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At least 775 records · Page 43Linked to original sources
PubMed2000

Inhibition of chromosome replication in Mycobacterium smegmatis: effect of the rpmH-dnaA promoter region.

In a previous study a functional mycobacterial origin of replication, oriC, was isolated on a plasmid. However, it was found that origin function was inhibited by the presence of the adjacent dnaA gene or its regulatory region, so that plasmids containing both of these regions next to the origin did not yield transformants. This inhibition could be due either to overexpression of dnaA on a plasmid being toxic, the transcription of dnaA into the downstream origin topologically inhibiting its function, or to the DnaA boxes upstream of dnaA somehow interacting with the DnaA boxes in the origin to prevent its function. To distinguish between these possibilities, plasmids were constructed lacking different parts of the dnaA gene: the promoter, the DnaA boxes, or both. Additionally, the putative dnaA promoter region was replaced by mycobacterial sequences that exhibit weaker or null promoter activity. The results indicate that the rpmH-dnaA promoter region, but not the DnaA boxes, is the principal cause of the incompatibility observed and suggest that this region could be playing a role in the inhibition of chromosome replication.

Bacterial Proteins↗
PubMed2005

Bacillus subtilis YabA is involved in determining the timing and synchrony of replication initiation.

It is shown here by flow cytometry that Bacillus subtilis YabA negatively regulates the timing of replication initiation. When the level of YabA was reduced, replication began at a decreased cell mass and when the level was increased, initiation was delayed. Synchrony of replication initiation was also disrupted at low levels of YabA. Yfp-YabA localized as foci in cells. Since YabA was reported to interact with DnaN (beta subunit of DNA polymerase III), co-localization of Yfp-YabA with the polymerase was examined using a Cfp fusion with DnaX (tau subunit of DNA polymerase III). It is reported that YabA appears to localize at the replication forks only at a late stage of DNA replication.

Bacillus subtilis↗
PubMed1984

Affinity of two different regions of the chromosome to the outer membrane of Escherichia coli.

It was found that DNA associated with the outer membrane of Escherichia coli K-12 is enriched for two different regions of the chromosome, which are both on the 5.9-megadalton EcoRI fragment containing the replication origin, oriC. One region overlaps oriC, whereas the other region was found to be associated with a 1-megadalton EcoRI-BamHI fragment located within the atp operon.

Base Sequence↗
PubMed1989

Chromosomal location and evolutionary rate variation in enterobacterial genes.

The basal rate of DNA sequence evolution in enterobacteria, as seen in the extent of divergence between Escherichia coli and Salmonella typhimurium, varies greatly among genes, even when only "silent" sites are considered. The degree of divergence is clearly related to the level of gene expression, reflecting constraints on synonymous codon choice. However, where this constraint is weak, among genes not expressed at high levels, divergence is also related to the chromosomal location of the gene; it appears that genes furthest away from oriC, the origin of replication, have a mutation rate approximately two times that of genes near oriC.

Bias↗
PubMed1975

Strains of Escherichia coli diploid for the chromosomal origin of DNA replication.

F' strains of E. coli have been isolated which are merodiploid for various chromosomal segments between 66 and 78 minutes. Strains diploid for the chromosomal DNA between the genes bgl and mtl grow slowly, have a reduced DNA/mass and an increased cell size. These properties could result if the chromosomal replication origin and a second, extrachromosomal, copy of the origin (located in this case on the F') were to compete for a substance required to initiate replication. We therefore suggest that these strains are diploid for the chromosomal origin of replication and that, therefore, the origin is located between bgl and mtl, that is between 71 and 73 minutes on the E. coli chromosome.

Bacterial Proteins↗
PubMed1969

The negative control mechanism for E. coli DNA replication.

Evidence is presented to show that the initiation of DNA replication in E. coli 555-7 requires synthesis of a protein whose production is correlated with total protein synthesis. Once replication is initiated, however, reinitiation will occur if all further protein synthesis is prevented; a small amount of protein synthesis is sufficient to prevent this unregulated reinitiation. This shows that the initiation of DNA replication is under negative control. A mechanism for the control of DNA replication is proposed; in this mechanism a replication repressor is synthesized periodically, while an antirepressor protein is synthesized continuously. Derepression of initiation results after sufficient accumulation of the antirepressor protein, and repression is re-established by repressor synthesis after the initiation of replication.

Bacterial Proteins↗
PubMed1972

Structure and replication of chromosomes in competent cells of Bacillus subtilis.

Competent cultures of Bacillus subtilis 168 were fractionated on gradients of Renografin-76 to obtain a population enriched for competent cells. The cells in this fraction contained two nuclear bodies. The competent cell fraction synthesized deoxyribonucleic acid and ribonucleic acid at reduced rates compared to the noncompetent cell fraction and appeared to divide synchronously upon incubation. The state of the chromosome in competent cells was determined by density transfer experiments and marker frequency analyses. The results are consistent with a competent cell possessing two, or a multiple of two, chromosomes, one complete and the other partially duplicated. During subsequent growth the partially completed chromosome replicates preferentially.

Bacillus subtilis↗
PubMed1970

Synchronous reinitiation of chromosome replication in E. coli B-r after nalidixic acid treatment.

Nalidixic acid has been used to interrupt DNA synthesis in exponentially growing cultures of E. coli B/r. Within three minutes after removal of the nalidixic acid block, premature rounds of chromosome replication are initiated at the normal origin of vegetative DNA synthesis. The new growing forks traverse the chromosome in about 40 minutes, the normal replication time. These rounds continue synchronously into the second generation after removal of the nalidixic acid. These phenomena are similar in some respect to the premature initiation of chromosomal replication observed after thymine starvation or after release of thermo-sensitive DNA synthesis mutants from the restrictive temperature that prevents DNA synthesis.

Chromosome Mapping↗
PubMed1982

Regulation of DNA synthesis and capacity for initiation in DNA temperature sensitive mutants of Escherichia coli. II. Requirements for acquisition and expression of initiation capacity.

This paper deals with the conditions that are necessary for the acquisition and expression of initiation potential in dnaA temperature sensitive mutants after they have been held for periods of time at nonpermissive temperature and then returned to permissive temperature in the presence of chloramphenicol. The following conditions were found to be essential: (1) 40-60 min at nonpermissive temperature during which time protein synthesis must occur; this period must be followed by (2) return to permissive temperature under which conditions active dnaA product is present, and (3) protein synthesis must be blocked during the first 10-20 min immediately after return to permissive temperature (when initiation takes place). In order for expression of the initiation potential (4) the chloramphenicol must be removed to allow the progression of the replication forks which had been initiated to occur and (5) the recA+ phenotype appears to be required for acquisition or expression (or both) of the initiation potential.

Bacterial Proteins↗
PubMed1989

DNA----DNA, and DNA----RNA----protein: orchestration by a single complex operon.

In Escherichia coli, the workhorse of molecular biology, a single operon is involved in the replication, transcription and translation of genetic information. This operon is controlled in a complex manner involving multiple cis-acting regulatory sequences and trans-acting regulatory proteins. It interacts with global regulatory networks by mechanisms which are presently being dissected.

Amino Acid Sequence↗
PubMed1998

Replication of lambda plasmid DNA in the Escherichia coli cell cycle.

The Cro repressor autoregulatory loop has long been considered the main regulatory process in controlling lambda plasmid replication initiation in Escherichia coli. However, we found recently that lambda plasmids can be maintained at a constant copy number in the absence of Cro function. Here we demonstrate that shortly after inactivation of the Cro repressor, the synthesis of lambda plasmid DNA increases significantly but is then stabilized at a level similar to that observed in the presence of the Cro function. We found that replication initiation of lambda plasmids carrying a functional cro gene proceeds randomly in the host cell cycle, but in the absence of Cro function the replication initiation of lambda plasmid DNA appears to be cell cycle dependent. The host DnaA protein appears to be at least one of the factors involved in the cell-cycle-specific control of lambda cro- plasmid replication. Therefore, it seems that the lambda cro- plasmid may serve as an amazingly simple model for studies on the regulation of DNA replication in the cell cycle.

Bacterial Proteins↗
PubMed1975

Revision of the linkage map of Bacillus subtilis 168: indications for circularity of the chromosome.

A revision of the linkage map of the Bacillus subtilis 168 chromosome has been undertaken with the use of the generalized transducing phage PBS1. The mapping of four new markers (narB1, mtlB1, aroI906, and tre-12) has allowed a determination of the relative orientation of the purB-dal segment and its linkage with the lin markers. The chromosomal segment comprised between the sacQ36 and gtaA12 markers has been linked with the narA1, ctrA1, and sacA321 markers. The recA1 marker has been mapped relative to the thyA and citB17 markers. Indications of linkage have been found between the tre-12 and catA markers and the aroG932 and sacQ36 markers. According to these results, a circular genetic map of the chromosome of B. subtilis 168 is presented. Taken together, the transduction data and the order of marker replication determined by Harford in the accompanying paper support strongly the hypothesis of a symmetrical and fully bidirectional mode of replication for the B. subtilis 168 chromosome.

Bacillus subtilis↗
PubMed2002

oriC region and replication termination site, dif, of the Xanthomonas campestris pv. campestris 17 chromosome.

A 13-kb DNA fragment containing oriC and the flanking genes thdF, orf900, yidC, rnpA, rpmH, oriC, dnaA, dnaN, recF, and gyrB was cloned from the gram-negative plant pathogen Xanthomonas campestris pv. campestris 17. These genes are conserved in order with other eubacterial oriC genes and code for proteins that share high degrees of identity with their homologues, except for orf900, which has a homologue only in Xylella fastidiosa. The dnaA/dnaN intergenic region (273 bp) identified to be the minimal oriC region responsible for autonomous replication has 10 pure AT clusters of four to seven bases and only three consensus DnaA boxes. These findings are in disagreement with the notion that typical oriCs contain four or more DnaA boxes located upstream of the dnaA gene. The X. campestris pv. campestris 17 attB site required for site-specific integration of cloned fragments from filamentous phage phiLf replicative form DNA was identified to be a dif site on the basis of similarities in nucleotide sequence and function with the Escherichia coli dif site required for chromosome dimer resolution and whose deletion causes filamentation of the cells. The oriC and dif sites were located at 12:00 and 6:00, respectively, on the circular X. campestris pv. campestris 17 chromosome map, similar to the locations found for E. coli sites. Computer searches revealed the presence of both the dif site and XerC/XerD recombinase homologues in 16 of the 42 fully sequenced eubacterial genomes, but eight of the dif sites are located far away from the 6:00 point instead of being placed opposite the cognate oriC. The differences in the relative position suggest that mechanisms different from that of E. coli may participate in the control of chromosome replication.

Amino Acid Sequence↗
PubMed1984

Impediment to replication fork movement in the terminus region of the Bacillus subtilis chromosome.

The terminus regions of the chromosomes of three strains of Bacillus subtilis 168 were radioactively labelled by supplying [3H]thymine towards the end of a round of replication. These strains lacked or contained the prophage SP beta c2. Following restriction endonuclease digestion of the purified DNA and fluorography, an SP beta c2-related perturbation of the terminus-labelling profile was observed, which was completely consistent with the previously suggested existence of an impediment to replication fork movement (terC) within a BamHI 24.8 X 10(3) base fragment (Weiss & Wake, 1983). The present data suggest that terC is located within the 11.4 X 10(3) base BamHI + SalI double-digest portion of this BamHI fragment.

Bacillus subtilis↗
PubMed1987

Proofreading by DNA polymerase III of Escherichia coli depends on cooperative interaction of the polymerase and exonuclease subunits.

The polymerase subunit (alpha) of Escherichia coli DNA polymerase III holoenzyme and the 3'----5' exonuclease subunit (epsilon) are each less active separately than together in the holoenzyme core (an assembly of alpha, epsilon, and theta subunits). In a complex formed from purified alpha and epsilon subunits, polymerase activity increased 2-fold, and that of the 3'----5' exonuclease increased 10- to 80-fold. The alpha-epsilon complex contains one each of the subunits as does the core. Stimulation of 3'----5' exonuclease activity is due mainly to a greatly increased affinity of the epsilon subunit for the 3'-hydroxyl terminus, resulting from DNA binding by the alpha subunit. Proofreading in the course of DNA synthesis by the alpha-epsilon complex was indistinguishable from that of the core. These findings identify the participation of the alpha subunit in proofreading by polymerase III holoenzyme and suggest that the fidelity of DNA replication may be influenced by the relative levels of the alpha and epsilon subunits in the cell.

Bacterial Proteins↗