Dependence of mammalian DNA synthesis on DNA supercoiling. III. Characterization of the inhibition of replicative and repair-type DNA synthesis by novobiocin and nalidixic acid

Novobiocin and nalidixic acid, inhibitors of the bacterial enzyme DNA gyrase, inhibit DNA, RNA and protein synthesis in several human and rodent cell lines. The sensitivity of DNA synthesis (both replicative and repair) to inhibition by novobiocin and nalidixic acid is greater than that of protein synthesis. Novobiocin inhibits RNA synthesis about half as effectively as it does DNA synthesis, whereas nalidixic acid inhibits both equally well. Replicative DNA synthesis, as measured by incorporation of [3H]thymidine, is blocked by novobiocin in a number of cell strains; the inhibition is reversible with respect to both DNA synthesis and cell killing, and continues for as long as 20--30 h if the cells are kept in novobiocin-containing growth medium. Both novobiocin and nalidixic acid inhibit repair DNA synthesis (measured by BND-cellulose chromatography) induced by ultraviolet light or N-methyl-N'-nitro-N-nitrosoguanidine (but not that induced by methyl methanesulfonate) at lower concentration (as low as 5 micrograms/ml) than those required to inhibit replicative DNA synthesis (50 micrograms/ml or greater). Neither novobiocin nor nalidixic acid alone induces DNA repair synthesis. Incubation of ultraviolet-irradiated cells with 10--100 micrograms/ml novobiocin results in little, if any, further reduction of colony-forming ability (beyond that caused by the ultraviolet irradiation). Novobiocin at sufficiently low concentrations (200 micrograms/ml) apparently generates a quiescent state (in terms of cellular DNA metabolism) from which recovery is possible. Under more drastic conditions of time in contact with cells and concentration, however, novobiocin itself induces mammalian cell killing.     

Effect of the bacterial DNA gyrase inhibitors, novobiocin, nalidixic acid, and oxolinic acid, on oxidative phosphorylation

When incubated with isolated intact rat liver mitochondria, novobiocin and nalidixic acid act as uncouplers of oxidative phosphorylation; they stimulate oxygen uptake and inhibit ATP synthesis. Novobiocin is about as powerful an uncoupler as is 2,4-dinitrophenol, nalidixic acid is somewhat less powerful, and oxolinic acid exerts no inhibition whatsoever at the concentrations used. The three inhibitors are without effect on oxidative phosphorylation in Escherichia coli nor does novobiocin affect this process in a novobiocin-permeable mutant of yeast. While it would appear that oxolinic acid may be a relatively specific tool for the manipulation of the superhelicity of DNA in complex systems such as mammalian mitochondria and intact mammalian cells, the specificity of each of these inhibitors may depend upon the particular conditions and species used and such experiments require adequate controls on oxidative phosphorylation.     

The effect of preincubation of HeLa cell nuclei with ATP on the degradation of mononucleosomal DNA by micrococcal nuclease.

HeLa cell nuclei with DNA labeled with [3H] thymidine have been preincubated under varying conditions and then incubated with micrococcal nuclease. Aliquots, removed at increasing times, were analyzed for mononucleosomal size DNA and for acid-soluble DNA, the ratios were plotted and a slope was determined. Preincubation with ATP and a regenerating system increased the slope 2 fold. Optimum ATP concentrations were above 0.25 mM. The ATP effect was reversed by novobiocin. No inhibition of the ATP effect was observed with nalidixic acid, coumermycin, oxolinic acid, VM-26, aphidicolin, or 3 amino-benzamide. NAD or cAMP or cGMP had no effect with or without ATP. Other nucleoside triphosphates could substitute to varying degrees for ATP as could ATP analogues. Nuclei from log phase cells showed no ATP effect, but log phase cells, partially depleted of ATP by incubation with deoxyglucose, showed the effect. The effect was lost in nuclei on long-term storage. No evidence was found for differential degradation of core histones, histone H-1 or DNA, and there was no evidence of nucleosome sliding.     

An evaluation of the evidence for H+ pumping by reconstituted cytochrome c oxidase in the light of recent criticism

Caffeine inhibited DNA synthesis in toluene-treated Escherichia coli K12 strains to the same extent as in intact cells using the incorporation of [3H]thymidine as a measure of DNA synthesis. The inhibition was found to be competitive with ATP, and it was not influenced by the concentrations of deoxynucleoside triphosphates to any extent. When caffeine was added together with other DNA synthesis inhibitors such as novobiocin, nalidixic acid or actinomycin D, the inhibition in all cases was non-additive. It is suggested that caffeine inhibits one of the ATP-requiring enzymes in the DNA replication machinery, possibly DNA polymerase III or one of the DNA helicases.     

Inhibition of recovery from potentially lethal damage by chemicals in Chinese hamster V79 A cells

Summary The inhibition of recovery from potentially lethal damage and the influence of mutation induction by lactate, pyruvate, novobiocin, and nalidixic acid was studied in the stationary phase of Chinese hamster V79 A cells. Lactate and pyruvate were selected to elucidate their possible involvement in the inhibition of recovery from PLD since high levels of lactate and pyruvate accumulate due to increased aerobic and anaerobic glycolysis in tumours. Effects of novobiocin and nalidixic acid were also studied to elucidate the possible role of an enzyme similar to DNA gyrase in the potentially lethal damage recovery of V79 cells. The inhibition of recovery depends on drug concentration and is complete with 20 mM of lactate and pyruvate and 20 µM of nalidixic acid and novobiocin. The chemicals seem to interfere with an early step in the recovery process. Incubation with novobiocin in a post-irradiation period does not change the mutation frequency significantly whereas lactate and pyruvate demonstrate a slight increase. Cells incubated with nalidixic acid showed a significant increase in mutation frequency at 24 h post-irradiation recovery time.Alexander von Humboldt Fellow: Present address: Department of Bio-Science, H. P. University, Summer-Hill, Simla, India     

Effect of nalidixic acid and novobiocine on the metabolism of suspension cultured carrot cells

Suspension cells of Daucus carota L. cv. Lunga di Amsterdam are extremely sensitive to both nalidixic acid and novobiocine. The synthesis of DNA, RNA and protein are inhibited within minutes of exposure even at concentrations less than 0.1 mM of both drugs. Moreover, uptake of deoxythymidine by cells is impaired more severely than by sodium azide. Reduction of oxygen consumption caused by the two drugs is slower than in the case of NaN₃ and occurs a few minutes after the inhibition of macromolecular biosynthesis. This excludes the possibility that the block in oxidation is the primary cause of the observed inhibition of cellular functions and suggests that the inhibition of ATP synthesis, which is immediately affected in both cases, may be responsible for these effects. A possible interaction with other cellular targets may be secondary to the uncoupling effect. Cell growth is completely inhibited by 0.3 mM concentration of both drugs, but this inhibition is irreversible only in the case of novobiocine. The irreversibility of cell growth inhibition by novobiocine can be explained by the total disappearance of ATP from the cell.     

Mechanism of action of nalidixic acid on Escherichia coli. Vi. Cell-free studies

The effects of nalidixic acid in vitro on deoxyribonucleic acid (DNA)- polymerase (deoxyribonucleosidetriphosphate: DNA deoxynucleotidyltransferase, EC 2.7.7.7), deoxyribonucleotide kinases (ATP: deoxymono- and diphosphate phosphotransferases), and deoxyribosyl transferase (nucleoside: purine deoxyribosyltransferase, EC 2.4.2.6) were examined employing partially purified and crude extracts of Escherichia coli ATCC 11229 and E. coli 15TAU. Nalidixic acid had no inhibitory effect on the DNA-polymerase of the wild-type strain E. coli ATCC 11229 at concentrations of 1.4 x 10(-3) to 2.8 x 10(-3)m. No inhibition of deoxyribonucleotide kinase activity was observed at concentrations of nalidixic acid ranging from 2 x 10(-3) to 8.6 x 10(-3)m. Nalidixic acid (0.43 x 10(-4) to 0.43 x 10(-3)m) had no inhibitory effect on the deoxyribosyl transferase activity of crude extracts obtained from E. coli ATCC 11229 or E. coli 15TAU. Analytical CsCl density gradient centrifugation demonstrated that the DNA obtained after treatment of E. coli 15TAU with nalidixic acid was not cross-linked. These results suggest that the prevention of DNA synthesis in vivo by nalidixic acid is not attributable to inhibition of DNA polymerase, deoxyribonucleotide kinase, deoxyribosyl transferase, or to cross-linking of the DNA of treated cells.     

The effect of various inhibitors of DNA synthesis on the repair of DNA photoproducts

The effect on DNA repair of several inhibitors of DNA synthesis has been investigated in CHO cells. Three assays were employed following ultraviolet irradiation of G₁ cells: unscheduled DNA synthesis, removal of antibody binding sites and alkaline elution. Cytosine arabinoside and aphidicolin were found to reduce unscheduled DNA synthesis in a dose-dependent manner without affecting the removal of antibody-binding sites. Strand rejoining was also inhibited. These results are consistent with the hypothesis that inhibition is due to premature chain termination during repair synthesis some time after excision of the lesion. Conversely, inhibition of unscheduled DNA synthesis by novobiocin is paralleled by inhibition of excision of the lesion. However, no inhibition of incision was apparent. Since nalidixic acid, an inhibitor of topoisomerase II, did not inhibit excision, it is unlikely that the primary site of action of novobiocin is this topoisomerase. The possibility that a second topoisomerase and/or a polymerase are affected is discussed in the light of previously published data.     

The effect of various inhibitors of DNA synthesis on the repair of DNA photoproducts

The effect on DNA repair of several inhibitors of DNA synthesis has been investigated in CHO cells. Three assays were employed following ultraviolet irradiation of G1 cells: unscheduled DNA synthesis, removal of antibody binding sites and alkaline elution. Cytosine arabinoside and aphidicolin were found to reduce unscheduled DNA synthesis in a dose-dependent manner without affecting the removal of antibody-binding sites. Strand rejoining was also inhibited. These results are consistent with the hypothesis that inhibition is due to premature chain termination during repair synthesis some time after excision of the lesion. Conversely, inhibition of unscheduled DNA synthesis by novobiocin is paralleled by inhibition of excision of the lesion. However, no inhibition of incision was apparent. Since nalidixic acid, an inhibitor of topoisomerase II, did not inhibit excision, it is unlikely that the primary site of action of novobiocin is this topoisomerase. The possibility that a second topoisomerase and/or a polymerase are affected is discussed in the light of previously published data.     

DNA Synthesis in Chloroplasts: III. THE DNA GYRASE INHIBITORS NALIDIXIC ACID AND NOVOBIOCIN INHIBIT BOTH THYMIDINE INCORPORATION INTO DNA AND PHOTOSYNTHETIC OXYGEN EVOLUTION BY ISOLATED CHLOROPLASTS

The influence of two DNA gyrase inhibitors, nalidixic acid andnovobiocin, on DNA synthesis in isolated pea chloroplasts wasexamined. Novobiocin at 1–5 mol m^–3 markedly lowered[³H]thymidine incorporation into DNA (30–95% inhibition);while less effective, nalidixic acid at similar concentrationsalso diminished incorporation (25–35% inhibition). Theinhibition of chloroplast DNA (ctDNA) biosynthesis by nalidixicacid and novobiocin was confirmed by autoradiography and densitometry.These data are consistent with the view that chloroplasts containa DNA gyrase-like enzyme which is necessary for DNA replication.Despite this, interpretation of the results is not straightforward,as both nalidixic acid and novobiocin also inhibited photosyntheticactivity. Each substance (at millimolar levels) reduced ferricyanide-dependentO₂ evolution in isolated chloroplasts. However, at lower concentrations(0.05–0.3 mol m^–3) they slightly enhanced photosyntheticelectron flow; thus, these compounds may act as uncouplers ofphotophosphorylation as well as inhibitors of electron transport.Nalidixic acid and novobiocin at relatively low (0.1 mol m^–3)concentrations also strongly reduced CO₂-dependent O₂ evolution(an index of CO₂ photo-assimilation) in isolated plastids. Thus,caution must be exercised in assessing results from studiesin which nalidixic acid and novobiocin are used with whole plants,cells, protoplasts or isolated chloroplasts. Key words: Chloroplast, DNA replication, novobiocin, nalidixic acid, DNA gyrase     

Evidences for the existence of two steps in DNA replication obtained in toluene-treated Escherichia coli.

Toluene-treated Escherichia coli can synthesize DNA in the presence of precursors and ATP [Moses, R.E. & Richardson, C.C. (1970) Proc. Natl Acad. Sci. U.S.A. 67, 674--681]. The replacement of ATP by another NTP or dNTP leads to the premature arrest of the reaction. Residual synthesis in the presence of an NTP or dNTP other than ATP differs from the complete reaction in the presence of ATP because it is less sensitive to nalidixic acid and novobiocin and because its maximal activity can be obtained with lower concentrations of dNTP or shorter times of toluene treatment. However, like the complete reaction, residual synthesis occurs at the replication fork pre-existing in vivo at the time of toluenization, produces short and long pieces of DNA, is inhibited by arabinosyl-adenine triphosphate, azide or mitomycin C, and is dependent on the dnaE, DNAB and dnaG gene products. We conclude from these data that ATP is specifically required for a step in DNA replication which involves the activity of DNA gyrase, the target of nalidixic acid and novobiocin [Higgins, N.P., Peebles, C.L., Sugino, A. & Cozzarelli, N.R. (1978) Proc. Natl Acad. Sci. U.S.A. 75, 1773-1777]. In the absence of DNA gyrase activity, short DNA pieces are formed and sealed but only a limited amount of the chromosome can be replicated (residual synthesis). In the presence of DNA gyrase activity, DNA synthesis can occur on a longer portion of the chromosome (complete synthesis).     

DNA synthesis in vivo and in vitro in Escherichia coli irradiated with ultraviolet light

DNA synthesis was followed in vivo and in permeable Escherichia coli after ultraviolet light irradiation, irradiation and incubation in a growth medium containing chloramphenicol and in unirradiated cells. In vitro, replicative type DNA synthesis was partially restored after incubation of cells in medium containing chloramphenicol, but not in vivo. The DNA was pulse-labeled in permeable cells in the presence of deoxyribonucleoside triphosphates and ribonucleoside triphosphates. dCTP was replaced by 5-Hg-dCTP as a substrate for DNA synthesis. Hg-DNA was separated from cellular nucleic acids on thiol-agarose affinity columns. The 5' termini of newly synthesized DNA were analyzed after treatment with alkaline phosphatase and rephosphorylation with polynucleotide kinase and [gamma-32P]ATP. DNA synthesis in unirradiated permeable E. coli represents a replicative process dependent on ATP and inhibited by novobiocin. About 70% of the nascent DNA carried terminally labeled RNA moiety at its 5' end. In vitro DNA synthesis in irradiated cells was suppressed and hardly influenced by the presence of ATP or novobiocin. The 5'-RNA content of this cell population was less than 5%.     

Variable effects of DNA-synthesis inhibitors upon DNA methylation in mammalian cells.

Post-synthetic enzymatic hypermethylation of DNA was induced in hamster fibrosarcoma cells by the DNA synthesis inhibitors cytosine arabinoside, hydroxyurea and aphidicolin. This effect required direct inhibition of DNA polymerase alpha or reduction in deoxynucleotide pools and was not specific to a single cell type. At equivalently reduced levels of DNA synthesis, neither cycloheximide, actinomycin D nor serum deprivation affected DNA methylation in this way. The topoisomerase inhibitors nalidixic acid and novobiocin caused significant hypomethylation indicating that increased 5-mCyt content was not a necessary consequence of DNA synthesis inhibition. The induced hypermethylation occurred predominantly in that fraction of the DNA synthesized in the presence of inhibitor; was stable in the absence of drug; was most prominent in low molecular weight DNA representing sites of initiated but incomplete DNA synthesis; and occurred primarily within CpG dinucleotides, although other dinucleotides were overmethylated as well. Drug-induced CpG hypermethylation may be capable of silencing genes, an effect which may be relevant to the aberrantly expressed genes characteristic of neoplastic cells.     

Mode of Action of Novobiocin in Escherichia coli

The mechanism of action of novobiocin was studied in various strains of Escherichia coli. In all strains tested except mutants of strain ML, the drug immediately and reversibly inhibited cell division, and later slowed cell growth. The previously described impairment of membrane integrity, degradation of ribonucleic acid (RNA), and associated bactericidal effect were found to be peculiar to ML strains. The earliest and greatest effect in all strains was an inhibition of deoxyribonucleic acid (DNA) synthesis; RNA synthesis was inhibited to a lesser extent, and cell wall and protein synthesis were affected later. The inhibition of nucleic acid synthesis was accompanied by an approximately threefold accumulation of all eight nucleoside triphosphates. Since novobiocin does not inhibit nucleoside triphosphate synthesis, degrade DNA, or immediately affect energy metabolism, it must inhibit the synthesis of DNA and RNA by direct action on template-polymerase complexes.     

DNA dependence and inhibition by novobiocin and coumermycin of the nucleolar adenosine triphosphatase (ATPase) of human fibroblasts

We have recently demonstrated by electron microscopic cytochemical methods that unfixed human fibroblasts exhibit intense MG2+ dependent adenosine triphosphatase (nATPase) activity in circumscribed areas of the cell nucleoli. The nATPase was specific for ATP and dATP and was inhibited by other ribonucleoside triphosphates. Its intranucleolar localization relative to nucleolar chromatin, and segregation into nucleolar zones after actinomycin treatment of the cells, suggested that the reaction took place in fibrillar centers. This ATPase has now been further characterized by electron microscopic cytochemistry. It was determined that short fixation permitted retention of most of the ATPase activity, and that the enzyme was active at high ionic strength (up to 400 mM KCl), but that the enzyme activity was very sensitive to elevated temperatures. DNA dependence of the enzyme was shown by inhibition of the reaction by DNase pretreatment in parallel with the removal of DNA from the cell, while pretreatment with RNase had no significant effect. The nATPase activity was also selectively inhibited by treatment of the cells with antagonists of the B subunit of DNA gyrase, novobiocin, and coumermycin, but not by nalidixic or oxolinic acids, which interfere with the A subunit of gyrase. Inhibitors of RNA synthesis, actinomycin D and aminonucleoside of puromycin, potentiate rather than inhibit nATPase reaction. The results suggest that nATPase functions to alter the degree of supercoiling or catenation of nucleolar organizer DNA, and is in reality a DNA topoisomerase that hydrolyzes ATP during its action.     

Enhancement of ribosomal ribonucleic acid synthesis by deoxyribonucleic acid gyrase activity in Escherichia coli.

The effect of the deoxyribonucleic acid (DNA) gyrase inhibitors coumermycin A1, novobiocin, and oxolinic acid on ribonucleic acid (RNA) synthesis in Escherichia coli was studied in vivo and in vitro. Preferential inhibition of ribosomal RNA (rRNA) synthesis was observed. No effect of oxolinic acid and coumermycin on rRNA synthesis was seen in mutants having a DNA gyrase which is resistant to these inhibitors. In a temperature-sensitive DNA gyrase mutant rRNA synthesis was decreased at nonpermissive temperatures. Thus, a functional DNA gyrase is required for rRNA synthesis. Purified DNA gyrase had no effect on rRNA synthesis in a purified system. However, DNA gyrase does show preferential stimulation of rRNA synthesis in a system supplemented with other proteins. Apparently, DNA gyrase stimulation of rRNA synthesis requires another protein.     

Toxicity of methylglyoxal towards rat enterocytes and colonocytes.

Effect of methylglyoxal, a bacterial metabolic product, on protein, DNA, and RNA synthesis in rat enterocytes and colonocytes was investigated. Results showed that 1 mM methylglyoxal inhibited protein, DNA, and RNA synthesis to the extent of 65-85, 65-80, and 10-20 per cent, respectively, in villus and crypt cells and colonocytes. The inhibitory pattern was similar in these various cell types. The inhibitory effect on protein and DNA synthesis was more marked than that on RNA synthesis. Inclusion of thiol compounds up to 4 mM concentration did not protect the cells from the inhibitory effect of methylglyoxal. No alteration in the level of cellular reduced glutathione and glyoxalase enzyme activity was observed when cells were incubated with 2 mM methylglyoxal. These results suggest that the antiproliferative action of methylglyoxal on eukaryotic cells may be through the inhibition of macromolecular synthesis.     

Inhibition of Ribonucleic Acid Synthesis by Nalidixic Acid in Escherichia coli

The effect of low concentrations of nalidixic acid on ribonucleic acid (RNA) synthesis in Escherichia coli was examined. It was observed that RNA synthesis in exponentially growing cells was not significantly affected, in harmony with previous studies. However, RNA synthesis was markedly depressed by nalidixic acid during starvation for an amino acid or during chloramphenicol treatment. This effect was not caused by increased killing or inhibition of nucleoside triphosphate synthesis by nalidixic acid. The pattern of radioactive uracil incorporation into transfer RNA or ribosomes was not changed by the drug. The sensitivity of RNA synthesis to nalidixic acid in the absence of protein production may be useful in probing the amino acid control of RNA synthesis.     

The DNA gyrase inhibitors,nalidixic acid and oxolinic acid,prevent iron-mediated repression of catechol siderophore synthesis inAzotobacter vinelandii

Summary Low concentrations of nalidixic acid and oxolinic acid that were just inhibitory toAzotobacter vinelandii growth promoted the production of the catechol siderophores azotochelin and aminochelin, in the presence of normally repressive concentrations of Fe³⁺. There was a limited effect on the pyoverdin siderophore, azotobactin, where low concentrations of Fe³⁺ were rendered less repressive, but the repression by higher concentrations of Fe³⁺ was normal. These drugs did not induce high-molecular-mass iron-repressible outer-membrane proteins and similar effects on the regulation of catechol siderophore synthesis were not produced by novobiocin, coumermycin, or ethidium bromide. The timing of nalidixic acid and Fe³⁺ addition to iron-limited cells was critical. Nalidixic acid had to be added before iron-repression of catechol siderophore synthesis and before the onset of iron-sufficient growth. Continued production of the catechol siderophores, however, was not due to interference with normal iron uptake. These data indicated that nalidixic acid prevented normal iron-repression of catechol siderophore synthesis but could not reverse iron repression once it had ocurred. The possible roles of DNA gyrase activity in the regulation of catechol siderophore synthesis is discussed.