Benzo(a)pyrene 7,8-dihydrodiol-9,10-oxide modification of DNA: Relation to chromatin structure and reconstitution

Purified duck reticulocyte DNA was incubated in vitro with a 7,8-dihydrodiol-9,10-oxide derivative of benzo(a)pyrene (BPDE). The carcinogen-modified DNA was somewhat more susceptible to partial digestion by the single strand specific endonuclease S₁ than unmodified DNA, suggesting slight denaturation of the helix at sites of modification. Chromatin was reconstituted in vitro utilizing this carcinogen-modified DNA and unmodified-chromatin associated proteins. This reconstituted chromatin showed the same kinetics and extent of digestion by Staphylococcal nuclease, and similar nucleosome profiles on sucrose density gradient centrifugation, as those obtained with native chromatin or chromatin reconstituted with unmodified DNA. Moreover, polyacrylamide gel electrophoresis of DNA fragments obtained from nuclease digests gel electrophoresis of DNA fragments obtained from nuclease digests of the reconstituted chromatins suggested that the chromatin containing carcinogen-modified DNA had the same subnucleosome structure as that reconstituted with unmodified DNA. In a separate set of studies intact duck reticulocyte chromatin was reacted directly with BPDE. Nuclease digestion studies indicated that 65% of the carcinogen was bound to the ‘open’ regions of chromatin, and 35% to ‘closed’ regions.These results indicate that although covalent binding of a benzo(a)pyrene (BP) derivative to DNA produces local distortions in conformation of the helix, this modification does not appear to interfere with the ability of the DNA to associate with histones to form nucleosome structures. In addition, although DNA in the open regions of chromatin is more susceptible to reaction with the BP derivative, there is appreciable reaction with the DNA associated with histones.     

The induction of cytochrome P-450 and monooxygenase activities in the chick embryo by 2-acetylaminofluorene

Administration of 2-acetylaminofluorence to chick embryos increases the cytochrome P-450 level 3.4 fold but causes no increase in total epoxide hydrase activity or other microsomal electron transport enzymes. The induction response shows some similarity to that elicited by phenabarbitone both in terms of the monooxygenase activities induced and their inhibition characteristics. Induction of a specific cytochrome P-450 subform by this agent may increase its detoxification and in part account for the resistance of avian species to its hepatocarcinogenic effect.     

A umuDC-independent SOS pathway for frameshift mutagenesis.

Summary The chemical carcinogen N-acetoxy-N-2-acetylaminofluorene induces mainly frameshift mutations, which occur within two types of sequences (mutation hot spots): –1 frameshift mutations within contiguous guanine sequences and –2 frameshift mutations within alternating GC sequences such as the NarI and BssHII restriction site sequences. We have investigated the genetic control of mutagenesis at these sequences by means of a reversion assay using plasmids pW17 and pX2, which contain specific targets for contiguous guanine and alternating GC sequences, respectively. Our results suggest that mutations at these hot spot sequences are generated by two different genetic pathways, both involving induction of SOS functions. The two pathways differ both in their LexA-controlled gene and RecA protein requirements. In the mutation pathway that acts at contiguous guanine sequences, the RecA protein participates together with the umuDC gene products. In contrast, RecA is not essential for mutagenesis at alternating GC sequences, except to cleave the LexA repressor. The LexA-regulated gene product(s), which participate in this latter mutational pathway, do not involve umuDC but another as yet uncharacterized inducible function. We also show that wild-type RecA and RecA430 proteins exert an antagonistic effect on mutagenesis at alternating GC sequences, which is not observed either in the presence of activated RecA (RecA^*), RecA730 or RecA495 proteins, or in the complete absence of RecA as in recA99. It is concluded that the –1 mutation pathway presents the same genetic requirements as the pathway for UV light mutagenesis, while the –2 mutation pathway defines a distinct SOS pathway for frameshift mutagenesis.     

Age-related changes in mutagen activation by rat tissues

Age-related changes in drug metabolism of the liver, lung and kidney of adult female Long-Evans rats were determined by measuring changes in mutagen formation. Activation of aflatoxin B1 (AFB1), 2-aminofluorene (AF) and 2-acetylaminofluorene (AAF) to mutagenic derivatives was assayed using the Ames Salmonella test system. The promutagens were incubated with tissue fractions from rats ranging in age from 2.5 to 25 months. With all three compounds, hepatic, renal and pulmonary activation was lower in the senescent than in the young adult animals. The largest decrease, however, occurred prior to middle-age, i.e. before 9-13 months. In liver and kidney, little change was detectable between the middle-aged and the old (20-25 months) animals. However, pulmonary metabolism in the oldest animals was slightly higher than in the extracts from the middle-aged rats. The observed decline in mutagen activation may thus be a function of maturation rather than senescence.     

The effect of nicotinamide on unscheduled DNA synthesis in cultured hepatocytes

The synthesis of $\text{E. coli}$ proteins was examined, by two-dimensional O'Farrell gels, in mutant strains defective in all possible combinations of the RNA processing enzymes RNase III, RNase E and RNase P. We found that the synthesis of most proteins was unaffected; however, the synthesis of a significant number of proteins, 21 out of 80 tested, was drastically reduced in the strain defective in all three enzymes. It appears that the two enzymes RNase III and RNase E are responsible for most of these changes.     

Acute response of the mouse bladder to derivatives of 4-ethylsulphonylnaphthalene-1-sulphonamide and bladder carcinogens measured by the uptake of (125 I)5-iodo-2 -deoxyuridine

The structural features of 4-ethylsulphonylnaphthalene-1-sulphonamide (ENS) responsible for the induction of DNA synthesis in the mouse bladder have been investigated using a method in which DNA synthesis is measured by the uptake of a thymidine analogue, [¹²⁵I]5-iodo-2′-deoxyuridine (IUdR). The ability to stimulate DNA synthesis was unaffected by the nature of the alkyl group in 4-alkylsulphonylnaphthalene-1-sulphonamide. The sulphonamide group appeared to be essential to the activity of the molecule because naphthalene-1,4-disulphonamide was active whereas 1,4-diethylsulphonylnaphthalene was not. Maximum activity was found when the sulphonamide group was attached to an aromatic system (benzene or naphthalene) containing an alkylsulphonyl or a sulphonamide group. Bladder carcinogens other than ENS failed to stimulate the uptake of [¹²⁵I]IUdR sufficiently to produce statistically significant results. The reasons for the large variation in response between individual mice are discussed, as are the implications of the structure activity relationships to the mode of action of ENS.     

Modification of ribonucleic acid by chemical carcinogens. IV. Circular dichroism and proton magnetic resonance studies of oligonucleotides modified with N-2-acetylaminofluorene

The conformational properties of various oligonucleotides modified with the chemical carcinogen N-2-acetylaminofluorene have been investigated utilizing circular dichroism, proton magnetic resonance spectroscopy and computer-generated molecular models. Introduction of the carcinogen, specifically and covalently, at the C-8 position of guanosine residues results in dramatic changes in the ciruclar dichroism spectra of the oligonucleotides. The attachment of N-2-acetylaminofluorene also causes large higher-field shifts for the proton resonances of fluorene and bases adjacent to a modified guanosine residue. These results, together with substantial supporting evidence, show that the covalent binding of N-2-acetylaminofluorene causes important changes in the conformational properties of oligonucleotides in aqueous solution. The major changes include rotation of the guanine base around the glycosidic linkage and the intramolecular stacking of fluorene with an adjacent base. A computer-displayed model of a carcinogen-modified dinucleotide illustrating these effects is presented. The specific conformational changes noted for the oligonucleotides could clearly disrupt the normal biological activity of similarly modified naturally occurring nucleic acids.     

Identification of the persistently bound form of the carcinogen N-acetyl-2-aminofluorene to rat liver DNA in vivo

In this article the structural analysis of the persistently bound form of the carcinogen N-acetyl-2-aminofluorene (AAF) to rat liver DNA in vivo is described. This compound appears to result from the formation of a covalent bond between carbon-3 of the aromatic ring and the amino group of guanine. Experimental evidence from three different approaches has led to the identification of the structure of the persistently DNA-bound AAF moity. First, [3-³H, 9-¹⁴C]N-acetoxy-AAF was reacted with DNA in vitro. As reported previously, a minor product was isolated from enzymatic digests of the reacted DNA, which had chemical and chromatographic properties identical to those of the persistent—AAF moiety in DNA in vivo. The ration ³H/¹⁴C of this product had diminished to the same extent as 3-CH₃S-AAF resulting from the reaction of methionine with [3-³H, 9-¹⁴C]N-acetoxy-AAF.Secondly, reaction of [9-¹⁴C]N-acetoxy-AAF with DNA, which was tritiated in the C-8 positions of the purines, did not result in removal of tritium in the persistent fraction obtained after acid hydrolysis, thus excluding substitution at C-8 and N-7 of guanine. Finally, by reacting N-OSO₃-K-AAF with deoxyguanosine in dimethylsulfoxide-triethylamine, a compound could be isolated, which was identified as 3-(deoxyguanosin-N²-yl)-AAF based on its NMR spectrum and on the mass spectrum of the corresponding guanine derivative obtained after removing deoxyribose by acid hydrolysis. This compound appeared to be identical with the persistently bound form present in DNA hydrolysates from rat liver after injection of [2′-³H]N-hydroxy-AAF.     

Interplay among replicative and specialized DNA polymerases determines failure or success of translesion synthesis pathways

Living cells possess a panel of specialized DNA polymerases that deal with the large diversity of DNA lesions that occur in their genomes. How specialized DNA polymerases gain access to the replication intermediate in the vicinity of the lesion is unknown. Using a model system in which a single replication blocking lesion can be bypassed concurrently by two pathways that leave distinct molecular signatures, we analyzed the complex interplay among replicative and specialized DNA polymerases. The system involves a single N-2-acetylaminofluorene guanine adduct within the NarI frameshift hot spot that can be bypassed concurrently by Pol II or Pol V, yielding a −2 frameshift or an error-free bypass product, respectively. Reconstitution of the two pathways using purified DNA polymerases Pol III, Pol II and Pol V and a set of essential accessory factors was achieved under conditions that recapitulate the known in vivo requirements. With this approach, we have identified the key replication intermediates that are used preferentially by Pol II and Pol V, respectively. Using single-hit conditions, we show that the β-clamp is critical by increasing the processivity of Pol II during elongation of the slipped −2 frameshift intermediate by one nucleotide which, surprisingly, is enough to support subsequent elongation by Pol III rather than degradation. Finally, the proofreading activity of the replicative polymerase prevents the formation of a Pol II-mediated −1 frameshift product. In conclusion, failure or success of TLS pathways appears to be the net result of a complex interplay among DNA polymerases and accessory factors.     

Studies on the mechanism of inhibition of 2-acetylaminofluorene toxicity by butylated hydroxytoluene.

Male rats were placed on a diet containing 0.05% (w/w) of the hepatic carcinogen 2-acetylaminofluorene (AAF). They ceased to gain weight. However, when the carcinogenic diet was supplemented with butylated hydroxytoluene (BHT) (0.5% w/w), an antioxidant, the animals gained weight at approximately one-half of the normal rate. This observation led to a series of experiments aimed at elucidating the mechanism(s) by which BHT reduced the toxicity of AAF. These initial studies were directed towards the effect of BHT on the extent and duration of the covalent binding of AAF with DNA. BHT feeding was shown to reduce the binding of carcinogen to hepatic DNA. Studies employing cells in culture demonstrated that BHT does not influence either excision repair or post-replication repair of DNA. These data indicate that a potential mechanism of action of BHT is at the anti-initiation level of carcinogen-induced DNA damage.     

Metabolism and nucleic acid binding of 7-fluoro-2-acetamidofluorene in rats: oxidative defluorination and apparent dissociation from hepatocarcinogenesis of 8-(N-arylamide) guanine adducts on DNA

The significance in hepatocarcinogenesis of various arylamine/amide adducts with nucleic acid was investigated by the use of comparison studies on several different parameters. Female Fischer and Sprague-Dawley rats are comparably sensitive to hepatocarcinogenesis by 2-acetamidofluorene (AAF), while male rats are more sensitive. 7-Fluoro-AAF is more carcinogenic in Sprague-Dawley rats than is AAF, but is strikingly so toward the liver of the female rat. Based on these observations, binding of both compounds to liver nucleic acids was determined for male and female Fischer rats at 1 and 3 days after a single injection of carcinogen, and in female Sprague-Dawley rats from 1 to 28 days after a single injection. As shown by others, no 8-(N-2-fluorenylacetamido)guanine adduct could be found in RNA or DNA of female Sprague-Dawley rats treated with AAF (nor was the corresponding 7-fluoro derivative detectable). These adducts were present, however, in comparable amounts in both male and female Fischer rats. The binding of 7-fluoro-AAF derivatives was higher than that of AAF derivatives in female Sprague-Dawley rats. Feeding of either AAF or 7-fluoro-AAF to Sprague-Dawley rats for 4 weeks before a single injection of [3H]7-fluoro-AAF resulted in reduction of the 8-(N-2-(7-fluoro)fluorenylacetamido)guanine adduct in males to undetectable levels in DNA and to 10% of control level in RNA. Non-acetylated adducts were increased in males, but decreased in females by AAF prefeeding; 7-fluoro-AAF prefeeding resulted in little change in adduct formation in females and in a major increase in non-acetylated adducts in males. AAF adducts disappeared from DNA more rapidly than did 7-fluoro-AAF adducts. Assay of the urinary metabolites from the animals in the prefeeding experiment showed that all compounds fed (including the non-hepatocarcinogens 4-acetamidobiphenyl and 2-acetamidophenanthrene) increased the proportion of N-hydroxy-7-fluoro-AAF among the metabolites. Defluorination of 7-fluoro-AAF to 7-hydroxy-AAF was also demonstrated and the ratio of 7-hydroxy-AAF to 5-hydroxy-7-fluoro-AAF was comparable to that observed for 7-hydroxy-AAF/5-hydroxy-AAF and AAF itself, suggesting that fluoro substitution does not increase activity by preventing detoxication.     

Induction of single-strand breaks and interstrand cross-links in liver DNA after the administration of 2-acetylaminofluorene and trans-4-acetylaminostilbene to rats

2-Acetylaminofluorene (AAF) or trans-4-acetylaminostilbene (AAS) was orally or intraperitoneally administered to female Wistar rats. DNA from liver cells was analyzed for single-strand breaks by the alkaline elution assay. Only borderline effects were observed with doses (100 μMol/kg) used in animal carcinogenesis experiments. Even high doses of AAF (1,000 μMol/kg) were not effective. Methyl methanesulfonate (MMS) in vivo and gamma irradiation in vitro were shown to produce dose-dependent DNA single-strand breaks (positive control). Only a marginal effect was obtained with 100 μMollkg MMS. The elution rate of DNA was increased by a factor of 34 in liver cells in vitro with 400 rad of gamma irradiation. Only a fraction of this rate could be demonstrated immediately after irradiation in vivo, and no lesions were found two hours later. This strongly indicates the rapid repair of single-strand breaks. Additional experiments showed that AAS, a nonhepatocarcinogen, produced more interstrand cross-links in the rat liver DNA than did AAF.     

Induction of 6-thioguanine resistance in human cells treated with N-acetoxy-2-acetylaminofluorene

Induction of 6-thioguanine resistance was studied in human cells treated with the direct-acting chemical carcinogen N-acetoxy-2-acetylaminofluorene (NA-AAF). At low concentrations (2.5–7.5 μM) induction of resistant clones was linear and followed one-hit kinetics, while at 10 μM the yield of resistant clones was higher and appeared to result from the combination of one-hit and two-hit kinetics. A study of about 50 resistant clones revealed that most had reduced levels of hypoxanthine-guanine phosphoribosyl transferase (HGPRT) activity (25–85% of controls) and were able to use exogenous hypoxanthine for growth (“Type II mutants,” deMars, 1974); a few had very low HGPRT activity (1–8% of controls) and were unable to use exogenous hypoxanthine (“Type I mutants”). Use of [9-¹⁴C]NA-AAF allowed us to examine the frequency of induction of thioguanine resistance as a function of binding to DNA (μmole AAF/mole DNA-P). Calculations from these data suggest that most “hits” on the HGPRT locus do not result in detectable mutations: At three different levels of binding and induced mutation frequency, the yield was 2.5-3 detectable mutants/10 000 molecules of acetylaminofluorene bound to the HGPRT locus. These data suggest that most bound acetylaminofluorene molecules either produce no change in the primary sequence of DNA (possibly as a result of repair or correct “read through” by the DNA polymerase) or result in changes which are phenotypically undetectable.     

iDNA6mA-PseKNC: Identifying DNA N6-methyladenosine sites by incorporating nucleotide physicochemical properties into PseKNC

N⁶-methyladenine (6mA) is one kind of post-replication modification (PTM or PTRM) occurring in a wide range of DNA sequences. Accurate identification of its sites will be very helpful for revealing the biological functions of 6mA, but it is time-consuming and expensive to determine them by experiments alone. Unfortunately, so far, no bioinformatics tool is available to do so. To fill in such an empty area, we have proposed a novel predictor called iDNA6mA-PseKNC that is established by incorporating nucleotide physicochemical properties into Pseudo K-tuple Nucleotide Composition (PseKNC). It has been observed via rigorous cross-validations that the predictor's sensitivity (Sn), specificity (Sp), accuracy (Acc), and stability (MCC) are 93%, 100%, 96%, and 0.93, respectively. For the convenience of most experimental scientists, a user-friendly web server for iDNA6mA-PseKNC has been established at http://lin-group.cn/server/iDNA6mA-PseKNC, by which users can easily obtain their desired results without the need to go through the complicated mathematical equations involved.     

A novel pathway for transversion mutation induced by dCTP misincorporation in a mutator strain of CHO cells.

Intracellular imbalances of dCTP produce both T----C transitions and an unusual class of transversions (A----C) at the aprt locus of CHO cells. Our data suggest that this transversion pathway is the consequence of dCTP:T mispairs which are not efficiently proofread during DNA replication.     

Formation of electrophilic N-acetoxyarylamines in cytosols from rat mammary gland and other tissues by trans-acetylation from the carcinogen N-hydroxy-4-acetylaminobiphenyl

The 105 000 × g supernatant fractions of various rat tissues catalyze the transfer of the N-acetyl group of certain carcinogenic aromatic acethydroxamic acids to the O atom of aromatic hydroxylamines. The resulting N-acetoxyhydroxylamines are strongly electrophilic and have been detected and analyzed through their reaction with N-acetylmethionine to yield methylmercaptoaminoarenes.Of the rat tissues studied the liver had the highest activity; kidney and small intestinal mucosa were about 15–20% as active. The transacetylase activities of these tissues were similar with respect to their ability to use either N-hydroxy-2-acetylaminofluorene (N-hydroxy-AAF or N-hydroxy-4-acetylaminobiphenyl (N-hydroxy-AABP) as acetyl donors, their stability on storage at 2–3°C, and their elution patterns from Sephadex G-100 columns. Low transacetylase activity was found in spleen and muscle.Mammary tissue from 16–21 day pregnant rats had 20% of the transacetylase activity of rat liver when N-hydroxy-AABP was used as acetyl donor and N-hydroxy-4-aminobiphenyl (N-hydroxy-ABP) was the acetyl acceptor. This enzyme system from mammary tissue did not utilize the fluorene derivatives as either acetyl donor or acetyl acceptor, was much more labile than the liver, kidney, or intestinal mucosa systems, and had a pH optimum at 7.5, as compared to pH 6.8 for liver. The mammary tissue system was similar to the hepatic system in being inhibited by sulfhydryl reagents; it required a source of reduced pyridine nucleotides for maximum activity.     

A synonymous mutation in NOD2 gene was significantly associated with non-specific digestive disorder in rabbit

Nucleotide-binding oligomerization domain containing 2 (NOD2) plays a pivotal role in the host innate and adaptive immunity by recognizing the pathogenic agents. Therefore, its genetic polymorphisms and association with susceptibility to infectious diseases have been widely reported in human and farm animals. In the present study, we investigated the genetic polymorphisms in 3171 bp coding region of NOD2 gene and association with non-specific digestive disorder (NSDD) in rabbit. A total of four coding single-nucleotide polymorphisms (cSNPs) were detected. Among them, c.2961C>T was further genotyped for case (n = 176) and control (n = 130) based on association analysis, which revealed that C allele carried the potential protective role for susceptibility to NSDD with the odds ratio (OR) values of 0.52 (95% confidence interval (CI) 0.37–0.73, P < 0.01). Under the dominant inheritance model, CC genotype was associated with decreased susceptibility to NSDD (OR = 0.38, 95% CI 0.24–0.60, P < 0.01). Along with the aggravation of NSDD, we observed higher mRNA expression of NOD2 gene (P < 0.05). However, the mRNA expression pattern of CC genotype would be interacted by the different status of NSDD, which only showed the significantly increased level in severe NSDD group (P < 0.05). These results revealed by genetic association and gene expression analysis suggested that the NOD2 gene was associated with the susceptibility to NSDD in rabbit. However, the causative mutations linked to c.2961C>T and corresponding functional depiction should be further explored by performing exhaustive genetic studies.