Effect of p-Fluorophenylalanine on Chromosome Replication in Escherichia coli

The effect of p-fluorophenylalanine (FPA) on deoxyribonucleic acid (DNA) synthesis and chromosome replication was studied in a thymine-requiring mutant of Escherichia coli. The rate and extent of chromosome replication were followed by labeling the DNA with isotopic thymine and a density marker, bromouracil. The DNA was extracted and analyzed by CsCl gradient centrifugation. The block in chromosome replication caused by high concentrations of FPA occurred at the same point on the chromosome as that caused by amino acid starvation. In a random culture, DNA in cells treated with FPA replicated only slightly slower than the DNA from cells that were not exposed to the analogue. In cultures which had been previously starved for thymine, however, the DNA from the cells treated with FPA showed a marked decrease in the rate and extent of replication. It was concluded that the E. coli cell is most sensitive to FPA when a new cycle of chromosome replication is being initiated at the beginning of the chromosome.     

Initiation of Deoxyribonucleic Acid Synthesis After Thymine Starvation of Bacillus subtilis

Evidence for premature initiation of deoxyribonucleic acid (DNA) replication after thymine starvation of Bacillus subtilis W23T(-) is presented, based on (i) increase in the number of ade(+) relative to met(+) transformants yielded by the DNA isolated from cultures after starvation (the ade(-) marker being near the origin of replication, whereas met(-) is close to the terminus), and (ii) increase in both the initial rate and final level of tritiated thymine incorporation in the presence of chloramphenicol after release from starvation. The marker ratio data agree quantitatively with the hypothesis that the initiation is induced only on one arm of each chromosome which was replicating prior to starvation.     

Inititation and termination of chromosome replication in Escherichia coli subjected to amino acid starvation.

Initiation and termination of chromosome replication in an Escherichia coli auxotroph subjected to amino acid starvation were examined by following the incorporation of [3H]thymidine into the EcoRI restriction fragments of the chromosome. The pattern of incorporation observed upon restoration of the amino acid showed that starvation blocks the process of initiation prior to deoxyribonucleic acid synthesis within any significant portion of the EcoRI fragment which contains the origin of replication, oriC. In this experiment, no incorporation of [3H]thymidine into EcoRI fragments from the terminus of replication was observed, nor was it found when a dnaC initiation mutant was used to prevent incorporation at the origin which might have obscured labeling of terminus fragments. Thus amino acid starvation does not appear to block replication forks shortly before termination of replication. Attempted synchronization of replication initiation by including a period of thymine starvation subsequent to the amino acid starvation led to simultaneous incorporation of [3H]-thymidine into all EcoRI fragments within the 240-kilobase region that surrounds oriC. It is shown that the thymine starvation step allowed initiation and a variable, but limited, amount of replication to occur.     

Development of Competence in Thymine-starved Bacillus subtilis with Chromosomes Arrested at the Terminus

Tryptophan- and thymine-requiring cells of Bacillus subtilis, emerging from an amino acid starvation treatment which causes arrest of the chromosomes at the terminus, were not transformable. During subsequent incubation in a thymineless medium supplemented with amino acids, the cultures developed competence while retaining chromosome arrest. The competent subpopulation apparently shares the synchronous chromosome arrest of the bulk population. This was shown by different methods. The principal method was marker frequency analysis of the deoxyribonucleic acid extracted from a population enriched for competent cells by a column-chromatographic method. It is concluded that development of the competent state can occur in nondividing cells, and that the presence of a replication fork actively engaged in synthesis of deoxyribonucleic acid is not required for the development of this state.     

Rate stimulation of deoxyribonucleic acid synthesis after inhibition.

The degree to which the rate of deoxyribonucleic acid synthesis in thy- cultures of Escherichia coli is stimulated after a period of thymine starvation is shown to be a function of the concentration of thymine present as well as of the culture doubling time. Inhibition of deoxyribonucleic acid synthesis by nalidixic acid yields comparable results. Periods of thymine starvation exceeding one doubling time appear to cause an irreversible inactivation of a fraction of the replication forks in the culture.     

Genetic Mapping in Bacillus subtilis by 5-Bromouracil Sensitization to Ultraviolet Inactivation of Transforming Activities

A new method for chromosome mapping of Bacillus subtilis Marburg is presented which is based on the sensitization to ultraviolet irradiation of transforming deoxyribonucleic acid that has incorporated 5-bromouracil instead of thymine. Deoxyribonucleic acid was extracted at intervals from the outgrowing spores of a thymine-requiring mutant incubated with 5-bromodeoxyuridine and subjected to a definite dose of ultraviolet irradiation. The residual activities of various genetic markers were assayed by transformation. The marker activity of deoxyribonucleic acid that had incorporated 5-bromodeoxyuridine was approximately 10 times as sensitive to ultraviolet irradiation as that of normal deoxyribonucleic acid. The markers proximal to the replication origin were sensitized at earlier times of outgrowth than distal markers. The chromosome replication in outgrowing spores was sufficiently synchronous and allowed the definite determination of when a marker became sensitized by incorporation of 5-bromodeoxyuridine. The time, designated "sensitization time," was estimated by plotting the logarithmic values of relative residual activities versus incubation times. The map constructed with sensitization times as a measurement showed good agreement with those constructed by other methods. The replication of the chromosome under the described conditions appeared to occur in the following marker order: (purA, hisA)-(purB)-(thr, pyrA)-(metC)-(leuA)-(lys, trpC, metB).     

Anucleate cell production and surface extension in a temperature-sensitive chromosome initiation mutant of Bacillus subtilis.

At 45 C, in a temperature-sensitive initiation mutant (TsB134) of Bacillus subtilis 168 Thy- tryp-, growing in a glucose-arginine minimal medium, chromosome completion occurred over a period of 80 to 90 min, after which there was no further nuclear division. Normal symmetrical cell divisions continued for a generation afterwards, so that nuclei were segregated into separate cells. During this period asymmetric divisions started to occur. Septa appeared at 25 to 30% from one end of the cell, giving a small anucleate cell and a larger nucleate cell. During inhibition of deoxyribonucleic acid (DNA) synthesis by thymine starvation under the restrictive conditions, asymmetrical division also occurred until there was approximately one nucleus per cell (about one generation time). Asymmetric division, giving anucleate cells, then occurred. Similar results were obtained when DNA synthesis was inhibited by nalidixic acid. After 3 h at 45 C, the rate of anucleate cell production in the presence and absence of thymine was constant at one division per 85 min per chromosome terminus present when DNA synthesis stopped. In the absence of DNA synthesis (during thymine starvation) at 35 C, growth in cell length was linear (i.e., the rate was constant), but at 45 C during thymine starvation the rate gradually increased by more than twofold. It is suggested that this was due to the establishment of new sites of growth associated with anucleate cell production. In the presence of thymine at 45 C, the rate of length extension increased by more than fourfold, which it is suggested was caused by the appearance of new growth zones as a result of chromosome termination and a contribution associated with anucleate cell production. If the mutant was incubated at 45 C for 90 min, both in the presence and absence of thymine, then anucleate cell formation could continue on restoration to 35 C in the absence of thymine...     

Bi-Directional Chromosomal Replication in Salmonella typhimurium

Transducing frequencies of phage P22 lysates prepared from Salmonella typhimurium exponential cultures in minimal and nutrient broth media were compared. The assumption is that cells grown in a minimal medium will have one replication fork per replication unit, but cells in nutrient broth will have multiple replication forks; therefore, the frequency of genetic markers near the origin of replication will be higher in the nutrient broth culture. Analysis of transduction showed a gradient of marker frequencies from the highest (the cysG-ilv region) to the lowest (purE-trpB region) in both clockwise and counter clockwise directions. This supports our previous observation that chromosome replication proceeds bidirectionally from the origin between cysG (109 min on S. typhimurium map) and ilv (122 min) to a terminus in purE-trpB region (20 to 53 min). Since this method avoids possible artifacts of other methods, the results are assumed to reflect the sequence of chromosome replication in exponentially growing cells. Evidence for the existence of multiple replication forks in nutrient broth-grown cells was supported by the following: (i) the marker frequency data fitted the assumption of multiple replication fork formation; (ii) residual deoxyribonucleic acid increase after inhibition of protein synthesis to complete a round of chromosome synthesis which was 44% in cells grown in a minimal medium and 82% in those in nutrient broth; (iii) segregation patterns of the (3)H-thymidine-labeled chromosome strands during subsequent growth in non-radioactive medium were studied by autoradiography, and the number of replication points per chromosome per cell was estimated as 5.6 for the nutrient broth culture and 2.5 for the minimal medium culture. These data support a model of symmetrical and bidirectional chromosome replication.     

Replication of the Bacterial Chromosome: Location of New Initiation Sites After Irradiation

New loci of replication along the bacterial chromosome are observed after irradiation of Escherichia coli. It was conjectured that, after X-irradiation, the new initiation site was random with respect to the fixed-origin, whereas, after ultraviolet light exposure, it was selective and appeared to be from the fixed-origin. Evidence presented here shows that, after X-irradiation of E. coli, the new initiation site(s) for the onset of deoxyribonucleic acid replication is induced at chromosomal regions not restricted to the fixed-origin. After ultraviolet light exposure, the new initiation site is preferentially from the fixed-origin. In these studies amino acid starvation was used to synchronize chromosome replication and to allow for differential radioisotopic labeling of the chromosomal origin and terminus. To facilitate interpretation, growing cells actively replicating their chromosome were compared with cells lacking growth points at the time of irradiation. The role of these new replication sites in the observed kinetics of deoxyribonucleic acid replication following X-ray or ultraviolet light exposure is discussed.     

More Precise Mapping of the Replication Origin in Escherichia coli K-12

The origin of replication in Escherichia coli K-12 was mapped by determining the rate of marker replication during a synchronous round of replication. Four isogenic strains were made lysogenic for lambdaind(-) and for phage Mu-1, with Mu-1 integrated into a different chromosomal location in each strain. Cultures were starved for amino acids to allow completion of chromosome replication cycles and then starved for thymine in the presence of amino acids, and a synchronous cycle of replication was initiated by the addition of thymine. Samples were exposed to radioactive thymidine at intervals, deoxyribonucleic acid was extracted, and the rate of marker replication was determined by deoxyribonucleic acid-deoxyribonucleic acid hybridization to filters containing Mu-1, lambda, and E. coli deoxyribonucleic acid. The results confirm that the origin of replication is near ilv. The travel times of the replication forks, calculated from the data obtained for cultures with doubling times of approximately 40 and 61 min, are 40 and 52 min, respectively.     

Temperature-Sensitive Initiation of Chromosome Replication in a Mutant of Bacillus subtilis

A mutant of Bacillus subtilis Ts37 has been isolated in which deoxyribonucleic acid (DNA) synthesis is inhibited at high temperature. The results presented here indicate that the process of initiation of DNA replication is temperature sensitive in this mutant. After shifting to 45 C, DNA increases 40 to 50% before synthesis ceases; an inhibition of protein synthesis permits an equivalent amount of DNA to be synthesized. A density shift experiment coupled with a marker frequency analysis shows that DNA synthesized at 45 C is highly enriched in the markers situated at the end of the chromosome. Transforming DNA extracted from a culture which has been incubated at 45 C exhibits the relative transforming efficiency for origin and terminus markers characteristic of completed chromosomes. After a shift back from 45 C to 30 C, reinitiation appears to occur always in the same region of the bacterial chromosome; in addition, replication as well as cell division is synchronized.     

Membrane enrichment of genetic markers close to the origin and terminus during the deoxyribonucleic acid replication cycle in Bacillus subtilis.

A temperature-sensitive Bacillus subtilis initiation mutant was used to achieve one cycle of synchronized deoxyribonucleic acid (DNA) replication. Markers near the origin of replication and the terminus were assayed for association with the cell membrane at intervals during the DNA replication cycle. DNA near the origin and terminus was found to be enriched in the membrane fraction throughout the DNA replication cycle. The magnitude of membrane enrichment or origin and terminus markers varied coincidentally, possibly as a consequence of incubating the cells at 45 degrees C.     

Regulation of Chromosome Replication in Bacillus subtilis: Effects of Amino Acid Starvation in Strain 168

Regulation of chromosome replication in Bacillus subtilis strain 168, in response to starvation for an essential amino acid, was found to differ from that reported for Escherichia coli. Not all replication points stop at the terminus during amino acid starvation. There is some evidence, however, to indicate that preferred stopping sites might exist. Initiation at the origin can occur in the absence of total protein synthesis as well as when the deoxyribonucleic acid (DNA)- mass ratio is unbalanced. DNA synthesis appears to be controlled independently of the initiation event by a second regulatory circuit, that may utilize the DNA-mass ratio. Once initiated, chromosome replication does not always go to completion in an uninterrupted sequence.     

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.     

Control of the Synthesis of Macromolecules During Amino Acid and Thymine Starvation in Bacillus subtilis

Studies of Maal?e, Lark, and others with amino acid- and thymine-starved cultures revealed successive steps in the biosynthesis of Escherichia coli chromosomes. In this study, the corresponding mechanisms in Bacillus subtilis 168 were examined. Using a strain requiring both thymine and tryptophan, we found that, 3 hr after the start of amino acid starvation, when the deoxyribonucleic acid (DNA) content of the culture had increased 40 to 50%, DNA synthesis ceased. After 4 to 5 hr, 100% of the cells were immune to thymineless death; their chromosomes had presumably been completed. Immune cultures slowly incorporated (3)H-thymine. Thymine incorporation increased 20-fold 30 min after readdition of amino acids, indicating reinitiation of chromosome synthesis. Simultaneous presence of amino acids and thymine was required for reinitiation. If 5-bromouracil (5-BU) was added instead of thymine, newly replicated DNA segments could be separated by centrifugation in CsCl. Analysis of the CsCl fractions by a transformation assay showed that the order in which the markers were synthesized was ade-16, thr-5, leu-8, metB5. Less than half the chromosomes started resynthesis synchronously in 5-BU. Nevertheless, chromosome alignment in the amino acid-starved culture is probably very good: marker frequency analysis of its DNA gives the same normalized frequencies as DNA from "perfectly" aligned spores. Full viability is maintained in the chromosome-arrested culture for 10 hr in thymine-free medium in the absence or presence of amino acids. In the latter condition, protein synthesis proceeds, and the cells filament and become more lysozyme-sensitive. Such cells must be incubated and plated on hypertonic or on slow-growth media; otherwise, they undergo "quasiosmotic" thymineless death. This death is thus apparently not directly attributable to any damage of chromosomal DNA. Further, weakening of the teichoic acid portion of the cell wall is not involved, since (32)P incorporation into teichoic acid is normal. Chloramphenicol prevents quasiosmotic thymineless death and also inhibits (32)P incorporation into teichoic acid. Chromosome-synthesizing cultures suffer thymineless death of two types: quasiosmotic death, and death insusceptible to osmotic rescue.     

Control of cell length in Bacillus subtilis.

During inhibition of deoxyribonucleic acid synthesis in Bacillus subtilis 168 Thy-minus Tryp-minus, the rate of length extension is constant. A nutritional shift-up during thymine starvation causes an acceleration in the linear rate of length extension. During a nutritional shift-up in the presence of thymine, the rate of length extension gradually increases, reaching a new steady state at about 50 min before the new steady-state rate of cell division is reached. The steady-state rates of nuclear division and length extension are reached at approximately the same time. The ratio of average cell length to numbers of nuclei per cell in exponential cultures is constant over a fourfold range of growth rates. These observations are consistent with: (i) surface growth zones which operate at a constant rate of length extension under any one growth condition, but which operate at an absolute rate proportional to the growth rate of the culture, (ii) a doubling in number of growth zones at nuclear segregation, and (iii) a requirement for deoxyribonucleic acid replication for the doubling in a number of sites.     

Chromosome Replication in Salmonella typhimurium

The replication of the Salmonella typhimurium chromosome was studied. As with E. coli 15T(-), replication was sequential. After amino acid starvation, replication proceeded from a unique and heritable region of the chromosome. 5-Bromouracil, when substituted for thymine, did not disturb the sequence of replication nor did it initiate extra replication cycles. By labeling the origin and the terminus of the chromosome with (3)H- and (14)C-thymine, respectively, it was possible to determine that the rate of chain elongation decreases as the growth rate decreases. No gap in the replication cycle could be observed.     

Regulation of Chromosome Replication in Bacillus subtilis: Effects of Amino Acid Starvation in Strain W23

Amino acid starvation allows limited synthesis of deoxyribonucleic acid (DNA) in Bacillus subtilis strain W23. DNA synthesis increased by about 30% after leucine starvation and by about 60% after histidine starvation. Genetic analysis on the DNA synthesized after amino acid starvation showed that all genetic markers examined have replicated, regardless of which amino acid was starved for. Initially, all markers replicated equally, but upon further replication, the thr cysB and the argA to lys regions replicated ahead of their neighboring, proximal regions. This could indicate that preferred stopping sites exist in these regions or additional sites from which replication can originate reside there. The results suggest that chromosome replication continues from those sites where it had stopped during amino acid starvation.     

Cell wall synthesis and initiation of deoxyribonucleic acid replication in Bacillus subtilis.

We have observed a connection between cell wall synthesis and the initiation of chromosome replication in Bacillus subtilis. Initiation of chromosome replication was prevented in synchronous cultures in the presence of the cell wall synthesis inhibitor vancomycin. When vancomycin was added to the cultures after initiation of chromosome replication, one round of replication was completed but no reinitiation occurred. Similar results were obtained when cell wall synthesis was inhibited by ristocetin, cycloserine, cloxacillin, or cephaloridine. When sucrose was added to the medium, initiation of deoxyribonucleic acid replication occurred in the presence of vancomycin, to an extent which allowed replication of no more than approximately one-half of the deoxyribonucleic acid of the culture. The same was found in cultures of spheroplasts of B. subtilis. However, initiation of chromosome replication in spheroplasts was completely insensitive to cloxacillin.