Conjugal Deoxyribonucleic Acid Replication by Escherichia coli K-12: Stimulation in dnaB(ts) Donors by Minicells

R64-11(+) donor cells that are thermosensitive for vegetative DNA replication will synthesize DNA at the restrictive temperature when recipient minicells are present. This is conjugal DNA replication because it is R64-11 DNA that is being synthesized and there is no DNA synthesis if minicells that cannot be recipients of R64-11 DNA are used. The plasmid DNA present in the donor cells before mating is transferred to recipient minicells within the first 20 min of mating, but additional copies of plasmid DNA synthesized during the mating continue to be transferred for at least 90 min. However, the transfer of R64-11 DNA to minicells is not continuous because the plasmid DNA in minicells is the size of one R64-11 molecule or smaller, and there are delays between the rounds of plasmid transfer. DNA is synthesized in minicells during conjugation, but this DNA has a molecular weight much smaller than that of R64-11. Thus, recipient minicells are defective and are not able to complete the synthesis of a DNA strand complementary to the single-stranded R64-11 DNA received from the donor cell.     

Isolation of Deoxyribonucleic Acid Methylase Mutants of Escherichia coli K-12

Fourteen deoxyribonucleic acid (DNA) and 10 ribonucleic acid (RNA) methylation mutants were isolated from Escherichia coli K-12 by examining the ability of nucleic acids prepared from clones of unselected mutagenized cells to accept methyl groups from wild-type crude extract. Eleven of the DNA methylation mutants were deficient in 5-methylcytosine (5-MeC) and were designated Dcm. Three DNA methylation mutants were deficient in N(6)-methyladenine (N(6)-MeA) and were designated Dam. Extracts of the mutants were tested for DNA-cytosine:S-adenosylmethionine and DNA-adenine:S-adenosylmethionine methyltransferase activities. With one exception, all of the mutants had reduced or absent activity. A representative Dcm mutation was located at 36 to 37 min and a representative Dam mutation was located in the 60-to 66-min region on the genetic map. The Dcm mutants had no obvious associated phenotypic abnormality. The Dam mutants were defective in their ability to restrict lambda. None of the mutations had the effect of being lethal.     

Effect of Thymine Starvation on Deoxyribonucleic Acid Repair Systems of Escherichia coli K-12

Thymine starvation of Escherichia coli K-12 results in greatly increased sensitivity to ultraviolet light (UV). Our studies, using isogenic strains carrying rec and uvr mutations, have shown the following. (i) Common to all strains tested is a change from multihit to single-hit kinetics of survival to UV after 60 min of thymine starvation. However, the limiting slope of UV survival curves decreases in the rec(+)uvr(+) strain and changes very little in several rec mutant strains and one uvrB mutant strain. Thus, when either the rec or uvr system is functioning alone, the limiting slopes of the UV survival curves are relatively unaffected by thymine starvation. (ii) Thymine starvation does not significantly inhibit repair processes carried out by either repair system alone; i.e., host cell reactivation of irradiated phage (carried out by the uvr system), excision of thymine dimers (uvr), or X-ray repair (rec). (iii) In a rec(+)uvr(+) strain, repair appears to be a synergistic rather than additive function of the two systems. However, after thymine starvation, repair capacity is reduced to about the sum of the repair capacities of the independent systems. (iv) The kinetics of thymineless death are not changed by rec and uvr mutations. This indicates that the lesions responsible for thymineless death are not repaired by rec or uvr systems. (v) Withholding thymine from thy rec(+)uvr(+) bacteria not undergoing thymineless death has no effect on UV sensitivity. Under these conditions one sees higher than normal UV resistance in the presence or absence of thymine. This is due to increased repair carried out by the uvr system. To explain these results we postulate that thymine starvation does not inhibit either the rec or uvr repair pathway directly. Rather it appears that thymine starvation results in increased UV sensitivity in part by inhibiting a function which normally carries out efficient coordination of rec and uvr pathways.     

Auxotroph Accumulation in Deoxyribonucleic Acid Polymeraseless Strains of Escherichia coli K-12

Spontaneous auxotrophs are found with high frequency in several strains of Escherichia coli K-12 deficient in Kornberg deoxyribonucleic acid polymerase. These include amino acid-, vitamin-, purine-, and pyrimidine-requiring strains. Although this was suggestive evidence that these strains might be mutators, reconstruction experiments demonstrate that auxotrophs possess a selective advantage over prototrophs in the same culture. Thus, despite the high frequency of auxotrophs in polymerase-deficient strains, it is not yet clear whether they have elevated mutation rates.     

Deoxyribonucleic Acid Transferred from Ultraviolet-Irradiated Excision-Defective Hfr Cells of Escherichia coli K-12

Deoxyribonucleic acid (DNA) transfer from (3)H-thymine-labeled Hfr cells has been measured by determining the amount of radioactivity remaining after selective lysis of the donor cells in the mating mixture. DNA transfer was less effectively reduced by ultraviolet irradiation of excision-defective Hfr cells than was the yield of recombinants. The buoyant density of DNA transferred from unirradiated and irradiated Hfr cells was equivalent to that of double-stranded DNA. Mating-dependent DNA synthesis in the recipient has been measured by mating Hfr cells deficient in thymidine kinase with irradiated thymine-requiring F(-) cells in the presence of (3)H-thymine. The extent of such DNA synthesis approximated the amount of DNA transferred from unirradiated donors. Neither DNA transfer nor mating-dependent DNA synthesis could be reliably measured when both parents were irradiated. It is proposed that transferred Hfr DNA is replicated in the recipient and that this replication still occurs when the Hfr DNA contains dimers.     

Deoxyribonucleic Acid-Deoxyribonucleic Acid Hybridization Assay for Replication Origin Deoxyribonucleic Acid of Escherichia coli

Deoxyribonucleic acid (DNA)-DNA hybridization on nitrocellulose filters can be used to assay for replication origin DNA from Escherichia coli if the DNA attached to the filters is enriched for the replication origin sequences. Such DNA can be readily isolated from very rapidly growing cells. When low amounts of this DNA were attached to filters, radioactively labeled DNA from the replication origin hybridized 1.7 times as well as radioactive replication terminus DNA. Under identical conditions, radioactively labeled DNA from exponentially growing cells hybridized only 1.3 times as well as radioactive replication terminus DNA. The replication origin, replication terminus, and randomly labeled DNA hybridized with similar efficiencies to filters containing DNA isolated from cells incubated in the absence of required amino acids. This DNA appeared to have all sequences present at equal frequencies. The hybridization assay was used to demonstrate that the DNA synthesized shortly after the addition of amino acids to cells previously deprived of required amino acids was primarily from the replication origin and then rapidly became similar to DNA synthesized by exponentially growing cells.     

Effect of Iododeoxyuridine upon Conjugation and the Fate of Transferred Deoxyribonucleic Acid in Escherichia coli K-12

The incorporation of 5-iododeoxyuridine (IUdR) into Escherichia coli K-12 deoxyribonucleic acid (DNA) has been found to decrease significantly the viability of female strains A288 and JC411(r) but to have only minor effect upon their ability to act as conjugational recipients and to perform recombination after conjugation. In contrast, IUdR incorporation into male strain HfrC appears to interfere with both chromosome transfer and genetic recombination. By using IUdR to densitylabel female DNA, and carrying out large-scale matings with (3)H-thymidine-labeled male cells, we examined the fate of transferred DNA. After a 30-min mating, the T6-sensitive male cells were lysed, and the DNA of the merozygotes and remaining female cells was isolated. Initial centrifugation of this DNA in a CsCl gradient showed that the male and female DNA species were associated. The nature of this association of the parental DNA species was determined by formaldehyde denaturation followed by CsCl centrifugation. Denaturation of DNA isolated immediately after T6 lysis gave a peak of radioactivity banding at the density of light single-stranded DNA. However, denaturation of DNA isolated after T6 lysis and dilution of the cells into fresh medium, exhibited peaks of radioactivity banding at positions corresponding to single-stranded, density-labeled DNA. The results indicate that recombination after conjugation in E. coli takes place by a breakage-and-reunion mechanism. The process of recombination can be separated into two stages. In the first stage, the donor and recipient DNA molecules become associated. The second stage consists of the formation of phosphodiester bonds between the donor and recipient segments comprising the recombinant molecule.     

Effect of Mutations in Deoxyribonucleic Acid Repair Pathways on the Sensitivity of Escherichia coli K-12 Strains to Nitrofurantoin

Escherichia coli K-12 strains that carry mutations in one or more genes coding for proteins involved in repair of deoxyribonucleic acid lesions are more sensitive to the antibiotic nitrofurantoin than are the nonmutant parent strains.     

Deoxyribonucleic Acid Replication and Cell Division in Escherichia coli at 33 C

At 33 C (60-min generation time) the time required to replicate the chromosome is C = 60 min. The time between the end of a round of replication and cell division is D = 20 min, as at 37 C. Nalidixic acid and a temperature shift in a dnaB mutant give identical results for the determination of the end of a round of replication.     

Acid response of exponentially growing Escherichia coli K-12

Induction of acid tolerance response (ATR) of exponential-phase Escherichia coli K-12 cells grown and adapted at different conditions was examined. The highest level of protection against pH 2.5 challenges was obtained after adaptation at pH 4.5-4.9 for 60 min. To study the genetic systems, which could be involved in the development of log-phase ATR, we investigated the acid response of E. coli acid resistance (AR) mutants. The activity of the glutamate-dependent system was observed in exponential cells grown at pH 7.0 and acid adapted at pH 4.5 in minimal medium. Importantly, log-phase cells exhibited significant AR when grown in minimal medium pH 7.0 and challenged at pH 2.5 for 2 h without adaptation. This AR required the glutamate-dependent AR system. Acid protection was largely dependent on RpoS in unadapted and adapted cells grown in minimal medium. RpoS-dependent oxidative, glutamate and arginine-dependent decarboxylase AR systems were not involved in triggering log-phase ATR in cells grown in rich medium. Cells adapted at pH 4.5 in rich medium showed a higher proton accumulation rate than unadapted cells as determined by proton flux assay. It is clear from our study that highly efficient mechanisms of protection are induced, operate and play the main role during log-phase ATR.     

Mapping of a Mutation, polB100, Affecting Deoxyribonucleic Acid Polymerase II in Escherichia coli K-12

Direct assay for deoxyribonucleic acid polymerase II in extracts has been used to screen recombinants for the polB allele in Hfr × F⁻ crosses, F-ductants in episome transfer, and transductants in generalized transduction by phage P1. The polB gene is located at 2 min on the Escherichia coli linkage map; it is 39 to 64% co-transducible with leu. A mutant, E. coli polA1 polB100 polC (ts), deficient in deoxyribonucleic acid polymerases I and II and having a thermolabile deoxyribonucleic acid polymerase III, has been prepared by the P1-mediated cross: P1 (HMS85 polB100) × E. coli BT1026 polA1 polC (ts) leu⁻.     

Pleiotropic Effect of the recA Gene of Escherichia coli: Uncoupling of Cell Division from Deoxyribonucleic Acid Replication

A defective recA gene, which is involved in recombination, is shown in this article to permit limited cell division, when deoxyribonucleic acid (DNA) synthesis is blocked. Thymidine starvation or nalidixic acid blocked DNA synthesis, and stopped cell division of a rec(+)thy(-) strain of Escherichia coli. However, with the same treatments, a recAthy(-) strain could continue to divide for at least 5 hr, and cell numbers increased 2.5- to 4-fold. After several hours of thymidine starvation, the culture contained very long cells (snakes) and small (normal-sized) cells. The short cells contained very little, if any, DNA. Cells of all ages divided in the absence of thymidine. Specific differences in membrane proteins were observed between thymidine-starved rec(+) and recA cells, as expected from previous experiments in which these proteins were associated with cell division and DNA synthesis. It is proposed that septum formation is controlled negatively by the recA(+) gene.     

Ionizing Radiation Damage to the Folded Chromosome of Escherichia coli K-12: Repair of Double-Strand Breaks in Deoxyribonucleic Acid

The extremely gentle lysis and unfolding procedures that have been developed for the isolation of nucleoid deoxyribonucleic acid (DNA; K. M. Ulmer et al., J. Bacteriol. 138:475-485, 1979) yield undamaged, replicating genomes, thus permitting direct measurement of the formation and repair of DNA double-strand breaks at biologically significant doses of ionizing radiation. Repair of ionizing radiation damage to folded chromosomes of Escherichia coli K-12 strain AB2497 was observed within 2 to 3 h of post-irradiation incubation in growth medium. Such behavior was not observed after post-irradiation incubation in growth medium of a recA13 strain (strain AB2487). A model based on recombinational repair is proposed to explain the formation of 2,200 to 2,300S material during early stages of incubation and to explain subsequent changes in the gradient profiles. Association of unrepaired DNA with the plasma membrane is proposed to explain the formation of a peak of rapidly sedimenting material (greater than 3,100S) during the later stages of repair. Direct evidence of repair of double-strand breaks during post-irradiation incubation in growth medium was obtained from gradient profiles of DNA from ribonuclease-digested chromosomes. The sedimentation coefficient of broken molecules was restored to the value of unirradiated DNA after 2 to 3 h of incubation, and the fraction of the DNA repaired in this fashion was equal to the fraction of cells that survived at the same dose. An average of 2.7 double-strand breaks per genome per lethal event was observed, suggesting that one to two double-strand breaks per genome are repairable in E. coli K-12 strain AB2497.     

Deoxyribonucleic Acid Degradation and the Lethal Effect by Myxin in Escherichia coli

Exposure of Escherichia coli 15T(-) cells to the antibiotic myxin results in the inhibition of deoxyribonucleic acid (DNA) biosynthesis, degradation of intracellular DNA, and death of the cells. Each of these effects was markedly enhanced when protein synthesis was simultaneously inhibited by chloramphenicol. In the continued presence of chloramphenicol, a brief (1 min) exposure to myxin resulted in a rate of DNA degradation and cell death equivalent to that found in the continued presence of myxin alone. Single-strand breaks were present in the DNA of cells exposed to myxin, but when chloramphenicol was also present the breaks were found much earlier. Degradation of DNA in cells exposed to myxin was found to be distributed randomly in both strands and extended over the genome with no restriction to the vicinity of the replication point. There was no release of DNA from its attachment to the cellular membrane in myxin-exposed cells. The possibility that the chloramphenicol effect is due to the inhibition of repair enzyme synthesis which is stimulated by exposure of the cells to myxin is discussed. These data indicate that the extent of the lethal and metabolic damage to the cells by an exposure to myxin represents the result of competition between damage to and repair of cellular DNA.     

Initiation and Termination of Bacterial Deoxyribonucleic Acid Replication in Low Concentrations of Chloramphenicol

Escherichia coli 15T(-) can initiate a cycle of deoxyribonucleic acid replication with equal efficiency in the presence of 25 or 50 mug of chloramphenicol/ml. However, these replication cycles are not completed in the presence of these drug concentrations, and the amount of replication decreases with increasing drug concentration.     

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.     

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.     

Relationships Between Bactericidal Effect and Inhibition of Ribonucleic Acid Nucleotidyl-transferase by Rifampicin in Escherichia coli K-12

The mechanism of action of rifampicin, an antibiotic which inhibits in vitro the polycondensation of ribonucleotides by ribonucleic acid (RNA) nucleotidyltransferase, was studied in vivo in Escherichia coli. It is argued that the inhibition of RNA nucleotidyltransferase represents the primary lesion and is responsible for the bactericidal effect. This conclusion is based on (i) the correlation between concentrations of the antibiotic which block in vivo incorporation of labeled uracil and the bactericidal concentrations, (ii) the evidence that the loss of viability of the cells immediately follows the block of RNA synthesis, and (iii) the observation that the reversal of the inhibition of RNA synthesis goes together with a reversal of the loss of viability.     

Effect of triethyltin on Escherichia coli K-12.

Triethyltin (TET) stimulated the basal respiration of Escherichia coli K-12 membrane vesicles in chloride (Cl-) medium but it had little effect on respiration in sulphate (SO4(2-)) medium. Since this uncoupling activity was Cl- dependent it was attributed to the Cl-/hydroxide (OH-) exchange reaction known to be mediated by TET [1,2]. TET inhibited the oxidation of succinate by intact E. coli in both Cl- and SO4(2-) medium, but at the same concentration of TET, inhibition was always more extensive in Cl- than SO4(2-) medium. In Cl- medium uncoupling in membrane vesicles and inhibition of succinate oxidation in intact bacteria occurred over the same concentration range and it appeared that the same mechanism, i.e. Cl-/OH- exchange, was responsible for both effects. Inhibition of succinate oxidation in SO4(2-) medium was not substantial until the concentration of TET was greater than 10(-5) M. Although the nature of this inhibition could not be determined by experiments with membrane vesicles indirect evidence from growth experiments indicated that it was due to impairment of oxidative phosphorylation. The relationship between these biochemical findings and the bacteriocidal action of TET was examined by using various concentrations of anion and substrate in the growth medium. Growth was inhibited in media containing either Cl- or SO4(2-) as the main anion but at a particular concentration of TET, inhibition was greater in Cl- medium. Growth was also inhibited to a greater extent in succinate than glucose medium. Furthermore in either Cl- or SO4(2-) glucose medium, lactic acid production increased as the concentration of TET was increased. These findings imply that the bacteriocidal action of TET is related to its effect(s) on oxidative phosphorylation.