Studies on the induction of thymine deficiency and on the effects of thymine and thymidine analogues in Escherichia coli

relA Inactivation Converts Sulfonamides Into Bactericidal Compounds

Folates are required for the de novo biosynthesis of purines, thymine, methionine, glycine, and pantothenic acid, key metabolites that bacterial cells cannot survive without. Sulfonamides, which inhibit bacterial folate biosynthesis and are generally considered as bacteriostats, have been extensively used as broad-spectrum antimicrobials for decades. Here we show that, deleting relA in Escherichia coli and other bacterial species converted sulfamethoxazole from a bacteriostat into a bactericide. Not as previously assumed, the bactericidal effect of SMX was not caused by thymine deficiency. When E. coli ∆relA was treated with SMX, reactive oxygen species and ferrous ion accumulated inside the bacterial cells, which caused extensive DNA double-strand breaks without the involvement of incomplete base excision repair. In addition, sulfamethoxazole showed bactericidal effect against E. coli O157 ∆relA in mice, suggesting the possibility of designing new potentiators for sulfonamides targeting RelA. Thus, our study uncovered the previously unknown bactericidal effects of sulfonamides, which advances our understanding of their mechanisms of action, and will facilitate the designing of new potentiators for them.

A balanced perspective on unbalanced growth and thymineless death

The early history of the esoteric phenomenon of thymineless death (TLD) is recounted, from the pioneering discovery by Seymour Cohen and Hazel Barner, through my graduate studies at Yale and postdoctoral research in Copenhagen. My principal contribution was the discovery that restricted synthesis of protein and RNA permits cultures of Escherichia coli to complete their DNA replication cycles without initiating new ones, and that cells held in this physiological state are immune to the lethality of thymine deprivation; unbalanced growth is not the fundamental cause of TLD. The successful synchronization of the DNA replication cycle contributed to formulation of the replicon concept. Studies at Stanford revealed a specific requirement for transcription and led to the discovery of a TLD-resistant mutant in a new gene, termed recQ, with important homologs in humans and most other organisms. The lessons learned from research on TLD underscore the value of basic research in bacterial systems that can have profound implications for human health.

Cancer chemotherapy by deoxynucleotide depletion and E2F-1 elevation

We propose that the lethality of commonly used anticancer drugs, e.g., methotrexate and cis-platinum are due, at least in part, to an increase of the E2F-1-mediated apoptotic cascade. The drugs directly or indirectly decrease deoxynucleoside triphosphates. The E2F family acts to provide control of S phase by transcribing genes required for deoxynucleoside triphosphate and DNA synthesis. Thus, a mechanism for control of E2F-1 is essential, a signal safeguarding against aberrant or uncontrolled cell proliferation. We have proposed a feedback control by NTPs that down-regulates E2F-1. Here, we provide evidence in support of this hypothesis.

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.

The autolytic ('suicidase') system of Enterococcus hirae: from lysine depletion autolysis to biochemical and molecular studies of the two muramidases of Enterococcus hirae ATCC 9790

Autolysis of Enterococcus hirae ATCC 9790 is the result of the action of endogenous enzymes that hydrolyze bonds in the protective and shape-maintaining cell wall peptidoglycan. It is thought that these potentially suicidal enzymes play a positive role(s) in wall growth and division and are expressed as autolysins when cell wall assembly and/or repair are inhibited. E. hirae possesses two potentially autolytic enzymes, both of which are muramidases. Although they hydrolyze the same bond as hen egg-white lysozyme, both are high-molecular-mass, complex enzymes. Muramidase-1 is synthesized as a zymogen, requiring protease activation. It is a glucoenzyme that is also multiply nucleotidylated with an unusual nucleotide, 5-mercaptouridine monophosphate. Muramidase-2 is almost certainly a product of a separate gene. The deduced amino acid sequence of a cloned gene for extracellular muramidase-2 showed several unusual features. It appears to be a two-, or perhaps three-domain protein with a putative glycosidase-active site near the N-terminal end and six 45-amino-acid-long repeats at the C-terminal end which are presumed to be involved with high-affinity binding to the insoluble peptidoglycan substrate. Muramidase-2 binds penicillin with low affinity. The presence of several amino acid groupings characteristic of serine-active site beta-lactam-interactive proteins is consistent with the possible presence of a penicillin-binding, third domain. Indirect evidence consistent with a role(s) for these enzymes in cell wall growth and division has been obtained. However, proof of such role(s) awaits modern genetic, molecular, and biochemical analyses.

A possible role for deoxyribonucleotide pool imbalances in carcinogenesis

Thymine nucleotide pool alterations, produced by attack on non-DNA primary targets, induce a variety of chromosome and chromatid aberrations. Specifically, in lower eukaryotes, thymidylate deprivation and excess are recombinagenic and dTMP depletion also produces DNA strand breakage. In higher eukaryotes, imbalances in thymine nucleotide pools provoke chromosome breaks and rearrangements, and inhibition of thymidylate biosynthesis causes morphological and oncogenic transformation in vitro. Thus, chromosomal rearrangements induced by dTMP deprivation may be the critical changes that lead to oncogenic transformation in response to thymine nucleotide depletion.

Induction of lethal damage in E. coli by Cerenkov emission associated with high-energy X-rays: the effect of bromouracil substitution

5.1. The damages induced in E. coli AB2487 recA by Cerenkov emission and ionizing radiation contribute in an additive fashion to the overall lethality, and do not interact in a synergistic fashion. 5.2. BU substitution enhances the lethal action of high energy X-irradiation on E. coli AB2487 recA by a mechanism involving enhanced radiosensitivity and enhanced photosensitivity.

Nonspecificity of some commonly used inhibitors of DNA synthesis in cultures of Streptococcus faecalis

The specificity of three commonly used inhibitors of DNA synthesis were tested in the batch culture of Streptococcus faecalis ATCC 8043 in rich broth medium. It was shown that nalidixic acid, mitomycin C and 6-(4-hydroxyphenylazo)uracil inhibit the growth of the cell mass as much as they decrease net DNA synthesis. Hence the drugs tested are highly unspecific inhibitors of DNA synthesis in S. faecalis; i.e. they all interfere with other processes as well as with DNA synthesis.

Inhibition of thymidine phosphorylase in vivo provides a rapid method for switching DNA labeling

Uridine blocks the in vivo conversion of thymine to thymidine in Escherichia coli, thus, one can change DNA labels by labelling first with a thymine label (e.g. 14C) and then, at the time of the change, adding 50 microgram uridine per ml and thymidine (e.g. 3H). The cells immediately start using the thymidine, ignore the thymine for several generations, and are not affected by the uridine.

Sensitization of Escherichia coli C to gamma-radiation by 5-bromouracil incorporation

Escherichia coli C cells, unifilarly substituted with 5-bromouracil (BrUra) were 2-25 times as sensitive as unsubstituted cells to killing by gamma-irradiation under aerobic conditions. The yield of DNA double-strand breaks in BrUra-substituted cells was increased by a factor only 1-55, suggesting that other lesions also contribute to cell-killing. Alkaline sucrose density gradient analysis of the 3H-thymine labelled DNA strand showed there was less repair of gamma-ray-induced single-strand breaks when BrUra was in the complementary strand. Since there are more of these unrepaired breaks than can be accounted for by BrUra-induced DNA double-strand breakage, some fraction of the lethal events in BrUra-substituted E. coli cells may be unrepaired DNA single-strand breaks.

Studies of intracellular thymidine nucleotides. Thymineless death and the recovery after re-addition of thymine in Escherichia coli K 12

In a thymine-deprived culture, the mutant cells (deficient in dTDP-glucose pyrophosphorylase activity and named Ter-15) lose viability at a faster rate, form longer filaments for the first 60 min and lose thymidine nucleotides and dTDP-sugar pools at a faster rate for the first 15 min than those of the parent cells, but the dTDP-sugar pool in the parent cells is maintained at high concentration for the first 90 min during thymine starvation. In the recovery of cell growth after re-addition of thymine into the thymine-deprived culture, parent cells recommence growth immediately, but the mutant cells (Ter-15) show a lag-phase for 45 min after which time their growth recommences. The rate of dTTP synthesis for the first 10 to 15 min after re-addition of thymine to thymine-deprived cultures of parent and mutant (Ter-15) cells is three-fold higher than that of thymine nondeprived culture (control), but the rates of dTMP and dTDP-sugar syntheses are the same as those of the control. The total DNA synthesis after re-addition of thymine is equal to that of the control, and the period of thymine starvation other than the number of viable cells during thymine starvation plays an important role. After separation of the filament cells from normal-sized cells by sucrose gradient centrifugation, the initial rate of DNA synthesis of filament cells is three-fold faster than that of normal-sized cells. These results show that the dependency of DNA synthesis upon dTTP concentration is maintained after re-addition of thymine into thymine-deprived culture.

5-Bromouridylyl-(3-5)-adenosine isolated from 5-bromouracil-induced filaments of Escherichia coli

A dinucleoside monophosphate was isolated from 5-bromouracil-induced filaments of a thymine auxotroph of Escherichia coli K-12. The dinucleoside monophosphate was fractioned from a [(14)C]5-bromouracil-labeled perchloric acid extract using Dowex-1-formate ion-exchange chromatography. Sephadex chromatography revealed its molecular weight to be 710. Snake venom phosphodiesterase digest of the dinucleoside monophosphate yielded [(14)C]5-bromouridine and adenosine 5'-monophosphate. The presence of [(14)C]5-bromouracil in bacterial ribonucleic acid indicates that ribonucleic acid, which had incorporated 5-bromouracil, was the probable source of this dinucleoside monophosphate, 5-bromouridylyl-(3' --> 5')-adenosine.

Interactions of polyoma and mouse DNAs. I. Lytic infection of bromodeoxyuridine-prelabeled mouse embryo cells

On CsCl isopycnic centrifugation of the DNA extracted from secondary mouse embryo (ME) cultures grown in the presence of 5-bromodeoxyuridine (BUdR) and 5-fluorodeoxyuridine (FUdR) for 40 h, 10 to 25% of the DNA was found to be unsubstituted, 70 to 80% was bromouracil-hybrid DNA, and 5 to 10% was heavy DNA. These results together with cell number determinations, autoradiography, and Feulgen microspectrophotometry revealed three types of cells in these cultures: (i) 60 to 80% of the cells replicated their DNA once, divided, and then stopped mitotic activity, (ii) 5 to 10% were going through a second round of DNA replication; whereas (iii) 10 to 30% did not replicate DNA during the BUdR-FUdR exposure. After the transfer of these cultures to normal medium (without BUdR-FUdR), up to 20% of the cells resumed DNA synthesis asynchronously within 60 h, but no increase in cell number was observed. BUdR-FUdR-treated cultures, which were infected with polyoma virus in the absence of the thymidine analogues, supported a lytic infection to the same extent as did untreated ME cultures. This was concluded from the similar number of cells, which were induced to synthesize DNA, from the similar replication rate of the viral DNA, from the similar number of cells containing polyoma capsid proteins, and from the similar yields of progeny virus determined by hemagglutination and plaque formation. Thus, BUdR-prelabeled ME cultures are suitable for the investigation of interactions of the polyoma and mouse genomes during the lytic infection.

5-Bromouracil-tolerant mutants of Bacillus subtilis

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 mug of BU/ml and 1 mug of thymine/ml. It is not known at what step or steps this reduction in selectivity occurs.

Method for restricting incorporation of radioactivity from 3 H-thymidine into deoxyribonucleic acid only during outgrowth of spores of Bacillus cereus T

When heat-activated spores of Bacillus cereus T (thy(-)) were germinated and grown in medium containing (3)H-thymidine, a significant amount of radioactivity was incorporated into ribonucleic acid and deoxyribonucleic acid (DNA). A method was developed to restrict the incorporation of radioactivity from (3)H-thymidine into DNA only. This was accomplished by labeling the cells with (3)H-thymidine in the presence of 2 mg of 2-deoxyadenosine per ml, 250 mug each of uracil, cytosine, and guanosine per ml, and 500 mug of adenosine per ml. Under these conditions, 97% of the radioactivity incorporated into cold trichloroacetic acid-insoluble material was associated with DNA only. In the absence of these compounds, DNA contained only 72% of the total radioactivity incorporated into cold acid-insoluble material.

Control of cell division in Escherichia coli: experiments with thymine starvation

This paper describes the kinetics of cell division in populations of cells which have been grown first under conditions which specifically inhibit deoxyribonucleic acid (DNA) synthesis (in the absence of thymine or the presence of nalidixic acid) and subsequently under conditions which allow DNA synthesis to recommence. Cell division does not take place during inhibition of DNA synthesis. There is a delay between recommencement of DNA synthesis and recommencement of cell division. The length of this delay increases as a function of the length of the preceding period of inhibition of DNA synthesis. The first division after this delay is partly synchronous, but all subsequent division is asynchronous. These observations are explained in terms of a model which supposes that the formation of initiator of chromosome replication during a period when DNA synthesis is inhibited results in a block to cell division. Division does not then occur until this "extra" round of DNA synthesis is completed.

The effect of cytotoxic agents on the passive transfer of cell-mediated immunity

A system involving the passive transfer of committed lymphoid cells from Listeria-immune donors has been used to study the phases of the immune response which are sensitive to the immunosuppressive action of various cytotoxic agents. The agents investigated included cyclophosphamide, vinblastine, methotrexate, azathioprine, and X-irradiation. Complete suppression of passive immunization was obtained by the administration of cyclophosphamide or vinblastine to recipients at the time of cell transfer or by prior X-irradiation of recipients a day before cell transfer. Methotrexate was only partially suppressive, whereas azathioprine had no effect at all. The donor cell responsible for the transfer of immunity to recipients was shown to be a resting cell which is sensitive to the action of cyclophosphamide but not to vinblastine. The results of this investigation suggest that the donor cells undergo multiplication in the tissues of the recipient, presumably in response to specific stimulation by Listeria antigens. This in turn results in the activation of host macrophages. The immunosuppressive action of cyclophosphamide, vinblastine, and irradiation in the cell-transfer system has been discussed in relation to a direct cytotoxic action on the immune lymphoid cells of the donor and specific interference with their proliferation in the recipient, as well as impairment of macrophage production on the part of the recipient itself.

Studies on chloroplast development and replication in Euglena. I. Vitamin B12 and chloroplast replication

When Euglena gracilis is grown under vitamin B(12) deficiency conditions, the amount of protein and of chlorophyll per cell increase with decrease of B(12) in the medium and consequently in the cell. The increase in cell protein is proportional to and precedes an increase in the number of chloroplasts per cell. This replication of the chloroplasts under deficiency conditions is not accompanied by nuclear or cell division. It is concluded that chloroplast replication in Euglena gracilis is independent of nuclear and cellular replication, at least under B(12) deficiency conditions. We established a graph of the growth of Euglena under different concentrations of vitamin B(12) added to the growth medium, which permitted us to calculate that at least 22,000 molecules of vitamin B(12) per cell are required to give normal growth.

Thymidine and thymine incorporation into deoxyribonucleic acid: inhibition and repression by uridine of thymidine phosphorylase of Escherichia coli

Thymidine is poorly incorporated into deoxyribonucleic acid (DNA) of Escherichia coli. Its incorporation is greatly increased by uridine, which acts in two ways. Primarily, uridine competitively inhibits thymidine phosphorylase (E.C.2.4.4), and thereby prevents the degradation of thymidine to thymine which is not incorporated into normally growing E. coli. Uridine also inhibits induction of the enzyme by thymidine. It prevents the actual inducer, probably a deoxyribose phosphate, from being formed rather than competing for a site on the repressor. The inhibition of thymidine phosphorylase by uridine also accounts for inhibition by uracil compounds of thymine incorporation into thymine-requiring mutants. Deoxyadenosine also increases the incorporation of thymidine, by competitively inhibiting thymidine phosphorylase. Deoxyadenosine induces the enzyme, in contrast to uridine. But this is offset by a transfer of deoxyribose from deoxyadenosine to thymine. Thus, deoxyadenosine permits incorporation of thymine into DNA, even in cells induced for thymidine phosphorylase. This incorporation of thymine in the presence of deoxyadenosine did not occur in a thymidine phosphorylase-negative mutant; thus, the utilization of thymine seems to proceed by way of thymidine phosphorylase, followed by thymidine kinase. These results are consistent with the data of others in suggesting that wild-type E. coli cells fail to utilize thymine because they lack a pool of deoxyribose phosphates, the latter being necessary for conversion of thymine to thymidine by thymidine phosphorylase.

Metabolism of thymineless mutants of Escherichia coli. I. Absence of thymidylate synthetase activity and growth characteristics of two sequential thymineless mutants

A study of optimal thymine and deoxythymidine (dThd) growth requirements of the thymineless mutants of Escherichia coli 15, E. coli 70-462 (strain 70), and a variant, E. coli 70V3-462 (strain 70V3), showed that for maximal turbidity (growth) strain 70 required 10-fold greater concentrations of thymine or dThd than did strain 70V3. On suboptimal concentrations of thymine or dThd, growth of strain 70 was greater on dThd than on thymine. In contrast, maximal growth of strain 70V3 was the same on equimolar concentrations of thymine and dThd. Growth rate of strain 70V3 was the same on equimolar concentrations of thymine and dThd up to 4 mum; at concentrations of 5 mum and greater, the "4-hr" growth was lower on dThd than on corresponding concentrations of thymine. Cultures of both thymineless mutants synthesized equal maximal amounts of DNA. Whereas strain 70V3 incorporated a maximum of 90% of the thymine or dThd in the media, strain 70 incorporated a maximum of only 10%. This poor utilization by strain 70 was neither a result of thymine or dThd conversion to a low-molecular-weight thymine derivative nor the production of a nonthymine inhibitory substance. Since strains 70 and 70V3 exhibited no thymidylate synthetase activity, the first mutation (strain 15 to strain 70) resulted in the loss of this activity. The second mutation (strain 70 to strain 70V3) probably brought about the loss of an enzyme(s) that catabolizes deoxyribose phosphate, permitting a greater net synthesis of dThd from thymine.

Effect of 9-beta-D-arabinofuranosyladenine on polymer synthesis in a polyauxotrophic strain of Escherichia coli

Leung, Hazel Barner (University of Pennsylvania School of Medicine, Philadelphia), Alice McGovern Doering, and Seymour S. Cohen. Effect of 9-beta-d-arabinofuranosyladenine on polymer synthesis in a polyauxotrophic strain of Escherichia coli. J. Bacteriol. 92:558-564. 1966.-Adenine-requiring mutants have been obtained from Escherichia coli strain 15 TAU, which also needs thymine, arginine, and uracil for growth. Some of these are killed by 9-beta-d-arabinofuranosyladenine (ara-A) in the absence of exogenous adenine; a particular mutant of this type, designated TAUAd, has been used in our studies. The lethality of ara-A, d-arabinosylhypoxanthine, and the 1-n-oxide of ara-A has been compared; ara-A is equally toxic in the presence or absence of thymine. Although the absence of uracil reduces ara-A toxicity, the lack of arginine almost eliminates lethality. It was found that ara-A completely inhibits deoxyribonucleic acid synthesis without markedly affecting ribonucleic acid (RNA) synthesis. Some inhibition of protein synthesis can be detected. However, the interpretation of these results is complicated because (i) exogenous adenine must be excluded, (ii) endogenous adenine is made available from RNA turnover, and (iii) ara-A is being rapidly converted to only slightly less toxic arabinosylhypoxanthine by the adenosine deaminase of E. coli. A suitable inhibitor for the bacterial deaminase has not yet been found.