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.
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 λind− 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, λ, 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.
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.
Studies of Maaløe, 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 3H-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 32P incorporation into teichoic acid is normal. Chloramphenicol prevents quasiosmotic thymineless death and also inhibits 32P incorporation into teichoic acid. Chromosome-synthesizing cultures suffer thymineless death of two types: quasiosmotic death, and death insusceptible to osmotic rescue.
Several thymineless Escherichia coli strains have been examined for their ability to replicate their deoxyribonucleic acid when bromouracil is substituted for thymine. The procedure we describe was used to identify a thymineless strain with characteristics relatively favorable to its use in bromouracil labeling experiments. In addition, mutants with an “absolute” thymine requirement could be easily distinguished from one with a “leaky” thymine requirement.
The chromosomes of a tryptophan−, thymine− double auxotroph of Bacillus subtilis were uniformly aligned at the chromosome terminus by an amino acid starvation treatment. By subsequent incubations, the starved culture was rendered competent, while its state of synchronous chromosome arrest was maintained by thymine starvation. The competent, chromosome-arrested cells were transformed for three unlinked markers, located in two different chromosome regions. Shortly after addition of deoxyribonucleic acid, the cell walls were removed with lysozyme in a medium containing deoxyribonuclease and no thymine, and the protoplasted culture was assayed for single and double transformants. It was found that markers both near and distant from the terminus entered freely into the cell interior. There was no important difference in the relative frequency of entry of different markers between synchronously arrested cells and nonsynchronized control cultures. It is concluded that entry of a given marker into the cell interior can occur even if the replication site of the chromosome is stationary at a location distant from the locus of the resident homolog of the entering marker. A mechanism of donor deoxyribonucleic acid entry involving homology at the replication fork is excluded.
Cultures of Escherichia coli 15T− and K-12 were labeled with 3H-thymine before, during, and after amino acid starvation. The number of labeled segregating units was measured by autoradiography of microcolonies derived from the labeled cells. In both strains, labels inserted before starvation and during starvation appeared to segregate as if incorporated into the same polynucleotide strands. However, labels inserted during and after starvation segregated as if incorporated into different polynucleotide strands. In view of previous data, it was concluded that replication after amino acid starvation originates from the region of the chromosome which serves as the origin for replication during normal growth and division.
Study of the replication pattern of a number of B. subtilis 168 strains under controlled physiological conditions revealed great interstrain variation in control of replication. Replication patterns were calculated from ratios of purA16/leu-8 and purA16/metB5 transformation frequency. The thymine-independent strains are under strict regulation with an average of one replication position per chromosome during log phase. After starvation for required amino acids or sporulation, the chromosome is in a completed state with no replication forks (class I). In contrast, several thymine-requiring strains (class III) have an average of three to four replication positions per chromosome during log phase (multiforked replication) of which one to two remain uncompleted after amino acid starvation or sporulation. The other thymine-requiring strains studied are intermediate (class II) in that they have an average of two replication positions per chromosome during log phase and one after amino acid starvation or sporulation. Pulse chase experiments indicate that the deoxyribonucleic acid which is close to the chromosomal origin on each branch of the multiforked chromosome is bound to a rapidly sedimenting cellular fraction, presumably membrane.
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.
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.
F plasmid replication during the Escherichia coli division cycle was investigated by using the membrane-elution technique to produce cells labeled at different times during the division cycle and scintillation counting for quantitative analysis of radioactive plasmid DNA. The F plasmid replicated, like the minichromosome, during a restricted portion of the bacterial division cycle; i.e., F plasmid replication is cell-cycle specific. The F plasmid replicated at a different time during the division cycle than a minichromosome present in the same cell. F plasmid replication coincided with doubling in the rate of enzyme synthesis from a plasmid-encoded gene. When the cell cycle age of replication of the F plasmid was determined over a range of growth rates, the cell size at which the F plasmid replicated followed the same rules as did replication of the bacterial chromosome--initiation occurred when a constant mass per origin was achieved--except that the initiation mass per origin for the F plasmid was different from that for the chromosome origin. In contrast, the high-copy mini-R6K plasmid replicated throughout the division cycle.
The variability of (i) the B period between birth and initiation of chromosome replication, (ii) the U period between initiation of chromosome replication and initiation of cell constriction, and (iii) the interdivision period (tau) have been estimated for slowly growing Escherichia coli B/r F. Cultures synchronized by the membrane elution technique were pulse-labeled with [3H]thymidine or continuously labeled with [3H]thymine. After fixation, the pattern of deoxyribonucleic acid replication was analyzed by electron microscopic radioautography. Cell length was found to increase exponentially with age at two different slow growth rates. The coefficient of variation of the B period was estimated to be 60%, that of the U period was 29%, and that of the interdivision period was 12%. From these values and the coefficient of variation of length at different cell cycle events were calculated a negative correlation between the B and U period (r = -0.9) and a positive correlation between length at birth and cell separation (r = 0.6). Initiation of chromosome replication and cell constriction were strictly correlated both with respect to age (r = 0.7) and length (r = 0.8). On the other hand, length at initiation of chromosome replication was distantly correlated with age (r = 0.1) or length at birth (r = 0.3). This low correlation excludes a model in which chromosome initiation is controlled by a random event in the B period. It favors a model in which chromosome initiation occurs at a particular distributed size independent of cell division.
Starvation for DNA precursor dTTP, known as ‘thymineless death’ (TLD), kills bacterial and eukaryotic cells alike. Despite numerous investigations, toxic mechanisms behind TLD remain unknown, although wrong nucleotide incorporation with subsequent excision dominates the explanations. We show that kinetics of TLD in Escherichia coli is not affected by mutations in DNA repair, ruling out excision after massive misincorporation as the cause of TLD. We found that the rate of DNA synthesis in thymine-starved cells decreases exponentially, indicating replication fork stalling. Processing of stalled replication forks by recombinational repair is known to fragment the chromosome, and we detect significant chromosomal fragmentation during TLD. Moreover, we report that, out of major recombinational repair functions, only inactivation of recF and recO relieves TLD, identifying the poisoning mechanism. Inactivation of recJ and rep has slight effect, while the recA, recBC, ruvABC, recG and uvrD mutations all accelerate TLD, identifying the protection mechanisms. Our epistatic analysis argues for two distinct pathways protecting against TLD: RecABCD/Ruv repairs the double-strand breaks, whereas UvrD counteracts RecAFO-catalyzed toxic single-strand gap processing.
The synthesis of φX174-specific RNA has been studied in infected cells in which the thymine of the viral (+) strand of the parental RF*, of the complementary (−) strand of the parental RF, or of both strands of the progeny RF molecules has been replaced with 5-bromouracil (5 BU). By irradiation of such cells with UV light at a wavelength of 313 nm it was possible to affect, specifically, the 5 BU-labeled strands. When the progeny RF molecules contain thymine, irradiation has no effect upon the synthesis of viral-specific RNA, regardless of 5 BU substitution in either strand of parental RF. If, however, progeny RF is labeled with 5 BU, irradiation produces a major decrease of viral RNA synthesis. It is concluded that many progeny RF molecules can serve as templates for transcription at late times of infection. Irradiation, prior to RF replication, of cells in which, particularly, the complementary strand of RF contains 5 BU, appears to decrease the ability of the parental RF to replicate.
Slowly growing Escherichia coli cells have a simple cell cycle, with replication and progressive segregation of the chromosome completed before cell division. In rapidly growing cells, initiation of replication occurs before the previous replication rounds are complete. At cell division, the chromosomes contain multiple replication forks and must be segregated while this complex pattern of replication is still ongoing. Here, we show that replication and segregation continue in step, starting at the origin and progressing to the replication terminus. Thus, early-replicated markers on the multiple-branched chromosomes continue to separate soon after replication to form separate protonucleoids, even though they are not segregated into different daughter cells until later generations. The segregation pattern follows the pattern of chromosome replication and does not follow the cell division cycle. No extensive cohesion of sister DNA regions was seen at any growth rate. We conclude that segregation is driven by the progression of the replication forks.
5-Bromouracil (BU)-tolerant mutants of Bacillus subtilis 23 (thy his) have been isolated. Several classes of tolerant mutants were obtained by a sequential selection procedure. The classes can be distinguished by their relative BU tolerance as well as several other phenotypic characteristics. The mutants can grow for an extended period of time in minimal medium supplemented with amino acids and BU, in which the sensitive parental strain (Bu+) undergoes rapid cell death. Both mutants But-1 and But-1310 have a greater rate of deoxyribonucleic acid (DNA) synthesis by a factor of two in the presence of BU than Bu+, But-1 being somewhat faster than But-1310. The preferential incorporation of thymine to BU of But-1 is about half that of the Bu+ strain during DNA replication in minimal medium supplemented with 10 μg of BU/ml and 1 μg of thymine/ml. It is not known at what step or steps this reduction in selectivity occurs.
Billen, Daniel (University of Texas M. D. Anderson Hospital and Tumor Institute, Houston, Tex.), and Roger Hewitt. Influence of starvation for methionine and other amino acids on subsequent bacterial deoxyribonucleic acid replication. J. Bacteriol. 92:609–617. 1966.—A study has been made of the subsequent replicative fate of deoxyribonucleic acid (DNA) synthesized during amino acid starvation by several multiauxotrophic strains of Escherichia coli. Using radioisotopic and density labels and a procedure whereby total cellular DNA is analyzed, we have confirmed and extended a recent report that the DNA made during amino acid starvation behaves anomalously during subsequent DNA replication. When 5-bromouracil (BU) serves as the density lable, 40% or more of the DNA synthesized during starvation will subsequently fail to replicate during three cell generations. Selective amino acid effects were noted. In two methionine-requiring bacteria, methionine deprivation appeared to be of singular importance in influencing the subsequent replicative fate of the DNA made in its absence.
When a non-BU density label (N15, C13) was utilized, the effects of amino acid starvation were less obvious. Although the DNA synthesized during complete amino acid starvation in a methionine-requiring E. coli was subsequently more slowly replicated, most of the DNA was finally duplicated during three generations of growth. If methionine was present during starvation for other required amino acids, the subsequent replication rate of the DNA synthesized during this time was more nearly normal, and complete replication was observed. The results have been interpreted as indicating that DNA synthesized during amino acid starvation, and especially during methionine starvation, is somehow altered, and that BU substitution for thymine may interfere with the restoration of such DNA to its replicative state.
In synchronized culture of Escherichia coli, the specific arrest of phospholipid synthesis (brought about by glycerol starvation in an appropriate mutant) did not affect the rate of ongoing DNA synthesis but prevented the initiation of new rounds. The initiation block did not depend on cell age at the time of glycerol removal, which could be before, during, or after the doubling in the rate of phospholipid synthesis (DROPS) and as little as 10 min before the expected initiation. We conclude that the initiation of DNA replication is not triggered by the preceding DROPS but requires active phospholipid synthesis. Conversely, when DNA replication initiation was specifically blocked in a synchronized culture of a dnaC(Ts) mutant, two additional DROPS were observed, after which phospholipid synthesis continued at a constant rate for at least 60 min. Similarly, when DNA elongation was blocked by thymine starvation of a synchronized culture, one additional DROPS was observed, followed by linear phospholipid accumulation. Control experiments showed that specific inhibition of cell division by ampicillin, heat shock, or induction of the SOS response did not affect phospholipid synthesis, suggesting that the arrest of DROPS observed was due to the DNA replication block. The data are compatible with models in which the DROPS is triggered by an event associated with replication termination or chromosome segregation.
DNA replication is highly regulated in most organisms. Although much research has focused on mechanisms that regulate initiation of replication, mechanisms that regulate elongation of replication are less well understood. We characterized a mechanism that regulates replication elongation in the bacterium Bacillus subtilis. Replication elongation was inhibited within minutes after amino acid starvation, regardless of where the replication forks were located on the chromosome. We found that small nucleotides ppGpp and pppGpp, which are induced upon starvation, appeared to inhibit replication directly by inhibiting primase, an essential component of the replication machinery. The replication forks arrested with (p)ppGpp did not recruit the recombination protein RecA, indicating that the forks are not disrupted. (p)ppGpp appear to be part of a surveillance mechanism that links nutrient availability to replication by rapidly inhibiting replication in starved cells, thereby preventing replication fork disruption. This control may be important for cells to maintain genomic integrity.
Billen, Daniel (The University of Texas, Houston), and Roger Hewitt. Physiological aspects of modification and restoration of chromosomal synthesis in bacteria after X irradiation. J. Bacteriol. 90:1218–1225. 1965.—A study was made of the effect of amino acid deprivation or chloramphenicol on the character of postirradiation deoxyribonucleic acid (DNA) replication in bacteria with the use of radioisotopes and 5-bromouracil as a density label. CsCl density-gradient studies of DNA showed that postirradiation incubation of amino acid-requiring Escherichia coli in an amino acid-free medium interfered with continued linear chromosomal replication. In the presence of the required amino acids, linear chromosomal replication was shown to resume. Addition of chloramphenicol was found to prevent this resumption. Deletion of the required amino acids or the presence of chloramphenicol in a fully supplemented medium allowed the detection of altered DNA synthesis in bacteria at X-ray doses as low as 500 r. The character of the limited DNA made in the presence of the density label after irradiation is described. The results are interpreted as showing that the synthesis of a protein(s) is required for restoration of linear chromosomal replication in the irradiated cells.
The relationship between termination of chromosome replication and cell division was investigated in Escherichia coli B/r. Synchronous cultures of E. coli B/r growing in glucose minimal medium or subjected to a nutritional shift-up were exposed to chloramphenicol, rifampin, mitomycin C, or nalidixic acid, and the ability of cells to divide in the presence of the inhibitors was measured. It was found that cell division became resistant to inhibitors of ribonucleic acid (RNA) and deoxyribonucleic acid (DNA) synthesis at approximately the same stage in the division cycle in all situations investigated. When the synchronous glucose-grown cultures were temporarily exposed to chloramphenicol early in the division cycle and then exposed to mitomycin C or nalidixic acid immediately after removal of chloramphenicol, the cells did not divide. In contrast, when DNA synthesis was inhibited by thymine starvation immediately after temporary exposure to chloramphenicol, cells divided. The results suggest that DNA chain elongation is completed in some cells in the absence of protein synthesis, but that additional steps involving specific RNA or protein synthesis, or both, may be required for processing the chromosomal structures to the form which is necessary for division. This processing, which normally occurs concurrent with DNA synthesis and is prevented by inhibitors of DNA synthesis, may trigger division. Alternatively, in the absence of protein synthesis, all aspects of chromosome formation may be completed, but final transcriptional events which are essential for division cannot take place until the complete synthesis of a critical amount of specific proteins.
The effects of pyrimidine limitation on chromosome replication and the control of ribosomal and transfer ribonucleic acid syntheses were investigated. Chromosome replication was studied by autoradiography of 3H-thymine pulse-labeled cells. Pyrimidine limitation did not affect the fraction of cells incorporating radioactive thymine during a short pulse, indicating that when growth is limited by the supply of pyrimidine, the time required for chromosome duplication increases in proportion to the time required for cell duplication. Control of ribosomal RNA and transfer RNA syntheses was examined by chromatographing cell extracts on methylated albumin kieselguhr columns. When growth was controlled by carbon-nitrogen limitation, the ratio of tRNA to total RNA remained roughly constant at growth rates above 0.5 doublings per hour. During pyrimidine limitation, however, the control of rRNA synthesis was apparently dissociated from the control of tRNA synthesis: the ratio of tRNA to total RNA increased as the growth rate decreased.
DNA replication is regulated in response to environmental constraints such as nutrient availability. While much is known about regulation of replication during initiation, little is known about regulation of replication during elongation. In the bacterium Bacillus subtilis, replication elongation is paused upon sudden amino acid starvation by the starvation-inducible nucleotide (p)ppGpp. However, in many bacteria including Escherichia coli, replication elongation is thought to be unregulated by nutritional availability. Here we reveal that the replication elongation rate in E. coli is modestly but significantly reduced upon strong amino acid starvation. This reduction requires (p)ppGpp and is exacerbated in a gppA mutant with increased pppGpp levels. Importantly, high levels of (p)ppGpp, independent of amino acid starvation, are sufficient to inhibit replication elongation even in the absence of transcription. Finally, in both E. coli and B. subtilis, (p)ppGpp inhibits replication elongation in a dose-dependent manner rather than via a switch-like mechanism, although this inhibition is much stronger in B. subtilis. This supports a model where replication elongation rates are regulated by (p)ppGpp to allow rapid and tunable response to multiple abrupt stresses in evolutionarily diverse bacteria.
The relationship between chromosome replication and cell division was investigated in a thymineless mutant of Escherichia coli B/r. Examination of the changes in average cell mass and DNA content of exponential cultures resulting from changes in the thymine concentration in the growth medium suggested that as the replication time (C) is increased there is a decrease in the period between termination of a round of replication and the subsequent cell division (D). Observations on the pattern of DNA synthesis during the division cycle were consistent with this relationship. Nevertheless, the kinetics of transition of exponential cultures moving between steady states of growth with differing replication velocities provided evidence to support the view that the time of cell division is determined by termination of rounds of replication under steady-state conditions.
5-Bromouracil (BU) was pulsed into the genome of synchronously growing cells of an F− strain of Salmonella typhimurium of LT2. BU-labeled genes were transduced with P22 phage to a series of recipient auxotrophs. When BU was incorporated early in the replication cycle, the transducing markers that had hybrid densities were those that lie between 9 and 12 o'clock on the genetic map. When BU was incorporated during the terminal period of the synchronous cycle, the transducing particles had hybrid densities for genes that lie from 1 to 8 o'clock clockwise. When phages were prepared on cells in which the middle period was BU-labeled, transducing particles with hybrid densities appeared for genes that lie in two separate regions: between 7 and 9 o'clock and between 12 and 2 o'clock. Analysis of the map sequences of the transduced BU genes, the relative frequency of transduction for each marker, and the time sequence of replication led to a hypothesis that the origin of replication is near the isoleucine-valine gene on the chromosome map. As for direction of replication, several models were considered, including the possibility that replication may proceed in both directions in the same chromosome. It was also found that the aroB, cysG, and strA genes are cotransduced and strA and aroC are also cotransduced. The relative order of the four genes was found to be aroB, cysG, strA, aroC, but the orientation in the circular map was not determined.