The molecular mechanism of benzimidazole mutagenicity: In vitro studies on transcription and translation

Benzimidazoles are weak mutagens acting through base substitutions; they are incorporated into nucleic acids. Experiments with deoxyribohomopolymers as templates demonstrated that benzimidazole nucleoside triphosphate is polymerized by RNA polymerase only in the presence of poly dC, i.e., instead of guanine. In plasmolyzed Escherichia coli cells, benzimidazole ribonucleoside diphosphate is polymerized by polynucleotide phosphorylase and can, after blocking of the normal mRNA synthesis with actinomycin D, be used as a messenger for polypeptide formation. The addition of radioactive amino acids to this system showed that benzimidazole is not read preferentially as guanine, as would have been expected from the RNA polymerase results. Instead, the reading was position dependent and benzimidazole is recognized (1) in the first codon position as adenine, (2) in the second as purine, and (3) in the third possibly only as base. Benzimidazole mutagenicity is thus explained as a G » A transition.     

Effects of benzimidazole on the purine and pyrimidine metabolism of yeast.

Yeast cells inhibited by benzimidazole accumulate hypoxanthine with associated efflux of xanthine. Unlike control cells, inhibited cells contain no detectable free UMP and CMP. Benzimidazole decreases uptake of [8-14C]hypoxanthine into the intracellular pool of hypoxanthine and xanthine but causes radioactive xanthine to accumulate in the medium. In inhibited cultures there is a threefold increase in incorporation of [8-14C]hypoxanthine into the total (intracellular plus extracellular) xanthine. Uptake of [8-14C]hypoxanthine into free nucleotides and into bound adenine and guanine was inhibited by 70%. Uptake of [U-14C]glycine into IMP, AMP, GMP, DNA and RNA was also substantially decreased. Incorporation of [2-14C]uracil into the intracellular uracil pool was inhibited by 30% and into free uridine and cytidine by over 90%. Benzimidazole inhibited incorporation of [8-3H]IMP into AMP and GMP, and decreased substantially the activity of glutamine-amidophosphoribosyltransferase (EC 2.4.2.14). Yeast cultures were shown to N-ribotylate benzimidazole. Results are consistent with benzimidazole inhibiting yeast growth by competing for P-rib-PP and so depriving other ribotylation processes such as the 'salvage' pathways and de novo synthesis of purines and pyrimidines.     

Biosynthesis of caffeine in tea callus tissue

1. A study of caffeine biosynthesis has been made by following the incorporation of radioactive carbon dioxide and methionine into the methylated purines produced by tea callus tissue. 2. The uptake of the radioactive labels into nucleic acid and caffeine was followed over a period of approximately 9h. 3. The distribution of the radioactive labels in both nucleic acid and caffeine was determined after incorporation and subsequent incubation of the tissue in a non-radioactive medium. 4. The results of the experiments indicated that the caffeine arose from purines released from the breakdown of nucleic acids rather than that it was formed directly from a purine pool. 5. A metabolic scheme to show the production of caffeine from the nucleotides of the nucleic acid is discussed.     

Tritium labelling of nucleic acids accompanied by conversion of cytosine to uracil.

A new method of incorporation of tritium into nucleic acids with an accompanying conversion of cytosine to uracil is proposed. The method is based on the reaction of nucleic acids with bisulfite in the presence of 3H2O. Under certain conditions poly(C) is quantitatively converted to a radioactive poly(U), whereas similar bisulfite treatment of poly(U) does not result in any tritium incorporation. Specificity of the reaction is confirmed by the results of analysis of modified tRNA and rRNA. Incubation of tRNA with bisulfite and 3H2O does not lead to cleavage of the polynucleotide chain. Similar treatment of the denatured DNA results in tritium incorporation into DNA which is accompanied by a conversion of cytosine to uracil. There is virtually no reaction between native DNA and bisulfite. Only certain cytosone residues in yeast tRNAVal/2a interact with bisulfate providing that reaction is carried out under sufficiently mild conditions.     

Effects of benzimidazole on the purine and pyrimidine metabolism of yeast

Yeast cells inhibited by benzimidazole accumulate hypoxanthine with an associated efflux of xanthine. Unlike control cells, inhibited cells contain no detectable free UMP and CMP. Benzimidazole decreases uptake of [8-¹⁴C]-hypoxanthine into the intracellular pool of hypoxanthine and xanthine but causes radioactive xanthine to accumulate in the medium. In inhibited cultures there is a threefold increase in incorporation of [8-¹⁴C]hypoxanthine into the total (intracellular plus extracellular) xanthine. Uptake of [8-¹⁴C]hypoxanthine into free nucleotides and into bound adenine and guanine was inhibited by 70%. Uptake of [U-¹⁴C]glycine into IMP, AMP, GMP, DNA and RNA was also substantially decreased. Incorporation of [2-¹⁴C]uracil into the intracellular uracil pool was inhibited by 30% and into free uridine and cytidine by over 90%. Benzimidazole inhibited incorporation of [8-³H]IMP into AMP and GMP, and decreased substantially the activity of glutamine-amidophosphoribosyltransferase (EC 2.4.2.14). Yeast cultures were shown to N-ribotylate benzimidazole. Results are consistent with benzimidazole inhibiting yeast growth by competing for P-rib-PP and so depriving other ribotylation processes such as the ‘salvage’ pathways and de novo synthesis of purines and pyrimidines.     

Biosynthesis of proteins, nucleic acids and glycosphingolipids by synchronized KB cells

The biosynthesis of glycosphingolipids and various types of proteins and nucleic acids at specific periods of the cell cycle was studied by using synchronized KB cells. Maximum incorporation of radioactive galactose, leucine and thymidine into several proteins and nucleic acids occurred as has been reported previously (6,11). Maximum incorporation of $\text{D}$-1[¹⁴C] galactose into glycosphingolipids was observed during the M and G-1 phases. There was a 5 fold increase in the levels of gangliosides and combined neutral glycosphingolipids during the M and G-1 phases. Thus, regulated biosynthesis of glycosphingolipids and macromolecules might be important in the cyclic expression of some of the functional properties which are characteristic of these compounds.     

5-Hydroxylation of benzimidazole by micromycetes I. Strains selection

Summary The ability of 610 strains of micromycetes to introduce a hydroxy-group into benzimidazole substrate has been investigated. Among them, 232 micromycetes have been selected and cultivated in a liquid synthetic medium. Convenient hydroxylation of benzimidazole was obtained with 78 fungi. Finally, 8 strains of micromycetes have been chosen for further investigation and optimization of this bioconversion.     

Synthesis of alanyl nucleobase amino acids and their incorporation into proteins

Proteins which bind to nucleic acids and regulate their structure and functions are numerous and exceptionally important. Such proteins employ a variety of strategies for recognition of the relevant structural elements in their nucleic acid substrates, some of which have been shown to involve rather subtle interactions which might have been difficult to design from first principles. In the present study, we have explored the preparation of proteins containing unnatural amino acids having nucleobase side chains. In principle, the introduction of multiple nucleobase amino acids into the nucleic acid binding domain of a protein should enable these modified proteins to interact with their nucleic acid substrates using Watson-Crick and other base pairing interactions. We describe the synthesis of five alanyl nucleobase amino acids protected in a fashion which enabled their attachment to a suppressor tRNA, and their incorporation into each of two proteins with acceptable efficiencies. The nucleobases studied included cytosine, uracil, thymine, adenine and guanine, i.e. the major nucleobase constituents of DNA and RNA. Dihydrofolate reductase was chosen as one model protein to enable direct comparison of the facility of incorporation of the nucleobase amino acids with numerous other unnatural amino acids studied previously. The Klenow fragment of DNA polymerase I was chosen as a representative DNA binding protein whose mode of action has been studied in detail.     

Theoretical studies on protein-nucleic acid interactions. II. Hydrogen bonding of amino acid side chains with bases and base pairs of nucleic acids

With a view to understanding the role of hydrogen bonds in the recognition of nucleic acids by proteins, hydrogen bonding between the bases and base pairs of nucleic acids and the amino acids (Asn, Gln, Asp and Glu, and charged residues Arg⁺, Glu^?, and Asp^?) has been studied by a second-order perturbation theory. Binding energies have been calculated for all possible configurations involving a pair of hydrogen bonds between the base (or base pair) and the amino acid residue. Our results show that the hydrogen bonding in these cases has a large contribution from electrostatic interaction. In general, the charged amino acids, compared to the uncharged ones, form more stable complexes with bases or base pairs. The hydrogen-bond energies are an order of magnitude smaller than the Coulombic interaction energies between basic amino acids (Lys⁺, Arg⁺, and His⁺) and the phosphate groups of nucleic acids. The stabilities of the complexes of amino acids Asn, Gln, Asp, and Glu with bases are in the order: G–X > C–X > A–X U–X or T–X, and G · C–X > A · T(U)–X, where X is one of these amino acid residues. It has been shown that Glu^? and Asp^? can recognize guanine in single-stranded nucleic acids; Arg⁺ can recognize G · C base pairs from A · T base pairs in double-stranded structures.     

Purine metabolism in mesophyll protoplasts of tobacco (Nicotiana tabacum) leaves.

The overall metabolism of purines was studied in tobacco (Nicotiana tabacum) mesophyll protoplasts. Metabolic pathways were studied by measuring the conversion of radioactive adenine, adenosine, hypoxanthine and guanine into purine ribonucleotides, ribonucleosides, bases and nucleic acid constituents. Adenine was extensively deaminated to hypoxanthine, whereupon it was also converted into AMP and incorporated into nucleic acids. Adenosine was mainly hydrolysed to adenine. Inosinate formed from hypoxanthine was converted into AMP and GMP, which were then catabolized to adenine and guanosine respectively. Guanine was mainly deaminated to xanthine and also incorporated into nucleic acids via GTP. Increased RNA synthesis in the protoplasts resulted in enhanced incorporation of adenine and guanine, but not of hypoxanthine and adenosine, into the nucleic acid fraction. The overall pattern of purine-nucleotide metabolic pathways in protoplasts of tobacco leaf mesophyll is proposed.     

The labelling of nucleic acids by radioactive precursors in the blue-green algae Anacystis nidulans and Synechocystis aquatilis Sanv.

Summary The labelling of nucleic acids of growing cells of the blue-green algae Anacystis nidulans and Synechocystis aquatilis by radioactive precursors has been studies. A. nidulans cells most actively incorporate radioactivity from [2-¹⁴C]uracil into both RNA and DNA, while S. aquatilis cells incorporate most effectively [2-¹⁴C]uracil and [2-¹⁴C]thymine.Deoxyadenosine does not affect incorporation of label from [2-¹⁴C]thymidine into DNA, but weakly inhibits [2-¹⁴C]thymine incorporation into both nucleic acids and significantly suppresses the incorporation of [2-¹⁴C]uracil.The radioactivity from [2-¹⁴C]uracil and [2-¹⁴C]thymine is found in RNA uracil and cytosine and DNA thymine and cytosine. The radioactivity of [2-¹⁴C]thymidine is incorporated into DNA thymine and cytosine. These results and data of comparative studies of nucleic acid labelling by [2-¹⁴C]thymine and [5-methyl-¹⁴C]thymine suggest that the incorporation of thymine and thymidine into nucleic acids of A. nidulans and S. aquatilis is accompanied by demethylation of these precursors. In this respect blue-green algae resemble fungi and certain green algae.     

Synthesis and oligonucleotide incorporation of fluorescent cytosine analogue tC: a promising nucleic acid probe

The tricyclic cytosine, tC, is a fluorescent base analogue with excellent properties for investigating intrinsic characteristics of nucleic acid as well as interactions between nucleic acids and other molecules. Its unique fluorescence properties and insignificant influence on overall structure and dynamics of nucleic acid after incorporation makes tC particularly interesting in fluorescence resonance energy transfer and anisotropy measurements. We here describe a straightforward synthesis of the standard monomer form of tC for DNA solid-phase synthesis, the tC phosphoramidite, and its subsequent incorporation into oligonucleotides. The total synthesis of the tC phosphoramidite takes approximately 8 days and its incorporation and the subsequent oligonucleotide purification an additional day.     

Amidino benzimidazole inhibitors of bacterial two-component systems.

Amidino benzimidazoles have been identified as inhibitors of the bacterial KinA/Spo0F two-component system (TCS). Many of these inhibitors exhibit good in vitro antibacterial activity against a variety of susceptible and resistant Gram-positive organisms. The moiety at the 2-position of the benzimidazole was extensively modified. In addition, the regioisomeric benzoxazoles, heterocyclic replacements for the benzimidazole, have been synthesized and their activity against the TCS evaluated.     

Artificial ribozymes and deoxyribozymes.

RNA and DNA molecules with catalytic properties have been isolated by in vitro selection from combinatorial nucleic acid libraries. A broad range of chemical reactions is catalyzed and nucleic acids can accelerate bond formation between small organic substrates. The catalytic performance of nucleic acids can be enhanced by the incorporation of additional functional groups.     

On molecular mechanisms of nucleic acid synthesis fidelity aspects. 1. Contribution of base interactions

This paper is concerned with the molecular mechanisms of spontaneous replacements of base pairs in the processes of template synthesis of nucleic acids. The method of atom-atom potential functions was used to calculate the energies of interaction in non-complementary base pairs arranged in a common plane so that the mutual position of the glycosidic bonds does not differ appreciably from their position for Watson-Crick pairs in the DNA double helix. A number of local minima of this energy have been found, which could occur in template synthesis and result in insertion of incorrect bases into the double helix. The calculation results are indicative of formation of purine-purine pairs with one of the purine nucleotides in syn-conformation, which can be regarded as a typical pathway of transversion, and that of wobble-pairs TG and AC, which can be regarded as a typical pathway of transition. The contribution of intramolecular interactions of nucleic acids as well as interactions of polynucleotide chains with an enzyme to the fidelity of template synthesis of nucleic acids is discussed. The calculation results are compared with the experimental data on the frequency of spontaneous mutations and the frequency of errors in template synthesis of nucleic acids in vitro.     

Heterogeneity of nucleoside kinases in marine microorganism cells

The incorporation of [³H]-thymidine and [³H]-uridine into nucleic acids of six marine microorganism strains belonging to different genera was studied. It was shown that the radioactive label of each of those exogenous precursors could be included into both the DNA and the RNA of bacterial cells. The activity of the nucleoside phosphorylation enzymes—thymidine and uridin kinases—was defined in bacterial cell extracts. The activity of thymidine kinase in the extracts is noticeably higher than the activity of uridine kinase, this enzyme, unlike uridine kinase, being present in all marine bacteria strains studied. After the partial purification of phosphorylation enzymes by means of ion-exchange chromatography, a number of enzymatic properties of nucleoside kinases and their substrate specificity were investigated. It was shown that the set of precursor phosphorylation enzymes in the strains under study differed in representatives of different marine bacterial genera.     

The fate of 7[14C]-methylguanine after administration to the rat

1. To assess the significance of the methylation of nucleic acids known to be caused by certain carcinogens, the metabolic fate of 7[¹⁴C]-methylguanine was studied, with special reference to its possible incorporation into RNA and DNA. 2. The major part (approx. 95%) of the dose was excreted unchanged in the urine. A small amount of N-demethylation took place, as evidenced by the formation of radioactive adenine and guanine, and expiration of ¹⁴C-labelled carbon dioxide. No evidence was obtained for the direct incorporation of 7-methylguanine into systems synthesizing nucleic acids, i.e. RNA in liver, DNA in intestine or in the foetus.     

Incorporation of label from radioactive uridine into the stylar nucleic acids of Lilium longiflorum thunb. as affected by heat, 6-methylpurine and actinomycin D

Summary 5-³H-uridine injected into the stylar canal of detached lily stigma-styles was taken up initially into the rapidly-labeled-RNA of the nucleic acid profile of a methylated albumin kieselguhr (MAK) column but with increasing time was found in all portions of the RNA profile, but not in the DNA. Heat treatment of the style before injection of 5-³H-uridine greatly reduced the rate of incorporation of label into and the ultimate amount of label found in the RNA species of the lily style. Translocation of 5-³H-uridine through the ovary into heattreated pistils and the injection of 5-³H-uridine into styles which had been incubated for 1 or 2 days after heat treatment resulted in stylar nucleic acids more highly labeled than nucleic acids in control styles, with an incorporation pattern different than control styles. Heat treatment of lily pistils resulted in detectable changes in the proportion of stylar RNA species as separated on MAK columns and measured as absorbance units. Actinomycin D and 6-methylpurine treated styles incorporated label from a stylar injection of radioactive uridine in patterns different than each other, different than heat-treated styles and different than non-treated styles. 6-methylpurine and heat treatment of styles only slightly reduced the rate at which 5-³H-uridine was removed from the stylar canal into the stylar tissue.Paper number 8917 of the Scientific Journal Series, Minn. Agr. Exp. Sta., St. Paul, MN 55108.     

Effect of Centchroman (67/20) and 78/224 on nucleic acid and protein biosynthesis during implantation in rats

The biosynthesis of nucleic acids and proteins was studied in rat uterus by following the incorporation of [³H]-thymidine, [³H]-uridineand[¹⁴C]-leucinein control and pregnant rats in the presence and absence of two anti-implantation drugs. One of the drugs, 78/224 caused a significant increase in incorporation whereas the other drug, Centchroman, caused an inhibition in incorporation of all the three precursors. The implications of these changes in the light of estrogenicity, agonist and antagonist actions of anti-estrogens have been analysed. The importance of homeostatic mechanisms involved in nucleic acids and proteins for the maintenance of constant internal milieu for blastocyst attachment has been discussed.