Effect of thymine starvation on messenger ribonucleic acid synthesis in Escherichia coli

Methylfolate Trap Promotes Bacterial Thymineless Death by Sulfa Drugs

The methylfolate trap, a metabolic blockage associated with anemia, neural tube defects, Alzheimer’s dementia, cardiovascular diseases, and cancer, was discovered in the 1960s, linking the metabolism of folate, vitamin B₁₂, methionine and homocysteine. However, the existence or physiological significance of this phenomenon has been unknown in bacteria, which synthesize folate de novo. Here we identify the methylfolate trap as a novel determinant of the bacterial intrinsic death by sulfonamides, antibiotics that block de novo folate synthesis. Genetic mutagenesis, chemical complementation, and metabolomic profiling revealed trap-mediated metabolic imbalances, which induced thymineless death, a phenomenon in which rapidly growing cells succumb to thymine starvation. Restriction of B₁₂ bioavailability, required for preventing trap formation, using an “antivitamin B₁₂” molecule, sensitized intracellular bacteria to sulfonamides. Since boosting the bactericidal activity of sulfonamides through methylfolate trap induction can be achieved in Gram-negative bacteria and mycobacteria, it represents a novel strategy to render these pathogens more susceptible to existing sulfonamides.

Sulfonamides were the first agents to successfully treat bacterial infections, but their use later declined due to the emergence of resistant organisms. Restoration of these drugs may be achieved through inactivation of molecular mechanisms responsible for resistance. A chemo-genomic screen first identified 50 chromosomal loci representing the whole-genome antifolate resistance determinants in Mycobacterium smegmatis. Interestingly, many determinants resembled components of the methylfolate trap, a metabolic blockage exclusively described in mammalian cells. Targeted mutagenesis, genetic and chemical complementation, followed by chemical analyses established the methylfolate trap as a novel mechanism of sulfonamide sensitivity, ubiquitously present in mycobacteria and Gram-negative bacterial pathogens. Furthermore, metabolomic analyses revealed trap-mediated interruptions in folate and related metabolic pathways. These metabolic imbalances induced thymineless death, which was reversible with exogenous thymine supplementation. Chemical restriction of vitamin B₁₂, an important molecule required for prevention of the methylfolate trap, sensitized intracellular bacteria to sulfonamides. Thus, pharmaceutical promotion of the methylfolate trap represents a novel folate antagonistic strategy to render pathogenic bacteria more susceptible to available, clinically approved sulfonamides.

Thymine Starvation and Single-Strand Breaks in Chromosomal Deoxyribonucleic acid of Escherichia coli

Single-strand breaks, as measured by the McGrath and Williams procedure, occur in chromosomal deoxyribonucleic acid of Escherichia coli cells during thymine starvation.

Thymine metabolism and thymineless death in prokaryotes and eukaryotes

For many years it has been known that thymine auxotrophic microorganisms undergo cell death in response to thymine starvation [thymineless death (TLD)]. This effect is unusual in that deprivation of many other nutritional requirements has a biostatic, but not lethal, effect. Studies of numerous microbes have indicated that thymine starvation has both direct and indirect effects. The direct effects involve both single- and double-strand DNA breaks. The former may be repaired effectively, but the latter lead to cell death. DNA damaged by thymine starvation is a substrate for DNA repair processes, in particular recombinational repair. Mutations in recBCD recombinational repair genes increase sensitivity to thymineless death, whereas mutations in RecF repair protein genes enhance the recovery process. This suggests that the RecF repair pathway may be critical to cell death, perhaps because it increases the occurrence of double-strand DNA breaks with unique DNA configurations at lesion sites. Indirect effects in bacteria include elimination of plasmids, loss of transforming ability, filamentation, changes in the pool sizes of various nucleotides and nucleosides and in their excretion, and phage induction. Yeast cells show effects similar to those of bacteria upon thymine starvation, although there are some unique features. The mode of action of certain anticancer drugs and antibiotics is based on the interruption of thymidylate metabolism and provides a major impetus for further studies on TLD. There are similarities between TLD of bacteria and death of eukaryotic cells. Also, bacteria have "survival" genes other than thy (thymidylate synthetase), and this raises the question of whether there is a relationship between the two. A model is presented for a molecular basis of TLD.

Thymineless death and genetic events in mammalian cells

Thymidylate synthase-negative mutants of cultured mouse FM3A cells were immediately committed to cell death upon thymidine deprivation especially when the cells were synchronized in the S-phase. Thymidine deprivation induced single strand breaks in parental DNA strands, as measured by alkaline sucrose gradient sedimentation, giving rise to two peaks, one with large and the other with short fragments. Increase in the short DNA fragments paralleled that of thymineless death. Thymidine deprivation also accumulated double strand DNA fragments as determined by a method of neutral filter elution, and their extent paralleled that of cell death. Double-strand DNA eluted through the filter sedimented as a single peak both in a neutral and in an alkaline sucrose gradient that coincided with that of the above short DNA fragments. Therefore, the double strand breaks seemed to occur in some defined portions of the genome and in some specific manners in contrast to those induced by X-ray, which occurred rather randomly. Cycloheximide blocked thymineless death and accumulation of the double stranded DNA fragments in parallel. The double strand breaks induced by thymidine starvation were not repaired, but instead advanced on subsequent incubation of the cells in growth medium containing thymidine. Cytogenetically, thymidine deprivation induced chromosome aberrations such as chromatid breaks, chromatid interchanges, and chromosome fragmentation. Also, 5-bromodeoxyuridine deprivation induced sister chromatid exchange. Thymidylate stress also induced loss of a stably integrated human gene in mouse cells, possibly by DNA rearrangements, under the conditions where no point mutations were induced.

Macromolecular synthesis in chromosome initiation mutants of Bacillus subtilis

Inactivation of the dna B or dna D gene product in Bacillus subtilis stimulates RNA and protein synthesis. Strains containing ts dna B and D mutations have been constructed by introducing the mutations by transformation into a thymine requiring strain which does not lyse during thymine starvation. The consequences of inactivation of these gene products have been assessed by comparing RNA and protein synthesis during thymine starvation at the restrictive temperature with the recipient strain. In the ts+ strain, there is a doubling in rate of RNA synthesis during thymine starvation. In the ts dna B and D mutations at the restrictive temperature the rate of RNA synthesis increases four fold. By preincubating the mutants in the absence of thymine for one generation at the permissive temperature the two fold increase in rate of RNA synthesis associated with inactivation of the initiation complex can be demonstrated under conditions where the ts+ strain shows a decrease in rate of RNA synthesis. The rate of protein synthesis observed largely reflects the rate of RNA synthesis in all strains. Completion of the chromosome at the restrictive temperature has no significant effect on the rate of RNA synthesis. It is suggested that inactivation of the initiation complex after chromosome initiation could play an important role in control of RNA synthesis in relation to the cell cycle.

[Escherichia coli K12 mutant with increased RNA content and messenger RNA stability]

A strain of Escherichia coli has been isolated from a E. coli HfrH after a treatment with nitrosoguanidine for a partial resistance to thymineless death. This strain shows, in addition, a global increase of the RNA content amounting to 50 per cent. The half-life of the unstable RNA as well as of the messenger RNA of the beta-galactosidase is increased to a considerable degree. The RNA polymerase of this strain is modified with respect to its resistance to rifampicin and its transcription efficiency in vitro of various DNA templates. Our working hypothesis is that the primary alteration of this strain lies at the RNA polymerase level with a consequent increase of the synthetic rate of the ribosomal RNA. The increase of the messenger RNA half-life may be an indirect consequence of this event via a saturation of the RNAase by the excess of ribosomal RNAs not associated to their proteins.

Thymineless death in Escherichia coli in various assay systems: viability determined in liquid medium

Thymineless death has been studied in four different Thy(-) strains of Escherichia coli by using various assay methods including conventional plating techniques as well as one performed entirely in liquid medium. Plating on L agar resulted in a greater loss in viability than the other assay methods, but this extrasensitivity of starved cells to L-agar plating quickly disappeared upon readdition of thymine to the starved cultures. This indicated that cellular damage responsible for the additional killing on L agar is reversible. The results obtained by three other assay methods, the liquid assay, plating on nutrient agar, or plating on tris(hydroxymethyl)aminomethane-minimal agar, did not differ significantly from each other with all strains tested except strain JG 151. In this strain thymineless death was much faster when assayed in the liquid system than by plating. It is suggested that thymineless death detected on nutrient or minimal agar is not a result of plating, but that the lethal event actually occurs during the period of thymine starvation.

Transforming ability of bacterial deoxyribonucleic acid in relation to the marker efficiencies in Diplococcus pneumoniae during thymidine starvation

Thymidine starvation induces a decrease in transforming activity of pneumococcus deoxyribonucleic acid. The integration of low- and high-efficiency markers seems to be equally affected.

Survival and macromolecular synthesis during incubation of Escherichia coli in limiting thymine

Survival and the synthesis of deoxyribonucleic acid (DNA), ribonucleic acid (RNA), and protein were measured during incubation of a thymine auxotroph of Escherichia coli in a series of media containing thymine concentrations below the optimal level of 2 mug/ml. The rate of increase in viable count gradually diminishes to no net growth with 0.2 mug/ml. With lower concentrations of thymine, the rate of cell death gradually increases, resulting in a typical thymineless death curve with 0.02 mug/ml. Both the rate of cell growth and the rate of cell inactivation vary linearly with the thymine concentration. Thirty minutes of incubation in media containing limiting concentrations of thymine before a shift to complete thymine starvation results in a progressive decrease in the length of the lag period preceding thymineless death. These data suggest that only one type of cellular damage occurs during the various degrees of thymine limitation. Prolonged preincubation in media containing 0.1 to 0.2 mug/ml of thymine results in an immunity to thymineless death. This immunity differs from that observed with amino acid-starved cells in its kinetics; ultraviolet irradiation of preincubated cells indicates that the cells are inactivated at the same rate as log-phase cells. These results suggest that the immunity is not associated with chromosome alignment. Thymine concentrations between 2 mug/ml and 0.2 mug/ml permit essentially the same amount of protein and RNA synthesis. The total amount of synthesis then decreases linearly to 40 to 50% of the control level with further reduction in the amount of thymine present. Protein and RNA synthesis are first affected at the same thymine concentration at which lethality is first detectable, and this correlation suggests that the synthesis of these macromolecules is involved in the mechanism of thymineless death. DNA synthesis, on the other hand, is directly dependent on the thymine concentration for levels of 0.5 mug/ml or less. There are no critical changes in DNA synthesis associated with lethality, and DNA synthesis is still occurring under conditions of thymine limitation which result in immunity. These observations suggest that DNA synthesis is not directly involved in thymineless death.

Methylated bases of Bacillus megaterium KM nucleic acids: comparison with Escherichia coli

Parallel studies were performed with methionineless derivatives of Escherichia coli 15 T(-) and Bacillus megaterium KM: T(-). Methylated bases are present in the total cell ribonucleic acid (RNA) of B. megaterium. The level of RNA methylation in E. coli is about 60% greater than that in B. megaterium. Although E. coli deoxyribonucleic acid (DNA) was found to contain 0.12% 5-methylcytosine (5-MC) and 0.24% 6-methylaminopurine (6-MA), methylated bases were not detected in the DNA of B. megaterium. Assuming a molecular weight of 7 x 10(9) daltons for B. megaterium DNA, it was calculated that this organism could not contain more than one molecule of 5-MC or 6-MA per genome, and that possibly no methylated bases were present. Methylated bases were also not detected in the DNA of thymine-starved B. megaterium. Crude extracts of this organism possess RNA methylase activity but no detectable DNA methylase activity.

Thymineless death in Escherichia coli: deoxyribonucleic acid replication and the immune state

Thymineless death (TLD) and nalidixic acid (NA) inactivation were studied in multiple auxotrophic strains of Escherichia coli B and B/r. As expected, it was found that both E. coli B and B/r exhibited an "immune state," i.e., a fraction of the population survived inactivation to both TLD and NA. With glucose as a carbon source in minimal medium, 0.1 to 0.3% of strain B and 0.2 to 0.5% of strain B/r survived inactivation; with acetate as the carbon source, the surviving fractions were increased to 1 to 2% and 5 to 7%, respectively. These immune fractions could be increased in magnitude by preincubation in minimal media containing thymine. Systematic analysis of the particular supplements necessary for the immune state indicated that the absence of the required amino acids was essential for the maximal expression of immunity. However, immunity was not abolished in acetate medium even in the presence of the required supplements. Further studies on the replication of deoxyribonucleic acid (DNA) during preincubation indicated that the degree of immunity did not necessarily correlate with the completion of a round of DNA replication. This finding was supported by examining the immune state in synchronous populations. In both glucose and acetate medium, there was no significant change in the degree of immunity to inactivation within the cell cycles of E. coli B and B/r. We concluded that some other event, possibly inhibition of protein synthesis, was necessary in determining the degree of the immune state. DNA replication was investigated after TLD and NA inactivation, and, as expected, it was found that both events led to premature initiation of replication. The only differences observed in the effects of these two processes on DNA synthesis were the following. (i) NA-induced replication was less sensitive to chloramphenicol than was TLD. (ii) TLD-induced replication was unaffected by pretreatment of the cells with mitomycin C, but this pretreatment prevented the replication of DNA after NA treatment. It was suggested that the mechanism of action of NA could involve a monofunctional attack on the DNA.

Effect of a recA gene on cell division and capsular polysaccharide production in a lon strain of Escherichia coli

InEscherichia colithe u.v. sensitivity generecAsuppressed u.v.-induced filamentation in alonu.v. sensitive strain without affecting capsular polysaccharide production.recAappears to prevent the stimulus that leads to filamentation in alonstrain.

Macromolecular synthesis and thymineless death in Mycoplasma laidlawii B

The relationships between macromolecular synthesis and viability have been studied in the pleuropneumonia-like organism Mycoplasma laidlawii B adapted to a semidefined grwoth medium. This organism exhibited an absolute growth requirement for the nucleosides uridine and thymidine, a partial requirement for guanosine and deoxyguanosine, but no requirement for adenosine, deoxyadenosine, cytosine, and deoxycytosine. Cytosine and deoxycytosine partially satisfied the requirement for uridine. Loss in viability resulted from thymidine deprivation, but not from a deficiency in other growth requirements. This phenomenon of thymineless death in a mycoplasma is similar in many respects to that reported in other bacterial systems. Chloramphenicol specifically inhibited protein synthesis and allowed deoxyribonucleic acid synthesis to proceed to only about 40% of that normally produced per generation period, while causing less inhibition of ribonucleic acid synthesis. Protein synthesis inhibition permitted thymineless death to a survival level of less than 0.5%, but ribonucleic acid synthesis inhibition resulted in a higher (10%) survival level. These results are consistent with previously noted aspects of thymineless death in Escherichia coli strains, which suggest that thymineless death is coupled to ribonucleic acid synthesis.

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.

Thymineless death in Escherichia coli: strain specificity

Thymineless death of various ultraviolet (UV)-sensitive strains of Escherichia coli B and K-12 was investigated. It was found that E. coli B, B(s-12), K-12 rec-21, and possibly K-12 Lon(-), all sensitive to UV, were also sensitive to thymine starvation. However, other UV-sensitive strains of E. coli were found to display the typical resistant-type kinetics of thymineless death. The correlation of these results with various other cellular processes suggested that the filament-forming ability of the bacteria might be involved in the mechanism of thymineless death. It was apparent from the present results that capacity for host-cell reactivation, recombination ability, thymine dimer excision, and probably induction of a defective prophage had little to do with determining sensitivity to thymine deprivation.