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PubMed1970

Temperature-sensitive mutants of Bacillus subtilis. I. Multiforked replication and sequential transfer of DNA by a temperature-sensitive mutant.

A temperature-sensitive mutant of Bacillus subtilis 168 was isolated. Its chromosome was found to undergo multiforked replication at normal temperature. The mutant cells then transferred chromosomes to recipient cells sequentially from the origin to the terminus of the chromosome at sublethal temperatures. Sequential transfer of the chromosome facilitated the determination of the relative positions of markers on the chromosome. Linkage between origin (adenine-16) and terminus (methionine) was demonstrated.

Adenine↗
PubMed1989

Delta dnaK52 mutants of Escherichia coli have defects in chromosome segregation and plasmid maintenance at normal growth temperatures.

Major heat shock proteins, such as the Escherichia coli DnaK protein, not only are required for cell growth after heat shock but seem to possess important functions in cellular metabolism at normal growth temperatures as well. E. coli delta dnaK52 mutants have severe cellular defects at 30 degrees C, one of which is in cell division (B. Bukau and G. C. Walker, J. Bacteriol, 171:2337-2346, 1989). Here we show that at 30 degrees C, delta dnaK52 mutants have defects in chromosome segregation and in maintenance of low-copy-number plasmids. Fluorescence microscopic analysis revealed that chromosomes were frequently lacking at peripheries of cell filaments of delta dnaK52 mutants and clustered at other locations. In other parts of the cell filaments, chromosomes were apparently normally distributed and they were also present in most of the small cells found in populations of delta dnaK52 cells. These defects might be at the level of DNA replication, since delta dnaK52 mutants have a threshold lower rate of DNA synthesis than wild-type cells. Chromosome segregation defects of delta dnaK52 mutants were also observed in an rnh dnaA mutant background, in which initiation of DNA replication is DnaA-oriC independent. We also found that low-copy-number P1 miniplasmids could not be stably maintained in delta dnaK52 mutants at 30 degrees C. delta par P1 miniplasmids that carry the P1-encoded rep functions required for their replication but lack the P1-encoded par functions required for faithful partitioning of the plasmids during cell division were also unstable in delta dnaK52 mutants. Taken together, our results indicate important, although not absolutely essential, functions for DnaK at 30 degrees C in one or more processes necessary for correct replication and/or partitioning of chromosomes and P1 miniplasmids. Furthermore, we found that P1 miniplasmids were also highly unstable in dnaJ259 mutants, indicating a role for the DnaJ heat shock protein in maintenance of these plasmids.

Cell Division↗
PubMed2005

Discovery of antagonist peptides against bacterial helicase-primase interaction in B. stearothermophilus by reverse yeast three-hybrid.

Developing small-molecule antagonists against protein-protein interactions will provide powerful tools for mechanistic/functional studies and the discovery of new antibacterials. We have developed a reverse yeast three-hybrid approach that allows high-throughput screening for antagonist peptides against essential protein-protein interactions. We have applied our methodology to the essential bacterial helicase-primase interaction in Bacillus stearothermophilus and isolated a unique antagonist peptide. This peptide binds to the primase, thus excluding the helicase and inhibiting an essential interaction in bacterial DNA replication. We provide proof of principle that our reverse yeast three-hybrid method is a powerful "one-step" screen tool for direct high-throughput antagonist peptide selection against any protein-protein interaction detectable by traditional yeast two-hybrid systems. Such peptides will provide useful "leads" for the development of new antibacterials.

Adenosine Triphosphatases↗
PubMed2001

Partitioning of the Escherichia coli chromosome: superhelicity and condensation.

Segregation in Escherichia coli, the process of separating the replicated chromosomes into daughter progeny cells, seems to start long before the duplication of the genome reaches completion. Soon after initiation in mid-cell region, the daughter oriCs rapidly move apart to fixed positions inside the cell (quarter length positions from each pole) and are anchored there by yet unknown mechanism(s). As replication proceeds, the rest of the chromosome is sequentially unwound and then refolded. At termination, the two sister chromosomes are unlinked by decatenation and separated by supercoiling and/or condensation. Muk and Seq proteins are involved in different stages of this replication-cum-partition process and thus can be categorized as important partition proteins along with topoisomerases. E. coli strains, lacking mukB or seqA functions, are defective in segregation and cell division. The nucleoids in these mutant strains exhibit altered condensation and superhelicity as can be demonstrated by sedimentation analysis and by fluorescence microscopy. As the supercoiling of an extrachromosomal element (a plasmid DNA) was also influenced by the mukB and seqA mutations we concluded that the MukB and SeqA proteins are possibly involved in maintaining the general supercoiling activity in the cell. The segregation of E. coli chromosome might therefore be predominantly driven by factors that operate by affecting the superhelicity and condensation of the nucleoid (MukB, SeqA, topoisomerases and additional unknown proteins). A picture thus emerges in which replication and partition are no longer compartmentalized into separable stages with clear gaps (S and M phases in eukaryotes) but are parallel processes that proceed concomitantly through a cell cycle continuum.

Bacterial Outer Membrane Proteins↗
PubMed1983

Role of the sfiA-dependent cell division regulation system in Escherichia coli.

Several authors have suggested that the SOS-associated (sfiA-dependent) system of division inhibition, normally induced by perturbations of DNA replication, also regulates steady-state (unperturbed) cell division. The present work shows that mean cell mass is identical in sfiA+ and sfiA mutant cultures during steady-state growth, that mass adjustment is identical after shift up, that sfiA expression is not induced by shift up, and that a sfiA mutation does not cause aberrant chromosome segregation.

Bacterial Proteins↗
PubMed1982

Primary structure of the chromosomal origins (oriC) of Enterobacter aerogenes and Klebsiella pneumoniae: comparisons and evolutionary relationships.

The nucleotide sequences of the Enterobacter aerogenes and Klebsiella pneumoniae DNA replication origins (oriC) were determined and compared with those of Escherichia coli and Salmonella typhimurium. Four interrelated, 9-base-pair repeats were identified from the conserved regions within the minimal origin. Evolutionary rates calculated from the minimal origin sequences yielded a quantitative phylogenic tree which agreed with the taxonomic classification of these genera.

Base Sequence↗
PubMed1988

Termination of DNA replication in Escherichia coli requires a trans-acting factor.

The terminus region of the Escherichia coli chromosome contains two sites that inhibit the progression of DNA replication forks. These termination sites, designated T1 and T2, are separated by 7.5 min (350 kilobases [kb]) on the genetic map and are located at the extremities of the terminus region. They demonstrate polarity (they stop replication forks traveling in one direction but not the other) and inhibit replication forks that have passed through and are about to leave the terminus. We have used deletion mutations in the terminus region to map the locations of T1 and T2 more accurately and to initiate studies on the mechanism of replication fork inhibition. We have narrowed the boundaries of T1 and T2 to 20 and 4 kb, respectively. T1 maps between kb 80 and 100 on the physical map of the terminus region (J. P. Bouché, J. Mol. Biol. 154:1-20, 1982), and T2 maps between kb 438 and 442. In addition, we report here that deletion of the region containing the T2 termination site inactivated T1. Supplying the T2 region on a plasmid restored T1 function, demonstrating that inhibition of replication at T1 requires a trans-acting factor which maps in the vicinity of termination site T2. We have called this newly identified terminus function the termination utilization substance (tus).

Chromosome Mapping↗
PubMed1991

In vitro type II binding of chromosomal DNA to membrane in Bacillus subtilis.

DNA-membrane association critical for initiation of DNA replication in Bacillus subtilis can be classified into two types. Type I is salt resistant and dependent on the initiation gene, dnaB, and type II is salt sensitive and independent of the dnaB gene. We found and sequenced two adjacent areas of type II binding within 1% of oriC on the B. subtilis chromosome.

Amino Acid Sequence↗
PubMed1997

CedA is a novel Escherichia coli protein that activates the cell division inhibited by chromosomal DNA over-replication.

We isolated and characterized a new gene related to the control of cell division regulation in Escherichia coli. At 30 degrees C, the dnaAcos mutant causes over-replication of the chromosome, and colony formation is inhibited. We found that, at this temperature, the dnaAcos cells form filaments; therefore, septum formation is inhibited. This inhibition was independent of SfiA, an inhibitor of the septum-forming protein, FtsZ. To identify factors involved in this pathway of inhibition, we isolated seven multicopy suppressors for the cold-sensitive phenotype of the dnaAcos mutant. One of these proved to be a previously unknown gene, which we named cedA. This gene encoded a 12 kDa protein and resided at 38.9min on the E. coli genome map. A multicopy supply of the cedA gene to the dnaAcos cells did not repress over-replication of the chromosome but did stimulate cell division of the host, the result being growth of cells with an abnormally elevated chromosomal copy number. Therefore, the expression level of the cedA gene seems to be important for inhibiting cell division of the dnaAcos mutant at 30 degrees C. We propose that over-replication of the chromosome activates a pathway for inhibiting cell division and that the cedA gene modulates this division control. In the dnaA+ background, cedA also seems to affect cell division.

Amino Acid Sequence↗
PubMed1980

The dnaA gene product is not required during stable chromosome replication in Escherichia coli.

Exposure of Escherichia coli dnaA strains to UV light results in a transient resumption of chromosome replication at 42 degrees C, the temperature restrictive to these mutants. Capability of dnaA mutants to replicate DNA at 42 degrees C can be stabilized, however, when either protein or RNA synthesis is inhibited 60 min after UV irradiation. DNA synthesis proceeds for several hours under these conditions. These results indicate that dnaA dependent transcription is not involved in initiation of chromosome cycles during stable DNA synthesis.

Chromosomes, Bacterial↗
PubMed1988

Identification of the DNA sequence from the E. coli terminus region that halts replication forks.

The terminus region of the E. coli chromosome contains two loci, T1 and T2, that inhibit the progress of replication forks and require the trans-acting factor tus. We have identified a 23 bp terminator signal at T1 and T2 that is within 100 bp of the sites of replication arrest. When an oligodeoxyribonucleotide containing the terminator signal was inserted into a plasmid, replication was halted only in a tus+ strain and when the terminator signal was oriented properly. We also found this terminator sequence in the terminus region of the plasmid R6K and in the origin region of RepFIIA class plasmids. In addition, we found striking similarities between the E. coli terminator signal and the terminator sequence of B. subtilis.

Base Sequence↗
PubMed1989

DNA replication in Escherichia coli mutants that lack protein HU.

DNA replication in Escherichia coli cells lacking protein HU was studied. HU has been suggested to be involved in the initiation of replication from in vitro studies. The isolated HU mutants, however, are viable under normal growth conditions (M. Wada, Y. Kano, T. Ogawa, T. Okazaki, and F. Imamoto, J. Mol. Biol. 204:581-591, 1988). Chromosomal replication in the mutants appeared to be normal with respect to bidirectional replication from oriC and to its dependence on dnaA and some other dna gene products. No significant defect was observed in DNA synthesis in vitro with a crude enzyme fraction prepared from the mutant cells. These results, along with the earlier in vitro studies, suggest that other histonelike protein(s) may substitute for HU in the initiation of replication in the mutant cells. Minichromosomes were more unstable in the mutants. In the absence of either the mioC promoter, from which transcription enters oriC, or the DnaA box (DnaA protein-binding site) just upstream of the mioC promoter, the minichromosomes were especially unstable in the HU mutant and were integrated into the chromosomal oriC region under conditions selective for the plasmid-harboring cells.

Bacterial Proteins↗
PubMed1990

Induction of the SOS response in Escherichia coli by azidothymidine and dideoxynucleosides.

A number of nucleosides with anti-human immunodeficiency virus (HIV) activity were evaluated in two colorimetric (beta-galactosidase) assays for induction of the SOS response in Escherichia coli. 3'-Azido-3'-deoxythymidine (azidothymidine; AZT), 2',3'-dideoxyadenosine (ddA), 2',3'-dideoxyguanosine (ddG), and 2',3'-dideoxyinosine (ddI) induced cell filamentation (sulA) and prophage lambda in well-agar diffusion and liquid microsuspension assays. AZT was approximately 100 times more potent than the dideoxypurine nucleosides, inducing sulA at less than 100 ng/ml. 2',3'-Dideoxythymidine (ddT) and 2',3'-dideoxy-2',3'-didehydrothymidine (D4T) induced sulA at 100 to 1,000 micrograms/ml, while 2',3'-dideoxycytidine (ddC) weakly induced prophage lambda. Activity relationships thus were AZT greater than ddA greater than or equal to ddI greater than or equal to ddG greater than ddT = D4T greater than ddC. ddA and ddI had equivalent activities in agar diffusion assays, but different activity profiles were observed in liquid microsuspension assays. The differences may be related to drug metabolism. AZT and ddA showed marginal effects in a DNA repair (preferential toxicity) assay in which E. coli WP2 and CM871 uvrA recA lexA were used. Furthermore, none of the agents was able to preferentially inhibit Bacillus subtilis M45 recA relative to wild-type strain H17. These data suggest that AZT and the dideoxynucleosides do not cause DNA lesions that are repairable by excision repair and/or error-free postreplication repair processes. Rather, the SOS response appears to be induced by DNA chain termination leading to the inhibition of DNA replication. Bacterial assays for induction of the SOS response may be useful as simple, rapid prescreens for the discovery of new anti-HIV agents. Moreover, such assays may provide an additional parameter in the evaluation of agents with demonstrated activity against HIV and other retroviruses.

Bacillus subtilis↗
PubMed1982

Kinetics of minichromosome replication in Escherichia coli B/r.

Replication control of the minichromosome pAL2 was found to differ from that of the chromosome in synchronously dividing populations of Escherichia coli B/r. Initiation of minichromosome replication took place at an increasing rate throughout synchronous growth. No coupling to initiation of chromosome replication was detected. Minichromosome replication was further examined in a dnaA5(Ts) temperature-sensitive initiation mutant. When cultures held at nonpermissive temperature (41 degrees C) for 60 min were shifted to permissive temperature (25 degrees C), initiation of both pAL2 and chromosome replication ensued in two waves spaced 25 to 35 min apart. Evidence is presented that minichromosomes terminate replication by passing slowly through a series of dimeric intermediate forms before reaching the closed circular monomeric form. The consequence of this slow passage as a rate-limiting step in the initiation reaction is discussed.

Chromosomes, Bacterial↗
PubMed1979

Isolation and characterization of dnaX and dnaY temperature-sensitive mutants of Escherichia coli.

Escherichia coli mutants with temperature-sensitive (ts) mutations in dnaX and dnaY genes have been isolated. Based on transduction by phage P1, dnaX and Y have been mapped at minutes 10.4--10.5 and 12.1, respectively, in the sequence dnaX purE dnaY. Both dna Xts36 and Yts10 are recessive to wild-type alleles present on episomes. F13 carries both dnaX+ and Y+; the shorter F210 carries dnaY+, but not X+. Lambda tranducing phages that carry dnaX+ or Y+ have been isolated, and hybrid plasmids of Col E1 and E. coli DNA from the Clarke and Carbon (1976) collection also carry portions of the dnaX purE dnaY region. Results obtained with the lambda transducing phages and the hybrid plasmids suggest that dnaX is a different gene from the previously characterized dnaZ gene, which is also near minute 10.5--The dnaXts36 mutant, after a shift to 42 degrees, stopped DNA synthesis gradually, and the total amount of DNA increased two-fold. When this mutant was shifted to 44 degrees, the rate of DNA synthesis dropped immediately and the final increment of DNA was only 10% of the initial amount. Replicative DNA synthesis in toluene-treated cells was completely inhibited at 42 degrees and was partially inhibited even at 30 degrees.--When the dnaYts10 mutant was shifted to 42 degrees, DNA synthesis gradually stopped, and the amount of DNA increased 3.6-fold. At 44 degrees, residual DNA synthesis amounted to a two-fold increase. Replicative DNA synthesis in vitro in toluene-treated cells was inactivated after 20 minutes at 42 degrees or by "preincubation" of cells at 42 degrees before toluene treatment.--The dnaX and dnaY products probably function in polymerization of DNA, although participation also in initiation cannot be excluded.

Base Sequence↗
PubMed2003

Controlled initiation of chromosomal replication in Escherichia coli requires functional Hda protein.

Regulatory inactivation of DnaA helps ensure that the Escherichia coli chromosome is replicated only once per cell cycle, through accelerated hydrolysis of active replication initiator ATP-DnaA to inactive ADP-DnaA. Analysis of deltahda strains revealed that the regulatory inactivation of DnaA component Hda is necessary for maintaining controlled initiation but not for cell growth or viability.

Adenosine Triphosphatases↗
PubMed1974

Membrane attachment of the chromosome in Bacillus subtilis mutants temperature-sensitive in DNA replication.

We have examined three mutants of Bacillussubtilis temperature sensitive in DNA initiation and one temperature sensitive in DNA elongation, in order to investigate whether these lesions can cause or can result in a detachment of the membrane-bound chromosomal region. Our results argue against any effect of the mutations examined on the association between the chromosome and the membrane.

Bacillus subtilis↗