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At least 91 records · Page 5Linked to original sources
PubMed2002

Inhibition of DNA replication by berenil of bacterial plasmids containing poly(dA)-poly(dT) sequences. 2D gel analysis of replicative intermediates.

Berenil, an aromatic compound used in veterinary medicine to treat trypanosome infections in livestock, has been shown to interfere with kinetoplast DNA replication. The drug is thought to bind to the minor groove of DNA and form hydrogen bonds between opposite A/T pairs. Studies utilizing Trypanosoma cruzi, revealed that minicircle DNA, which is 60% A-T rich, and also the major component of kinetoplast DNA networks, is one of the targets for berenil. In order to better understand the mode of action of berenil and its effect on DNA replication, we have studied the effect of the drug on pBR322 derived plasmids containing poly(dA)-poly(dT) sequences. The resulting plasmids were pVL26, which contained 240 bp of poly(dA)-poly(dT) inserted at the EcoRV site of pBR322 and pKH47, which contained 100 bp of poly(dA)-poly(dT) inserted at the PvuII site of pBR322. When cultures containing all of these plasmids were exposed to berenil, plasmids pVL26 and pKH47 were found to have significantly lower yields than pBR322, with pKH47 being the most sensitive to berenil. In the present study we show that the poly(dA)-poly(dT) sequences in plasmids pVL26 and pKH47 are not very stably maintained. However, the resulting deletion mutants containing a fraction of the poly(dA)-poly(dT) sequences were still sensitive to berenil. We also analyzed by 2D agarose gel electrophoresis the progression of the replication fork through the homopolymer region in plasmid pVL26d but failed to detect a replication barrier in this region in the presence of berenil.

Base Sequence↗
PubMed1993

Participation of the bacterial membrane in DNA replication and chromosome partition.

The concept that the bacterial membrane plays an active role in the regulation of DNA replication and in segregation, or 'partition', of the bacterial chromosome at cell division was proposed in 1963. Membrane participation offered a relatively simple way to coordinate replication and partition. Some of the details of this model have been confirmed, while others have been changed. In fact, it appears that the membrane may play several distinct roles in these processes, and recent experiments have begun to identify the complexity of membrane involvement.

Journal Article↗
PubMed1996

Rifampin-induced initiation of chromosome replication in dnaR-deficient Escherichia coli cells.

The dnaR130 mutant of Escherichia coli, which was thermosensitive in initiation of chromosome replication, was capable of thermoresistant DNA synthesis in the presence of rifampin at a low concentration that allowed almost normal RNA synthesis. The DNA synthesis in the presence of the drug depended on protein synthesis at the high temperature. The protein synthesis in the dnaR-deficient cells provided a potential for thermoresistant DNA synthesis to be induced at a high dose of the drug that almost completely prevented RNA synthesis. The induced synthesis was synchronously initiated from oriC and proceeded semiconservatively toward terC. The replication depended on the dnaA function, which was essential for normal initiation of replication from oriC. The capability for drug-induced replication was abolished by certain rifampin resistance mutations in the beta subunit of RNA polymerase. Thus, the drug can induce the dnaA-dependent initiation of replication in the dnaR-deficient cells through its effect on RNA polymerase. This result implies that the dnaR product is involved in the transcription obligatory for the initiation of replication of the bacterial chromosome.

Bacterial Proteins↗
PubMed2001

The form of chromosomal DNA molecules in bacterial cells.

The circular concept of the bacterial chromosome was based initially on experiments involving conjugation mapping and autoradiographic imaging of DNA. This view was then supported by DNA fragment mapping, genome sequencing, and the analysis of linear DNA produced by a single cleavage of chromosomal DNA. A circular chromosome is also indicated by the existence of a mechanism for segregating dimeric chromosomes produced by recombination and the replication of DNA on both sides of the replication terminus. The evidence for circularity is reviewed here and found to be compatible with either a circular or a linear chromosomal DNA molecule. Moving pictures of ethidium-stained DNA revealed most chromosomal DNA as a rosette form with loops emanating from a dense node or as a network of strands lacking a node. This description applies to Escherichia coli, Agrobacterium tumefaciens, Pyrococcus endeavorii, Vibrio cholerae, and both the linear-mapping chromosome of Streptomyces lividans and its circular-mapping derivative. Networks without nodes were found for two linear-mapping Borrelia species. For the E. coli chromosome, open-form circles of various sizes were found only at extremely low frequency. The node of the rosette was reduced in size or eliminated in recA mutants, as well as by treatment with either ribonuclease, topoisomerase IV, 1 M NaCl, or lysozyme. A model is presented for the bacterial chromosome in which the DNA is compacted by many points of strand association (including recombination junctions, tangles and knots) created during the repair of DNA damage that occurs many times in each chromosome replication cycle.

Bacteria↗
PubMed2001

Evolution rates of genes on leading and lagging DNA strands.

One of the main causes of bacterial chromosome asymmetry is replication-associated mutational pressure. Different rates of nucleotide substitution accumulation on leading and lagging strands implicate qualitative and quantitative differences in the accumulation of mutations in protein coding sequences lying on different DNA strands. We show that the divergence rate of orthologs situated on leading strands is lower than the divergence rate of those situated on lagging strands. The ratio of the mutation accumulation rate for sequences lying on lagging strands to that of sequences lying on leading strands is rather stable and time-independent. The divergence rate of sequences which changed their positions, with respect to the direction of replication fork movement, is not stable-sequences which have recently changed their positions are the most prone to mutation accumulation. This effect may influence estimations of evolutionary distances between species and the topology of phylogenetic trees.

Amino Acid Substitution↗
PubMed2000

Dynamic organization of chromosomal DNA in Escherichia coli.

We have revealed the subcellular localization of different DNA segments that are located at approximately 230-kb intervals on the Escherichia coli chromosome using fluorescence in situ hybridization (FISH). The series of chromosome segments is localized within the cell in the same order as the chromosome map. The large chromosome region including oriC shows similar localization patterns, which we call the Ori domain. In addition, the localization pattern of the large segment including dif is characteristic of the replication terminus region. The segment also shows similar localization patterns, which we call the Ter domain. In newborn cells, Ori and Ter domains of the chromosome are differentially localized near opposite cell poles. Subsequently, in the B period, the Ori domain moves toward mid-cell before the initiation of replication, and the Ter domain tends to relocate at mid-cell. An inversion mutant, in which the Ter domain is located close to oriC, shows abnormal subcellular localization of ori and dif segments, resulting in frequent production of anucleate cells. These studies thus suggest that the E. coli chromosome is organized to form a compacted ring structure with the Ori and Ter domains; these domains participate in the cell cycle-dependent localization of the chromosome.

Cell Division↗
PubMed2003

Coupling the initiation of chromosome replication to cell size in Escherichia coli.

Bacterial cells change size dramatically with change in growth rate, but the ratio between cell volume and the number of copies of the origin of chromosome replication (oriC) is roughly constant at the time of initiation of DNA replication at almost all growth rates. Recent research on the inactivation of initiator protein (DnaA) and depletion of DnaA pools by the high-affinity DnaA-binding locus datA allows us to propose a simple model to explain the long-standing question of how Escherichia coli couples DNA replication to cell size.

Adenosine Triphosphate↗
PubMed1998

Conversion to bidirectional replication after unidirectional initiation from R1 plasmid origin integrated at oriC in Escherichia coli.

The cell division phenotypes of Escherichia coli with its chromosome replication driven by oriR (from plasmid R1) were examined by fluorescence microscopy and flow cytometry. Chromosome replication patterns in these strains were followed by marker frequency analyses. In one of the strains, the unidirectional oriR was integrated so that the replication fork moved clockwise from the oriC region, and bacterial growth and division were similar to those of the wild-type parent. The bacteria were able to convert the unidirectional initiation from oriR into bidirectional replication. The site for conversion of uni- to bidirectional replication seemed to be localized and could be mapped genetically within 6 min to the immediate right of the minimal oriC. Replication starting in the counterclockwise direction from the R1 replicon integrated at the same site in the opposite orientation could not be described as either bi- or unidirectional, as no single predominant origin could be discerned from the more or less flat marker frequency pattern. These strains also showed extensive filamentation, irregular nucleoid distribution and the presence of anucleate cells, indicative of segregation and division defects. Comparison among intR1 derivatives differing in the position of the integrated oriR relative to the chromosome origin suggested that the oriC sequence itself was dispensable for the conversion to bidirectionality. However, passage of the replication fork over the 6 min region to the right of oriC seemed important for the bidirectional replication pattern and normal cell division phenotype.

Cell Division↗
PubMed1983

Biosynthetic mechanism of ribulose-1,5-bisphosphate carboxylase in the purple photosynthetic bacterium, Chromatium vinosum. III. Absence of extrachromosomal DNA.

Inducible formation of ribulose-1,5-bisphosphate (RuBP) carboxylase in the cells of Chromatium vinosum under autotrophic conditions was not affected by six different inhibitors of DNA synthesis. Photosynthetic CO2 fixation and RuBP carboxylase activities were not influenced by seven reagents known to eliminate plasmids. Plasmids were not detectable by agarose gel electrophoresis employing either the cleared lysate or alkaline sodium dodecyl sulfate method, nor were they detected by ethidium bromide-CsCl density gradient centrifugation. Overall experimental results tend to indicate that plasmids are absent in the Chromatium cells and that the induction of RuBP carboxylase is presumably not regulated in the DNA replication process.

Carboxy-Lyases↗
PubMed2003

Increasing the ratio of Soj to Spo0J promotes replication initiation in Bacillus subtilis.

The ParA and ParB protein families are well conserved in bacteria. However, their functions are still unclear. In Bacillus subtilis, Soj and Spo0J are members of these two protein families, respectively. A previous report revealed that replication initiated early and asynchronously in spo0J null mutant cells, as determined by flow cytometry. In this study, we examined the cause of this promotion of replication initiation. Deletion of both the soj and spo0J genes restored the frequency of replication initiation to almost the wild-type level, suggesting that production of Soj in the absence of Spo0J leads to early and asynchronous initiation of replication. Consistent with this suggestion, overproduction of Soj in wild-type cells had the same effect on replication initiation as in the spo0J null mutant, and overproduction of both Soj and Spo0J did not. These results indicate that when the ratio of Soj to Spo0J increases, Soj interferes with tight control of replication initiation and causes early and asynchronous initiation. Whereas replication initiation also occurred significantly earlier in the two spo0J mutants, spo0J14 and spo0J17, it occurred only slightly early in the sojK16Q mutant and was delayed in the sojG12V mutant. Although Soj localized to nucleoids in the spo0J mutants, the two Soj mutant proteins were distributed throughout the cell or localized to cell poles. Thus, interestingly, the promotion of replication initiation seems to correlate with localization of Soj to nucleoids. This may suggest that Soj inhibits transcription of some cell cycle genes and leads to early and asynchronous initiation of replication. In wild-type cells Spo0J counteracts this Soj function.

Bacillus subtilis↗
PubMed1984

Replication control of IncP plasmids.

Clones of Escherichia coli with a chromosomally integrated RP4-prime plasmid were isolated and characterized. Chromosome transfer was increased about 50-fold and the Hfr still carried an autonomous plasmid indistinguishable from the original RP4-prime. This could be eliminated by pRP64 or R751, two distinguishably marked incompatible plasmids, giving rise to strains which stably retained the resistance patterns of both plasmids and which continued to transfer the chromosome at enhanced levels. In both cases, however, the copy number of the autonomous plasmid was reduced by the presence of a chromosomal RP4 such that the total number of P plasmid genomes (integrated and autonomous) remained constant. The results are consistent with the idea that copy number is controlled by diffusible inhibitors or initiators of replication.

Chromosomes, Bacterial↗