotherapeutic agents that target DNA topoisomerase II. We show that, over its cytotoxic range, amsacrine is a potent mutagen of the S1 phenotype in the AL (human x hamster) hybrid cell line. By contrast, amsacrine induction of the HPRT- phenotype in AL cells is at least two decades less frequent and is not concentration dependent. Such differential mutation frequencies are hypothesized to reflect the concomitant loss of essential genes neighboring the hprt locus. It may be that some amsacrine cytotoxicity is due to the inactivation of essential genes by large deletions. The AL mutation system is well suited for the detection and mapping of mutations which are large deletions because its MIC1 locus, which controls the expression of the selectable cell surface antigen S1, is on a single human chromosome. This human chromosome 11 is in addition to the genome of the Chinese hamster ovary cell and is basically nonessential. Since there are no sister human chromosomes in AL cells, deletions which extend beyond the MIC1 locus may be conveniently and unambiguously mapped. We have detected the presence or absence of 9 different chromosome 11 markers in 48 S1- mutants cloned from amsacrine-treated cultures. We find that almost all (92%) of the mutants have deletions of at least 1.5-2 megabase pairs in length. The distribution of marker loss frequencies flanking the MIC1 locus does not appear symmetric with respect to distance from that locus. We speculate that amsacrine-induced deletions are mediated by a series of subunit exchanges between overlapping topoisomerase II dimers at the bases of replicons or larger chromosomal structures such as replicon clusters or chromosome minibands.

Amsacrine↗
PubMed1993

Critical steps for induction of chromosomal aberrations in CHO cells heated in S phase.

The following four effects on DNA replication are observed in cells heated in S phase of the cell cycle: (1) inhibition of replicon initiation, (2) delay in DNA chain elongation into multicluster-sized molecules > 160S, (3) reduction in fork displacement rate, and (4) increase in single-stranded regions in replicating DNA. Since cells heated in S phase manifest chromosomal aberrations when they enter metaphase, whereas cells heated in G1 do not, we attempted to determine if the effects on DNA replication are critical for the induction of chromosomal aberrations by studying these same effects during DNA replication when synchronous CHO cells had been heated (10 min at 45.5 degrees C) in G1 phase. Following a heat-induced G1 block (12 h), we found previously that when the cells entered S phase, replicon initiation was functional and chain elongation into multicluster-sized molecules > 160S was delayed but completed during S phase. In the present study, we find that the fork displacement rate was near normal and that there was no increase in single-stranded DNA. Additionally, an increase in excess nuclear protein induced in the heated G1-phase cells returns to a normal level by about 12 h, just prior to when the cells enter S phase. Since the excess nuclear protein remains for many hours in heated S-phase cells, we hypothesize that the excess nuclear protein is responsible for the drastic reduction in the fork displacement rate and the associated increase in single-stranded DNA. Furthermore, we hypothesize that this persistent increase in single-stranded DNA during replication is a critical step for the induction of chromosomal aberrations in heated S-phase cells. Consistent with this hypothesis, we observed that aphidicolin (1-2 micrograms/ml) treatment of S-phase cells for 13-16 h, which results in a twofold increase in single-stranded DNA during the inhibition of DNA synthesis, also induces chromosomal aberrations. Possibly, endogenous endonucleolytic attack occurs opposite these sites of single-stranded DNA, thus creating double-strand breaks which either can remain unrepaired or are misrepaired to account for the chromatid breaks and exchanges, respectively, observed as cells complete their cell cycle and enter metaphase.

Animals↗
PubMed1997

[A mobile genetic element on a Bordetella pertussis chromosome stimulates cointegrate formation in Escherichia coli strains].

This work continues a series of reports devoted to the study of a repeated sequence isolated from the Bordetella pertussis chromosome (RSBP--Repeated Sequence of Bordetella Pertussis). The RSBP was earlier demonstrated to have a structure similar to IS elements and exhibit some properties of mobile genetic elements. The results of this work demonstrate the ability of this novel genetic element to stimulate the formation of cointegrates between independent replicons. We have studied the structure of five cointegrates formed by integration of a resident RSBP-containing plasmid into three different sites of a recipient replicon. The studied cointegrates are capable of resolution with the release of a resident plasmid independent of the host cell RecA function.

Bordetella pertussis↗
PubMed1998

p53-dependent signaling sustains DNA replication and enhances clonogenic survival in 254 nm ultraviolet-irradiated human fibroblasts.

The cyclin-dependent kinase inhibitor p21(WAF1/CIP1/SDI1/CAP20) exists in normal human fibroblasts in a quaternary complex with a cyclin, a cyclin-dependent kinase, and proliferating cell nuclear antigen. A model was proposed in which, during p53-mediated suppression of cell proliferation following treatment with 254 nm UV radiation (UVC), the enhanced expression of p21 might inhibit DNA replication by virtue of its interactions with proliferating cell nuclear antigen. To test this model, we examined the mechanisms of inhibition of DNA replication in diploid human fibroblasts that express human papillomavirus type 16 E6, which inactivates p53. E6-expressing cells were defective in G1 checkpoint responses of induction of p21 and G1 arrest after ionizing radiation-induced damage to DNA. Accordingly, E6-expressing cells were resistant to inactivation of single-cell colony formation by ionizing radiation. E6 cells also displayed normal S-phase checkpoint responses of inhibition and recovery of replicon initiation following exposure to ionizing radiation and normal ability to bypass pyrimidine dimers during DNA replication soon after UVC irradiation (i.e., postreplication repair). However, DNA replication 6 h after UVC exposure was significantly inhibited in E6 cells in comparison to isogenic controls. This failure to maintain DNA replication in S-phase cells was associated with enhanced sensitivity to inactivation of single-cell colony formation by UVC. These results indicate that the p53-induced p21 pathway is not involved in the immediate S-phase responses to radiation-induced DNA damage of inhibition of replicon initiation and translesion bypass. However, our results demonstrate that p53 and, conceivably, p21 contribute to the ability of normal human fibroblasts to sustain DNA replication activity and form colonies following UVC irradiation.

Cell Line↗
PubMed1991

Mapping replication origins in yeast chromosomes.

The replicon hypothesis, first proposed in 1963 by Jacob and Brenner, states that DNA replication is controlled at sites called origins. Replication origins have been well studied in prokaryotes. However, the study of eukaryotic chromosomal origins has lagged behind, because until recently there has been no method for reliably determining the identity and location of origins from eukaryotic chromosomes. Here, we review a technique we developed with the yeast Saccharomyces cerevisiae that allows both the mapping of replication origins and an assessment of their activity. Two-dimensional agarose gel electrophoresis and Southern hybridization with total genomic DNA are used to determine whether a particular restriction fragment acquires the branched structure diagnostic of replication initiation. The technique has been used to localize origins in yeast chromosomes and assess their initiation efficiency. In some cases, origin activation is dependent upon the surrounding context. The technique is also being applied to a variety of eukaryotic organisms.

Blotting, Southern↗
PubMed1993

SV40 DNA replication intermediates: analysis of drugs which target mammalian DNA replication.

The simian virus 40 chromosome, a model for the mammalian replicon, is a uniquely powerful system for the study of drugs and treatments which target enzymes of the mammalian replication apparatus. High resolution gel electrophoretic analysis of normal and aberrant viral replication intermediates can be used effectively to understand the molecular events of replication failure. These events include breakage of replication forks, aberrant topoisomerase action, failure to separate daughter chromosomes, protein-DNA crosslinking, single and double strand DNA breakage, alterations in topology and inactivation of replication intermediates. The SV40 replication system can also be used to study the recombinational events which often follow drug-induced replication failure.

Animals↗
PubMed2002

Bioprocess applications of a Sindbis virus-based temperature-inducible expression system.

The production and study of toxic proteins requires inducible expression systems with low basal level expression and high inducibility. Here, we describe bioprocess applications of the pCytTS temperature-regulatable Sindbis virus replicon-based expression system. We used green fluorescent protein as a marker protein to optimize the selection of stable transfected clones with increased expression levels. Using the optimized protocol, clones were constructed that produced the growth-inhibiting, anti-viral protein interferon beta (beta-IFN). Selected clones were analyzed for temperature-dependent beta-IFN production in adherent and suspension cultures in serum free medium. Specific expression levels were around 1.0 x 10(5) IU/10(6) cells/day (0.5 microg/10(6) cells/day) in suspension cultures and over 1.5 x 10(6) IU/mL/day (7.5 microg/mL/day) in hollow fiber reactors using adherent cells. Hexahistidine-tagged beta-IFN purified from T-flask cultures was highly glycosylated and showed high specific activity. beta-IFN mRNA amplified by the viral replicase for 10 days did not show an accumulation of mutations. These data suggest the applicability of the pCytTS-inducible expression system for the production of high-quality glycoproteins in different reactors.

Animals↗
PubMed2006

Broad host range vectors for stable genomic library construction.

We describe the construction of 36 stable vectors for genomic library construction in gram-negative species. These vectors contain the pBBR1 replicon that has been shown to stably replicate in every gram-negative species tested. The plasmids also contain bidirectional, rho-independent transcriptional terminators flanking the multiple cloning site, which allows for greater insert stability, and thus, greater genomic representation. Each vector varies in its antibiotic resistance cassette, mobilization function, and promoter used to express insert sequences. These vectors should prove useful in the screening of highly representational genomic libraries in a broad variety of gram-negative species.

Cloning, Molecular↗
PubMed2005

A Markov model approach shows a large variation in the length of S phase in MCF-7 breast cancer cells.

BACKGROUND: The potential doubling time of a tumor has been suggested to be a measurement of tumor aggressiveness; therefore, it is of interest to find reliable methods to estimate this time. Because of variability in length of the various cell cycle phases, stochastic modeling of the cell cycle might be a suitable approach. METHODS: The relative movement curve and the DNA synthesis time were estimated by using local polynomial regression methods. Further, the rate of nucleotide incorporation was estimated by using a Markov pure birth process with one absorbing state to model the progression of the DNA distribution through S phase. RESULTS: An estimate of the DNA synthesis time, with confidence intervals, was obtained from the relative movement curve. The Markov approach provided an estimate of the distribution of the time to complete S phase given the initial distribution. Using the Markov approach we also made an estimate of the mean number of active replicons during S phase. CONCLUSIONS: A Markov pure birth process has shown to be useful to model the progression of cells through S phase and to increase knowledge about the variability in the length of S phase and a large variation is shown.

Analysis of Variance↗
PubMed1998

Leptospira genomics.

The bacterial species Leptospira interrogans (sensu stricto) has a complex genome containing two circular chromosomal replicons. Comparative analysis of the larger chromosome reveals a fluid genetic organization with many large rearrangements differentiating two closely related strains. In the present study new genes were identified by partial sequence analysis of randomly cloned fragments of L. interrogans DNA. These genes were localized in regions of the genome by nucleic acid hybridization with DNA fragments separated by pulsed-field gel electrophoresis. The resulting genetic maps provide improved resolution for each strain and provide evidence for additional chromosomal rearrangements. Insertion elements may be involved in recombination events, as several are near regions of the chromosome that have undergone rearrangement.

Chromosome Mapping↗
PubMed2005

Pulsed-field gel electrophoresis to study the diversity of whole-genome organization in the genus Ochrobactrum.

The alpha-proteobacterial genus Ochrobactrum groups together organisms that display varied life-styles, such as free-living bacteria, members of rhizosphere and soil, nitrogen-fixing bacteria in plant nodules, xenobiotic-degrading bacteria, colonizers of nematodes and insects, and opportunistic human pathogens. The genomes of nine strains of Ochrobactrum anthropi and eight strains of Ochrobactrum intermedium were analyzed by pulsed-field gel electrophoresis of the whole genome and of I-CeuI digestion fragments. All isolates and type strains of O. anthropi and O. intermedium possessed two high-molecular-weight circular replicons identified as two independent chromosomes on the basis of 16S rDNA hybridization. The genome of the type strain of Ochrobactrum tritici, Ochrobactrum grignonense, and Ochrobactrum gallinifaecis also contained two circular chromosomes. The megaplasmid content was highly variable even among strains in the same species, leading to whole-genome sizes that ranged from 5.060 to 8.300 Mbp and from 4.690 to 7.680 Mbp for O. anthropi and O. intermedium, respectively. This exceptional level of genomic diversity could be related to the adaptability of Ochrobactrum spp. to various ecological niches.

Chromosomes, Bacterial↗