Interactions of bleomycin with DNA

Functional annotation of chemical libraries across diverse biological processes

Chemical-genetic approaches offer the potential for unbiased functional annotation of chemical libraries. Mutations can alter the response of cells in the presence of a compound, revealing chemical-genetic interactions that can elucidate a compound's mode of action. We developed a highly parallel, unbiased yeast chemical-genetic screening system involving three key components. First, in a drug-sensitive genetic background, we constructed an optimized diagnostic mutant collection that is predictive for all major yeast biological processes. Second, we implemented a multiplexed (768-plex) barcode-sequencing protocol, enabling the assembly of thousands of chemical-genetic profiles. Finally, based on comparison of the chemical-genetic profiles with a compendium of genome-wide genetic interaction profiles, we predicted compound functionality. Applying this high-throughput approach, we screened seven different compound libraries and annotated their functional diversity. We further validated biological process predictions, prioritized a diverse set of compounds, and identified compounds that appear to have dual modes of action.

Potentiation of bleomycin cytotoxicity in Saccharomyces cerevisiae

Lesions introduced into cellular DNAs prelabeled with [2-14C]thymidine or [6-3H]thymidine, as well as cell killing, were inhibited by the presence of EDTA during 20-min reactions of Saccharomyces cerevisiae cells with the low-molecular-weight bleomycin family of anticancer antibiotics. In contrast, the level of killing by low concentrations of bleomycin was higher among cells which had grown for three generations in defined synthetic complete medium supplemented with ferrous sulfate than among cells grown without iron supplementation. In S. cerevisiae, the uptake of iron is facilitated by a plasma membrane ferric reductase activity and a high-affinity (Km = 5 x 10(-6) M) ferrous uptake system. Lethal effects of 1.3 x 10(-6) M bleomycin increased approximately 50% with 10(-5) M Fe(II), nearly twofold with 10(-4) M Fe(II), and 2.8 times with 10(-3) M Fe(II). Thus, iron preloading is a new experimental approach to increasing and studying the effects of the glycopeptides on cellular DNAs and other cellular targets. This approach could also be used for studying and better understanding DNA repair genes and could serve as a model for studies of redox active chemicals in biological systems.

Light-activated cleavage of DNA by cobalt-bleomycin

We have studied the light-activated cleavage of DNA by cobalt-bleomycin using a series of synthetic DNA fragments containing (AT)n and (GC)n. This cleavage reaction requires high concentrations of the antibiotic and appears to be a stoichiometric process rather than a catalytic process. We find that, in common with the iron-complex, cobalt-bleomycin can cleave at ApT steps within regions of alternating AT residues; ApT steps within other sequences including (AAT)n. (ATP)n are not good substrates for cobalt-bleomycin cleavage. Some repetitive regions display an alternating pattern of cleavage products, revealing the preferred arrangement of ligand molecules along a saturated DNA lattice. A similar repetitive pattern is found for diethylpyrocarbonate modification and hydroxyl-radical cleavage. Although cleavage of ApT and GpC proceeds at equivalent rates, the data suggest that bleomycin binds more tightly to the latter. Adenine residues on the 3' side of both GpC-cleavage and ApT-cleavage sites are rendered more reactive to diethylpyrocarbonate, consistent with a ligand-induced alteration in local DNA structure. The cobalt-bleomycin-binding site consists of not more than four base pairs, and may be as small as three base pairs.

DNA structure influences sequence specific cleavage by bleomycin

We have examined the cleavage of several synthetic DNA sequences by iron(II)-bleomycin. We find that, although bleomycin cuts mixed sequence DNAs with a preference for GC = GT > GA >> GG, it efficiently cleaves regions of (AT)n cutting exclusively at ApT, not TpA. Isolated ApT steps show very little cleavage while blocks of three or more contiguous ATs are cut as efficiently as GpT. This cleavage is specific for (AT)n, since sequences of the type (TAA)n.(TTA)n and (ATT)n.(AAT)n are hardly cut at all. No cleavage is observed at ApC or CpA within sequences of the type (AC)n.(GT)n; regions of An.Tn are also not cut. Although the cobalt-bleomycin complex (which binds to but does not cleave DNA) yields good DNase I footprints at GT and GC sites, no footprints are observed within (AT)n, suggesting that although the cleavage reaction is efficient, the binding affinity is relatively weak. We propose a model in which bleomycin cleavage is determined by local DNA structure, while strong binding requires the presence of a guanine residue.

Further characterizations of bleomycin-sensitive (blm) mutants of Saccharomyces cerevisiae with implications for a radiomimetic model

Direct selection for 12 mutations (blm) conferring hypersensitivities to lethal effects of bleomycins in Saccharomyces cerevisiae resulted in mutants exhibiting cross-hypersensitivity to ionizing radiation and hydrogen peroxide. Remaining mutations did not confer cross-hypersensitivity to radiation. All blm mutations were recessive, except codominant blm3-1, and were assigned to seven complementation groups.

Degradation of DNA and structure-activity relationship between bleomycins A2 and B2 in the absence of DNA repair

The contribution of DNA repair to the net number of DNA breaks produced during chemical degradation of DNA was determined by using temperature-sensitive mutant cells deficient in ATP-dependent DNA ligase [poly(deoxyribonucleotide):poly(deoxyribonucleotide) ligase, EC 6.5.1.1]. In a very sensitive assay for determining lesions introduced into Saccharomyces cerevisiae DNAs, 2-14C- and 6-3H-prelabeled DNAs from ligase-proficient and ligase-deficient cells were sedimented together through precalibrated, isokinetic alkaline sucrose gradients. DNA ligation was slower after chemical degradation of DNA by bleomycin than after gamma irradiation. DNA breaks increased approximately linearly with drug concentrations, and were approximately equivalent for ligase-proficient and ligase-deficient cells. These results were unexpected because ligase-deficient, but not ligase-proficient, cells lacked the capacity to eliminate DNA breaks produced by bleomycin. The results indicated that DNA repair did not occur during the chemical degradation of DNA under the experimental conditions. Bleomycin B2 produced considerably more DNA breaks than bleomycin A2 over a range of concentrations in ligase-proficient cells, which tolerated higher numbers of DNA breaks in general than ligase-deficient cells. The chemical analogues are structurally identical except for their cationic C-terminal amine. The actual number of DNA breaks produced by bleomycin A2 or bleomycin B2, and not the concentration of bleomycin A2 or bleomycin B2 per se, determined the amount of cell killing. DNA repair is critical in quantitating DNA breaks produced by chemicals, but was ruled out as a factor in the higher DNA breakage by bleomycin B2 than bleomycin A2.

The role of redox-active metals in the mechanism of action of bleomycin

Belomycin is a glycopeptide antibiotic routinely used to treat human cancer. It is commonly thought to exert its biological effects as a metallodrug, which oxidatively damages DNA. This review systematically examines the properties of bleomycin which contribute to its reaction with DNA in vitro and may be important in the breakage of DNA in cells. Because strand cleavage results from the reductive activation of dioxygen by metallobleomycins, the mechanism of this process is given primary attention. Current understanding of the structures of the coordination sites of various metallobleomycins, their thermodynamic stabilities, their propensity to form adduct species, and their properties in ligand substitution reactions provide a foundation for consideration of the chemistry of dioxygen activation as well as a basis for thinking about the metal-speciation of bleomycin in biological systems. Oxidation-reduction pathways of iron-bleomycin, copper-bleomycin, and other metal-bleomycin species with O2 are then examined, including information on photochemical activation. With this background, structural and thermodynamic features of the binding interactions of DNA with bleomycin, its metal complexes, and adducts of metallobleomycins are reviewed. Then, the DNA cleavage reaction involving iron-bleomycin is scrutinized on the basis of the preceding discussion. Particular emphasis is placed on the constraints which the presence of DNA places on the mechanism of dioxygen activation. Similarly, the reactions of other metalloforms of bleomycin with DNA are reviewed. The last topic is an analysis of current understanding of the relationship of bleomycin-induced cellular DNA damage to the model developed above, which has evolved on the basis of chemical experimentation. Consideration is given to the question of the importance of DNA strand breakage caused by bleomycin for the mechanism of cytotoxic activity of the drug.

Growth phase dependency of chromatin cleavage and degradation by bleomycin

Preferential cleavage of Saccharomyces cerevisiae chromosomes in internucleosomal (linker) regions and nonspecific degradation of chromatin by an anticancer antibiotic which degrades DNA were investigated and found to increase in consecutive stages of growth. Cleavage of DNA in internucleosomal regions and intensities and multiplicities of nucleosomal bands were dependent on drug concentration, growth phase of the cells, and length of incubation. Cellular DNA was least degraded during logarithmic phase. After cells progressed only one generation in logarithmic phase, low concentrations (6.7 x 10(-7) to 3.4 x 10(-6) M) of bleomycin produced approximately three to seven times more DNA breaks. Internucleosomal cleavage was highest, and the most extended oligonucleosomal series and extensive chromatin degradation were observed during stationary phase. It is concluded that the growth phase of cells is critical in determining amounts of the highly preferential cleavage in internucleosomal regions and overall breakage and degradation of DNA. Mononucleosomal bands were most intense, indicating the greatest accumulation of DNA of this size. Mean mononucleosomal lengths were 165.9 +/- 3.9 base pairs, in agreement with yeast mononucleosomal lengths. As high-molecular-weight chromatin was digested by bleomycin, oligonucleosomes and, eventually, mononucleosomes became digested. Therefore, it is also concluded that bleomycin degradation of oligonucleosomes and trimming of DNA linker regions proceed to degradation of the monosomes (core plus linker DNA).

Modifications of the effect of bleomycin in the somatic mutation and recombination test in Drosophila melanogaster

Exposure to oxygen has been implicated as an important mechanism of mutations, cancer and aging. Most data supporting this notion have been obtained in vitro, but the elaborate defense systems against oxygen stress in aerobic organisms make it difficult to extrapolate in vitro data to in vivo conditions. In the present investigation the somatic mutation and recombination test (SMART) in Drosophila with the wing spot system (Graf et al., 1984) has been used as an in vivo system to study the effect of oxygen radicals generated by bleomycin (BLM). BLM causes a dose-related increase of wing spots and this effect drastically increases by increasing oxygen in the atmosphere to 70%. Data from treatment of larvae of different ages, as well as post-treatment with oxygen, indicate that BLM can persist, presumably intercalated in DNA, and subsequently be activated by oxygen to generate free radicals. By the use of inversion heterozygosity, which eliminates somatic recombination, it was shown that the majority of wing spots induced by BLM emanate from somatic recombination. A small number of flies deviated from the rest by an abnormally high frequency of BLM-induced wing spots. Preliminary results from a selection of such flies indicate that this extreme response to BLM is genetically determined. Treatment with BLM was also combined with agents known to interfere with the defense mechanisms against radicals or function as radical scavengers. Only ascorbic acid cotreatment had a modifying effect on BLM mutagenicity. The other agents did not alter or at most had a marginal effect on BLM mutagenicity. These data indicate that the defense mechanisms do not constitute a limiting factor in this case. BLM intercalates between DNA bases, presumably giving little time and opportunity for modifying agents to react with radicals generated in direct contact with the gene targets. No effect of BLM was observed on male germ cells by measuring loss and non-disjunction of ring-X/Y, neither in air nor in a 70% oxygen atmosphere.

Bleomycin-induced DNA repair by Saccharomyces cerevisiae ATP-dependent polydeoxyribonucleotide ligase

In contrast to ligase-deficient (cdc9) Saccharomyces cerevisiae, which did not rejoin bleomycin-induced DNA breaks, ligase-proficient (CDC9) yeast cells eliminated approximately 90% of DNA breaks within 90 to 120 min after treatment. Experimental conditions restricted enzymatic removal of the unusual 3'-phosphoglycolate termini in DNA cleaved by bleomycin and involved doses producing equivalent numbers of DNA breaks or doses producing equivalent killing.

Bleomycin-induced mutagenesis in repackaged lambda phage: base substitution hotspots at the sequence C-G-C-C

DNA isolated from lambda phage was treated with bleomycin A2 plus Fe2+. The bleomycin-damaged DNA was added to lambda packaging extracts and the resulting phage were grown in SOS-induced E. coli. Under these conditions, treatment of the DNA with 0.8 microM bleomycin reduced the viability of the repackaged phage to 3% and increased the frequency of clear-plaque mutants in the progeny by a factor of 16. Bleomycin-induced mutations which mapped to the DNA-binding domain of the cI gene were subjected to DNA-sequence analysis. The most frequent events were single-base substitutions at G:C base pairs, nearly all of which occurred at cytosines in the sequence Py-G-C. Cytosines in the third position of the sequence C-G-C-C were particularly susceptible to mutation. At A:T base pairs, mutations were less frequent and were a mixture of single-base substitutions and -1 frameshifts, occurring primarily at G-T and A-T sequences. Thus, the overall specificity of bleomycin-induced mutations matches that of bleomycin-induced DNA lesions (strand breaks and apyrimidinic sites), which are formed at G-C (particularly Py-G-C), G-T and, to a lesser extent, A-T sequences. Furthermore, the frequency of various types of substitutions was consistent with selective incorporation of A and T residues opposite apyrimidinic sites at these sequences. The highly selective nature of bleomycin-induced mutations may explain the lack of mutagenesis by this compound in a number of reversion assays.

Inhibition of bleomycin-induced DNA strand breaks in V 79 Chinese hamster cells by the antioxidant propylgallate

Bleomycin induced DNA single-strand breaks in Chinese hamster V 79 cells which were detected by the alkaline filter elution assay. In the presence of propylgallate, an antioxidant, the amount of DNA single-strand breaks was significantly reduced. The production of DNA strand breaks by methylnitronitrosoguanidine used as a positive control was not influenced by propylgallate. It is suggested that propylgallate inhibits the generation of DNA single-strand breaks by trapping reactive oxygen species produced by the bleomycin-iron(II) complex.

Functional analogues of bleomycin: DNA cleavage by bleomycin and hemin-intercalators

New hemin-intercalators (Hem-G's) that cleave DNA were synthesized, on the basis of 2-amino-6-methyldipyrido[1,2-alpha:3',2'-d]imidazole (Glu-P-1) as an intercalator moiety. Hem-G's, which possess an intramolecular ligand of the ferrous ion (a histidine or imidazole moiety), cleave DNA very efficiently and act at guanine-pyrimidine sequences preferentially. Bleomycin (BLM) also cleaved DNA with the same base-sequence selectivity shown by Hem-G's. The 5'-terminus of the DNA fragments cleaved by Hem-G's or by BLM is a phosphoryl group, while the 3'-terminus of the cleaved DNA fragments does not possess a 3'-phosphoryl group. There are more than three kinds of 5'-end 32P-labeled DNA fragments, which can be substrates of terminal deoxynucleotidyl transferase (TdT). One of the 3'-termini of the cleaved DNA fragments is a 3'-hydroxy group. The mobility of the 3'-end 32P-labeled DNA fragment cleaved by Hem-G's or by BLM corresponds to the removal of pyrimidine bases having guanine at the 5'-side. The mobility of one kind of the cleaved 5'-end 32P-labeled DNA fragments corresponds to the removal of guanine having pyrimidine at the 3'-side, followed by 3'-dephosphorylation. We propose that there exist plural mechanisms for DNA cleavage by Hem-G's or by BLM. The deduced structures of the cleaved DNA fragments suggest that one of the mechanisms involves deletion of two nucleotide units from DNA.

Bleomycin--mode of action with particular reference to the cell cycle

Over the last four years, investigations into the mechanism of interaction between bleomycin and DNA have been pursued at a rapid pace. This is, no doubt, because of the potential of bleomycin as a tool for molecular biology. It seems likely that the precise nature of the interaction between Fe(II), oxygen and bleomycin will be elucidated in the near future together with the nature of the binding between the complex and DNA. More information on the mechanism of strand scission including the involvement of free radical mechanisms and sequence specificity may also be expected. In contrast to this picture of rapid progress at the molecular level, interest in studies of bleomycin action at the cellular level appears to have waned. This is despite the fact that most of the important questions which have been raised regarding effects of the drug on cell cycle progression, the possibility of a selective action on on-cycling cells and the nature of 'recovery from potentially-lethal damage' remain unresolved. There is no doubt that, for most cell types, bleomycin produces a block at the early G2 stage of the cell cycle. There is considerable doubt, however, as to how many of the cells blocked for a significant period remain clonogenically viable. This question is amenable to being answered using a vital DNA stain, such as Hoechst 33342, and cell sorting but this does not appear to have been done. The relationship between G2 blockage and repair of DNA damage has also not been resolved. Neither has the question of whether or not DNA breaks which remain unrepaired are different in nature from the majority of repairable lesions. The data on the relative sensitivity of exponential and plateau phase cells are conflicting and their in vivo significance unclear. Well designed experiments to examine the bleomycin sensitivity of those cells in solid tumors which survive radiation treatment could help to answer this question. Evidence that the phenomenon of 'recovery from potentially lethal damage' is therapeutically-exploitable is mainly lacking. It would be of great relevance to known whether or not the effect can be observed in normal tissues. However, the evidence that the effect is not simply an artefact of clonogenic assay procedures is scanty and this possibility must be borne in mind.(ABSTRACT TRUNCATED AT 400 WORDS)

Interactions of a fragment of bleomycin with deoxyribodinucleotides: nuclear magnetic resonance studies

Proton NMR spectroscopy was used to establish certain geometrical parameters of the complexes formed between N-(3-aminopropyl)-2'-(2-acetamidoethyl)-2,4'-bithiazole-4-carboxamide hydrochloride (BLMF), a fragment of bleomycin, and various deoxyribodinucleotides. All proton resonances in these compounds have been assigned; chemical shifts were recorded as functions of their concentration. In the complex formed between BLMF and pdG-dC, chemical shifts of the bithiazole protons (measured with respect to values extrapolated to infinite dilution) were displaced upfield by 0.4 ppm. Other proton resonances of BLMF were shifted upfield but to a lesser extent. After corrections are made for self-stacking, maximum values for induced chemical shifts of the bithiazole protons are reached at a dinucleotide/BLMF ratio of 2. Coupling sums for dinucleotides (12.5-13.7 Hz) were unchanged following complexation, suggesting that there is no marked change in sugar conformation when BLMF is bound. On the basis of these results and of molecular model building studies, we propose a three-dimensional structure for a BLMF:pdG-dc complex in which the thiazole rings are intercalated in the duplex and stack preferentially on the purines. Projected on the same plane, the horizontal axis connecting the center of both bithiazole rings in this configuration superimposes on the axis connecting the centers of the purine bases. In this complex, both thiazole protons extend into the minor groove and the positively charged terminal amine binds to the negatively charged phosphate group of DNA.

Photolability of bleomycin and its complexes

Bleomycin has been found to be very sensitive to photolysis and on irradiation with the full spectral range of a medium-pressure mercury lamp undergoes a number of photo-induced reactions; there is a process in which the absorbance at 310 nm decreases, and a slower process in which it increases with photolysis time. The faster process can be studied by irradiation at approximately 300-350 nm, is complete in approximately 8 min, obeys first order kinetics, but is itself biphasic. The Fe(II) and Cu(II) complexes of bleomycin are also photolabile, as is the bleomycin-DNA complex.