Effects of p-Fluorophenylalanine and Chloramphenicol on Chemotaxis in Escherichia coli

The effects of chloramphenicol and p-fluorophenylalanine (p-FPA) on growth, proportion of motile cells, average rate of motility, and the chemotactic response of a methionine auxotroph of Escherichia coli K-12 were studied. Kinetic studies revealed that the inhibition of chemotaxis by p-FPA can be explained by the effect on growth, proportion of motile cells, and average rate of motility rather than a selective inhibition of chemotaxis per se. The effect of chloramphenicol on chemotaxis could not be explained in terms of these characteristics. It is concluded that low concentrations of chloramphenicol, unlike p-FPA, selectively inhibit chemotaxis.     

Temperature-Sensitive Initiation of Chromosome Replication in a Mutant of Escherichia coli

The properties of Escherichia coli mutant D2-47LT indicate that it is temperature-sensitive for a protein required for the initiation of chromosome replication. The results of several different experiments are consistent with this hypothesis, and no support was found for the alternate hypotheses tested. Although the strain is usually unable to initiate replication at 42 C, some of the initiation proteins are apparently synthesized at the restrictive temperature. This can cause initiation on partially replicated, but not completed, chromosomes. It appears that the temperature-sensitive protein is required for initiation on completed chromosomes.     

Replication of Vibrio cholerae Chromosome I in Escherichia coli: Dependence on Dam Methylation

We successfully substituted Escherichia coli''s origin of replication oriC with the origin region of Vibrio cholerae chromosome I (oriCI_Vc). Replication from oriCI_Vc initiated at a similar or slightly reduced cell mass compared to that of normal E. coli oriC. With respect to sequestration-dependent synchrony of initiation and stimulation of initiation by the loss of Hda activity, replication initiation from oriC and oriCI_Vc were similar. Since Hda is involved in the conversion of DnaA^ATP (DnaA bound to ATP) to DnaA^ADP (DnaA bound to ADP), this indicates that DnaA associated with ATP is limiting for V. cholerae chromosome I replication, which similar to what is observed for E. coli. No hda homologue has been identified in V. cholerae yet. In V. cholerae, dam is essential for viability, whereas in E. coli, dam mutants are viable. Replacement of E. coli oriC with oriCI_Vc allowed us to specifically address the role of the Dam methyltransferase and SeqA in replication initiation from oriCI_Vc. We show that when E. coli''s origin of replication is substituted by oriCI_Vc, dam, but not seqA, becomes important for growth, arguing that Dam methylation exerts a critical function at the origin of replication itself. We propose that Dam methylation promotes DnaA-assisted successful duplex opening and replisome assembly at oriCI_Vc in E. coli. In this model, methylation at oriCI_Vc would ease DNA melting. This is supported by the fact that the requirement for dam can be alleviated by increasing negative supercoiling of the chromosome through oversupply of the DNA gyrase or loss of SeqA activity.The genomes of Vibrio cholerae and several related Vibrio spp. are distributed between two circular chromosomes. Characterization of the origins of replication of V. cholerae chromosomes I and II (oriCI_Vc and oriCII_Vc, respectively) has shown that oriCI_Vc is similar to the origin of replication of the Escherichia coli chromosome, oriC, whereas oriCII_Vc is completely different (20). Like oriC, oriCI_Vc has five R-type DnaA boxes (53) as well as boxes conforming to the I and τ types (52, 61), and the DnaA protein is the rate-limiting factor in the initiation of replication in both cases (18). In E. coli, DnaA associates with both ATP and ADP, and the ATP-bound form is absolutely required for initiation to take place (reviewed in reference 60). When reaching a critical level, DnaA^ATP (DnaA bound to ATP) protein is proposed to form a helical filament, anchored at one or more R-boxes (54, 69), in which origin DNA wraps around the outside of the DnaA core (21) or where the DnaA wraps around oriC (61). In both cases, the topology of the DnaA-oriC nucleoprotein complex leads to formation of compensatory negative supercoiling that facilitates unwinding of the adjacent AT-rich region resulting in initiation. In both models, DnaA^ATP is absolutely required for initiation, and in agreement with this, DnaA^ATP was found to be the rate-limiting factor for initiation in vivo (69).The V. cholerae oriCI_Vc also resembles oriC in having many potential sites for methylation by DNA adenine methyltransferase (Dam), although the number and position of the GATC sites differ slightly (see Fig. ​Fig.1).1). The role of Dam in initiation of chromosome replication has been studied mainly in E. coli. After initiation of DNA replication has occurred on a fully methylated oriC, the newly replicated hemimethylated origins are sequestered from the Dam methyltransferase and from reinitiation for approximately one-third of a doubling time. During this time interval, the activity and amount of DnaA available for initiation are reduced to prevent immediate reinitiation (reviewed in references 57 and 83). The sequestration is carried out by the SeqA protein that binds hemimethylated oriC GATC sequences with high affinity (48). In the absence of Dam methylation or SeqA, the same origin can be reinitiated in the same cell cycle, and initiations become asynchronous (9, 48).Open in a separate windowFIG. 1.Alignment of the E. coli minimal oriC with the corresponding region from V. cholerae chromosome I. The AT-rich sequence and the three 13-mer repeats L, M, and R found in E. coli (5) are indicated above the alignment. The 6-mer (A/T)GATCT boxes (80) are underlined. Other DnaA binding sites, i.e., R-boxes (53), I-boxes (52), and τ-boxes (61), are shown as boxed regions. Dam methylation sites (GATC) are shaded gray. The experimentally defined binding sites for integration host factor (IHF) (22) and factor for inversion stimulation (FIS) (65) in E. coli are indicated, and bases that match the consensus sequence are in boldface type. The single base difference between oriCI_Vc and oriCI_Vc* (see Materials and Methods) in the minimal origin region is shown below the two sequences. A gap introduced to maximize alignment of the two sequences is indicated by a dash in the sequence. Nucleotides that are identical in the two sequences are indicated by an asterisk below the two sequences.Genes encoding a Dam homologue and a SeqA homologue are present on Vibrio genomes, but there appear to be some differences between the functions of the proteins in E. coli and V. cholerae. dam has been found to be an essential gene in V. cholerae (33, 15), which is not the case in E. coli (48, 51). Conflicting data exist concerning the essentiality of seqA in V. cholerae (15, 72). The roles of Dam and SeqA in oriCI_Vc replication have been studied using minichromosomes, i.e., plasmids replicating exclusively from a cloned copy of oriCI_Vc (20). oriCI_Vc-based minichromosomes can replicate in wild-type E. coli cells but were unable to replicate in dam, seqA, and seqA dam mutants (20). The extrachromosomal existence of minichromosomes is dependent on their ability to initiate replication in synchrony with the chromosomal origin (46, 75). In E. coli cells mutated in dam or seqA, incompatibility exists between the oriC carried on minichromosomes and that of the chromosome due to origin competition (13), and when minichromosomes are maintained under selective pressure, they integrate into the origin region of the host chromosome (46, 75). Minichromosomes based on oriCI_Vc may also compete with the E. coli oriC for initiations in dam or seqA mutant cells. However, due to limited sequence identity, they may not be able to integrate into the E. coli chromosome. This could provide an explanation for the failure to introduce oriCI_Vc minichromosomes into dam and seqA mutant cells (20). Both dam and seqA genes could therefore be required for viability of V. cholerae for reasons not related to chromosome replication. In addition to its role in DNA replication, roles for Dam methylation in gene regulation and DNA repair have also been demonstrated in a number of bacteria (for reviews, see references 11, 45, 47, and 50). For V. cholerae as well as for Salmonella spp. and Yersinia pseudotuberculosis, Dam plays a role in virulence possibly through regulation of virulence gene expression (33). Less is known about the functions of seqA apart from its role in E. coli replication, but it has been suggested that SeqA functions as a nucleoid-organizing protein (for a review, see reference 83), and the E. coli chromosome has been demonstrated to have increased supercoiling in a seqA strain (85).Here we describe the first in vivo evidence that Dam plays an important role in the initiation of replication by facilitating the replication initiation at oriCI_Vc in E. coli. In addition, we show that SeqA does not carry an essential role in the initiation of replication.     

Replication of Deoxyribonucleic Acid in Escherichia coli C Mutants Temperature Sensitive in the Initiation of Chromosome Replication

An Escherichia coli HF4704S mutant temperature sensitive in deoxyribonucleic acid (DNA) synthesis and different from any previously characterized mutant was isolated. The mutated gene in this strain was designated dnaH. The mutant could grow normally at 27 C but not at 43 C, and DNA synthesis continued for an hour at a decreasing rate and then ceased. After temperature shift-up, the increased amount of DNA was 40 to 50%. When the culture was incubated at 43 C for 70 min and then transferred to 27 C, DNA synthesis resumed after about 50 min, initiating synchronously at a fixed region on the bacterial chromosome. The initiation step in DNA replication sensitive to 30 mug of chloramphenicol per ml occurs synchronously before the resumption of DNA replication after the temperature shift-down, being completed about 30 min before the start of DNA replication. When the cells incubated at 27 C in the presence of 30 mug of chloramphenicol per ml after the temperature shift-down to 27 C were transferred to 43 C with simultaneous removal of the antibiotic, no resumption of DNA replication was observed. When the culture was returned to 43 C after being released from high-temperature inhibition at 30 min before the start of DNA replication, no recovery replication was observed; whereas at 20 min, the recovery of replication was observed. These results indicated that HF4704S was temperature sensitive in the initiation of DNA replication. Analysis of HF4704S, by an interrupted conjugation experiment, indicated that gene dnaH was located at about 64 min on the E. coli C linkage map. In E. coli S1814 (a K-12 derivative), which was a dnaH(ts) transductant from HF4704S (C strain) with phage P1, the mutated gene (dnaH) was demonstrated to be closely linked to the thyA marker by conjugation and P1 transduction experiments and to be distinct from genes dnaA through dnaG.     

Analysis of Protein Synthesis Rates after Initiation of Chromosome Replication in Escherichia coli

The aim of this study was to investigate whether the synthesis rates of some proteins change after the initiation of replication in Escherichia coli. An intR1 strain, in which chromosome replication is under the control of an R1 replicon integrated into an inactivated oriC, was used to synchronize chromosome replication, and the rates of protein synthesis were analyzed by two-dimensional polyacrylamide gel electrophoresis of pulse-labeled proteins. Computerized image analysis was used to search for proteins whose expression levels changed at least threefold after initiation of a single round of chromosome replication, which revealed 7 out of about 1,000 detected proteins. The various synthesis rates of three of these proteins turned out to be caused by unbalanced growth and the synthesis of one protein was suppressed in the intR1 strain. The rates of synthesis of the remaining three could be correlated only to the synchronous initiation of replication. These three proteins were analyzed by peptide mass mapping and appeared to be the products of the dps, gapA, and pyrI genes. Thus, the expression of the vast majority of proteins is not influenced by the state of chromosome replication, and a possible role of the replication-associated expression changes of the three identified proteins in the cell cycle is not clear.     

Chromosome Replication and Cell Division in Escherichia coli at Various Temperatures of Growth

The effect of temperature on the growth rate and the pattern of chromosome replication during the division cycle of Escherichia coli B/r growing in various media was investigated. The time between divisions, the time for a round of replication (C), and the time between completion of a round and cell division (D) were threefold longer at 21 C than at 37 C. At all temperatures and in all media, D equalled one-half C, suggesting that a common mechanism controls chromosome replication and the progression of the cell toward division after completion of a round of replication.     

Chromosome Replication and the Division Cycle of Escherichia coli B/r

The average amount of deoxyribonucleic acid (DNA) per cell was measured in steady-state cultures of Escherichia coli B/r grown at 37 C in glucose-limited chemostats or in batch cultures in the exponential growth phase as maintained with one of several carbon sources. Within experimental errors, DNA content was dependent only on growth rate and independent of the type of culture, the carbon source, or the addition of growth factors. The amount of DNA per cell increased continuously with growth rate over the range of 0.02 to 3 divisions per hour. The data over the entire range of growth rates are in agreement with a constant time for a single replication point to traverse the entire genome, 47 min, and with cell division following 25 min after termination of replication. The measured amount of DNA per genome was 4.2 x 10(-15) g (or 2.5 x 10(9) daltons).     

Molecular Weight of Deoxyribonucleic Acid Synthesized During Initiation of Chromosome Replication in Escherichia coli

Alkaline sucrose gradients were used to study the molecular weight of deoxyribonucleic acid (DNA) synthesized during the initiation of chromosome replication in Escherichia coli 15 TAU-bar. The experiments were conducted to determine whether newly synthesized, replication origin DNA is attached to higher-molecular-weight parental DNA. Little of the DNA synthesized after readdition of required amino acids to cells previously deprived of the amino acids was present in DNA with a molecular weight comparable to that of the parental DNA. The newly synthesized, low-molecular-weight DNA rapidly appeared in higher-molecular-weight material, but there was an upper limit to the size of this intermediate-molecular-weight DNA. This limit was not observed when exponentially growing cells converted newly synthesized DNA to higher-molecular-weight material. The size of the intermediate-molecular-weight DNA was related to the age of the replication forks, and the size increased as the replication forks moved further from the replication origin. The results indicate that the newly synthesized replication origin DNA is not attached to parental DNA, but it is rapidly attached to the growing strands that extend from the replication fork to the replication origin, or to the other replication fork if replication is bidirectional. Experiments are reported which demonstrate that the DNA investigated was from the vicinity of the replication origin and was not plasmid DNA or DNA from random positions on the chromosome.     

Effect of Hydroxyurea on Replication of Bacteriophage T4 in Escherichia coli

Hydroxyurea inhibited the replication of bacteriophage T4 in Escherichia coli B. The concentration of hydroxyurea required to inhibit net deoxyribonucleic acid (DNA) synthesis 50% was about 50-fold less than that required in uninfected cells. Even in the presence of high hydroxyurea concentrations, phage DNA was readily synthesized from the products of breakdown of the E. coli DNA, and viable phage were made. Deoxyribonucleotide, but not ribonucleotide, synthesis was strongly inhibited in the presence of hydroxyurea. The data indicate that hydroxyurea specifically inhibits de novo DNA synthesis in E. coli infected with bacteriophage T4 by inhibiting the ribonucleoside diphosphate reductase system, but does not affect DNA synthesis at subsequent steps.     

Initiation and Velocity of Chromosome Replication in Escherichia coli B/r and K-12

The macromolecular composition and a number of parameters affecting chromosome replication were examined over a range of exponential growth rates in two common Escherichia coli strains, B/r and K-12 AB1157. Based on improved measurements of DNA after treatment of exponential cultures with rifampin, the cell mass per chromosomal replication origin (initiation mass) and the time required to replicate the chromosome from origin to terminus (C period) were determined. For these two strains, the initiation mass approached values of 8 × 10⁻¹⁰ and 10 × 10⁻¹⁰ units of optical density (at 460 nm) of culture mass per oriC, respectively, at growth rates above 1 doubling/h (at 37°C). The amount of protein per oriC decreased with increasing growth rate for AB1157 and remained nearly constant for the B/r strain. The C period decreased for both strains in an essentially identical manner from about 70 min at 0.6 doublings/h to about 33 min at 3 doublings/h. From the initiation mass and C period, relative or absolute copy numbers for genes with known map locations can be accurately determined at different growth rates. At growth rates above 2 doublings/h, when chromosomes are highly branched, genes near the origin are about threefold more prevalent than genes near the terminus. At a growth rate of 0.6 doubling/h, this ratio is only about 1.7, which reflects the lower degree of chromosome branching.     

Membrane Alteration and the Formation of Metachromatic Granules in Escherichia coli Treated with p-Fluorophenylalanine

The effect of p-fluorophenylalanine (FPA) on growing cultures of Escherichia coli was studied with regard to the composition and morphology of the cell envelope. A cell wall fraction was prepared by autolysis in hypertonic medium, and the resulting spheroplasts were osmotically lysed to obtain a cytoplasmic membrane fraction. Incorporation of labeled phenylalanine, FPA, and N-acetylglucosamine into both fractions of FPA-inhibited cells suggested that the composition of the membrane changed with time, whereas that of the cell wall remained relatively constant. Amino acid analysis revealed changes in the composition of the membrane fraction after FPA inhibition. Electron micrographs of shadowed cells and membranes revealed the presence of electron-dense metachromatic granules during the early stages of FPA inhibition.     

Replication restart in gyrB Escherichia coli mutants

Gyrase is an essential topoisomerase in bacteria that introduces negative supercoils in DNA and relaxes the positive supercoils that form downstream of proteins tracking on DNA, such as DNA or RNA polymerases. Two gyrase mutants that suffer partial loss of function were used here to study the need for replication restart in conditions in which gyrase activity is affected. We show that the preprimosomal protein PriA is essential for the viability of these gyrB mutants. The helicase function of PriA is not essential. The lethality of the gyrB priA double mutants is suppressed by a dnaC809 mutation, indicating a requirement for primosome assembly in gyrB strains. The lethality of gyrB priA combination of mutations is independent of the level of DNA supercoiling, as gyrB and priA were also co-lethal in the presence of a DeltatopA mutation. Inactivation of homologous recombination did not affect the viability of gyrB mutants, indicating that replication restart does not require the formation of a recombination intermediate. We propose that the replisome is disassembled from replication forks when replication progression is blocked by the accumulation of positive supercoils in gyrase mutants, and that replication restarts via PriA-dependent primosome assembly, directly on the in-activated replication forks, without the formation of a recombination intermediate.     

Effects of Chromosome Underreplication on Cell Division in Escherichia coli

The key processes of the bacterial cell cycle are controlled and coordinated to match cellular mass growth. We have studied the coordination between replication and cell division by using a temperature-controlled Escherichia coli intR1 strain. In this strain, the initiation time for chromosome replication can be displaced to later (underreplication) or earlier (overreplication) times in the cell cycle. We used underreplication conditions to study the response of cell division to a delayed initiation of replication. The bacteria were grown exponentially at 39°C (normal DNA/mass ratio) and shifted to 38 and 37°C. In the last two cases, new, stable, lower DNA/mass ratios were obtained. The rate of replication elongation was not affected under these conditions. At increasing degrees of underreplication, increasing proportions of the cells became elongated. Cell division took place in the middle in cells of normal size, whereas the longer cells divided at twice that size to produce one daughter cell of normal size and one three times as big. The elongated cells often produced one daughter cell lacking a chromosome; this was always the smallest daughter cells, and it was the size of a normal newborn cell. These results favor a model in which cell division takes place at only distinct cell sizes. Furthermore, the elongated cells had a lower probability of dividing than the cells of normal size, and they often contained more than two nucleoids. This suggests that for cell division to occur, not only must replication and nucleoid partitioning be completed, but also the DNA/mass ratio must be above a certain threshold value. Our data support the ideas that cell division has its own control system and that there is a checkpoint at which cell division may be abolished if previous key cell cycle processes have not run to completion.     

Changes in Cell Size and Shape Associated with Changes in the Replication Time of the Chromosome of Escherichia coli

Average cell mass is shown to be inversely related to the concentration of thymine in the growth medium of a thy⁻ strain of Escherichia coli. The kinetics of the transition from one steady-state average cell mass to another was followed in an attempt to determine the relationship between the chromosome replication time and the time between completion of a round of chromosome replication and the subsequent cell division. Differences in average cell mass are shown to be associated with similar differences in average cell volume. Changes in volume associated with changes in thymine concentration are shown to be due primarily to differences in the width of cells. It is proposed that extension in length of the cell envelope occurs at a linear rate which is proportional to the growth rate and which doubles at the time of termination of rounds of replication. Changes in volume not associated with a change in growth rate are therefore accommodated by a change in cell width. Conditions are described under which average cell mass can continue to increase in successive generations and no steady-state average cell mass is achieved.     

Chromosome structuring limits genome plasticity in Escherichia coli

Chromosome organizations of related bacterial genera are well conserved despite a very long divergence period. We have assessed the forces limiting bacterial genome plasticity in Escherichia coli by measuring the respective effect of altering different parameters, including DNA replication, compositional skew of replichores, coordination of gene expression with DNA replication, replication-associated gene dosage, and chromosome organization into macrodomains. Chromosomes were rearranged by large inversions. Changes in the compositional skew of replichores, in the coordination of gene expression with DNA replication or in the replication-associated gene dosage have only a moderate effect on cell physiology because large rearrangements inverting the orientation of several hundred genes inside a replichore are only slightly detrimental. By contrast, changing the balance between the two replication arms has a more drastic effect, and the recombinational rescue of replication forks is required for cell viability when one of the chromosome arms is less than half than the other one. Macrodomain organization also appears to be a major factor restricting chromosome plasticity, and two types of inverted configurations severely affect the cell cycle. First, the disruption of the Ter macrodomain with replication forks merging far from the normal replichore junction provoked chromosome segregation defects. The second major problematic configurations resulted from inversions between Ori and Right macrodomains, which perturb nucleoid distribution and early steps of cytokinesis. Consequences for the control of the bacterial cell cycle and for the evolution of bacterial chromosome configuration are discussed.     

Effect of Nalidixic Acid on Semiconservative Replication and Repair Synthesis After Ultraviolet Irradiation in Escherichia coli

Both semiconservative deoxyribonucleic acid replication and "extensive repair" synthesis, after ultraviolet irradiation, appear to be blocked by nalidixic acid. These findings suggest that the agent(s) responsible for both of these modes of replication, or some necessary common process or structure, is affected by this drug.