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Arylamine-DNA adducts in vitro and in vivo: their role in bacterial mutagenesis and urinary bladder carcinogenesis.

Hepatic N-oxidation, followed by N-glucuronidation, has been proposed as a route of metabolic activation for arylamine bladder carcinogens. It is postulated that the N-glucuronides are transported to the bladder lumen where they are hydrolyzed under slightly acidic conditions to release direct-acting carcinogenic and mutagenic N-hydroxyarylamines. In this study, 4-aminobiphenyl (ABP), 1-naphthylamine (1-NA), 2-naphthylamine (2-NA), 2-acetylaminofluorene (AAF), 4-nitrobiphenyl (NBP), benzidine (BZ), and N-acetylbenzidine (ABZ) were administered to male beagle dogs (60 mumole/kg), and the bladder epithelium DNA adducts were quantified at various times after treatment. At 24-48 hr after administration, the order of binding to bladder epithelium DNA was: ABP >> AAF > NBP congruent with 2-NA congruent withBZ congruent with ABZ >> 1-NA. The level of DNA modification by ABP remained constant for 7 days, whereas 2-NA and AAF residues decreased by 35% and 80%, respectively. The extent and relative persistence of total DNA binding correlated with the compounds' ability to induce bladder tumors in dogs. ABP, AAF, NBP, 2-NA and ABZ administration resulted in DNA binding sufficient for adduct analysis. Enzymatic hydrolysis of the DNA and examination of the adducts by high pressure liquid chromatography indicated that arylamine substitution at C8 of deoxyguanosine was the dominant product. Additional adducts were detected in animals treated with ABP, NBP, and 2-NA. Furthermore, the profiles of adducts obtained in vivo were remarkably similar to the profiles obtained when the N-hydroxy arylamine metabolites of these carcinogens were reacted with DNA in vitro at pH 5.0. To evaluate the mutagenic potential of these arylamine-DNA adducts, Salmonella typhimurium strains TA 1535 and TA 1538 were incubated with N-hydroxy-2-NA, N-hydroxy-2-aminofluorene (AF), N-hydroxy-ABP, and N-hydroxy-ABZ and the resulting DNA adducts and reversions were quantified. Arylamine-C8-deoxyguanosine substitution was correlated with frameshift reversions induced by these agents, with the lesions showing a relative order of mutagenic efficiency of ABZ>AF congruent with2-NA>ABP. These data suggest that mutagenic N-hydroxyarylamines may be ultimate carcinogens for the bladder epithelium. Furthermore, if one assumes that a mutagenic lesion is important for tumor initiation, then C8-deoxyguanosine substitution by these compounds may be significant for urinary bladder carcinogenesis.

Amines↗

[Specificity of new restrictases and methylases. Unusual modification of cytosine at position 4].

Fourteen restriction endonucleases and 4 methylases were isolated and purified from 14 strains of Citrobacter freundii and Escherichia coli, which were isolated from natural sources. To determine the nucleotide sequence recognized by the endonucleases a comparison of DNA cleavage patterns, the evaluation of the cleavage frequency of some DNA with known recognition sequences and mapping was used. It was determined that Cfr101 is a new enzyme recognizing 5'PuCCGGPy. Other restriction enzymes isolated were isoschizomers of: Cfr5I, Cfr11I, Eco60I, Eco61I--EcoRII; Cfr4I, Cfr8I, Cfr13I--Sau96I; Cfr6I--PvuII, Cfr9I--SmaI, Eco26I--HgiJII; Eco32I--EcoRV; Eco52I--XmaIII; Eco56I--NaeI. Some of the enzymes in C. freundii and E. coli were found for the first time. The methylases MCfrI; MCfr6I, MCfr9I and MCfr10I recognize the same nucleotide sequence as specific endonucleases isolated from the same strain. DNA modification in vitro by MCfrI and MCfr10I yields 5-methylcytosine and 4-methylcytosine by MCfr6I and MCfr9I.

Adenoviridae↗

Methods to detect DNA damage by free radicals: relation to exercise.

Epidemiological investigations repeatedly show decreased morbidity from regular exercise compared with sedentary life. A large number of investigations have demonstrated increased oxidation of important cellular macromolecules, whereas other investigators have found no effects or even signs of lowering of oxidation of macromolecules. In particular, extreme and long-duration strenuous exercise appears to lead to deleterious oxidation of cellular macromolecules. The oxidation of DNA is important because the oxidative modifications of DNA bases, particularly the 8-hydroxylation of guanine, are mutagenic and have been implicated in a variety of diseases such as ageing and cancer. The methodologies for further investigation of the relationship between DNA oxidation and exercise are available. The preferred methods rely on HPLC or GC-mass spectrometry; whereas the theoretically-attractive liquid chromatography-tandem mass spectrometry is being developed. Caution should be taken to avoid artifacts because of the six orders of magnitude of difference between oxidized and non-oxidized DNA bases in tissues. The methods can be used to estimate tissue levels, i.e. a local concentration of oxidized DNA, or to estimate the rate of body DNA oxidation by the urinary output of repair products, the latter being a method that is independent of repair. During exercise there appears to be a shifting of dietary-dependent antioxidant, e.g. vitamin C and vitamin E, from muscle to plasma, and an increased oxidation in plasma of these antioxidants. Supplementation trials with antioxidants have not been able to increase exercise performance; however, optimum nutrition with antioxidants and possibly supplementation, could be important in the prevention of diseases in the long term. The pattern from these observations appears to be quite consistent; immediately after exercise, regardless of how intense, there do not appear to be any signs of oxidative damage to DNA. Acute or prolonged moderate exercise does not produce signs of oxidative DNA damage and might even be associated with lowering of the levels of oxidation of tissue DNA; however, after long-duration and intense exercise an increase in oxidative DNA modifications is apparent. We suggest as a hypothesis that the relationship between exercise and health is U-shaped. This hypothesis needs to be tested in detail in order to establish the maximum beneficial exercise level with regard to oxidative DNA modification, and also the level that could be deleterious and might even increase the risk for cancer and other diseases.

8-Hydroxy-2'-Deoxyguanosine↗

Biomonitoring of aquatic systems.

The 32P-postlabelling analysis provides a sensitive means for detecting pollution-related DNA adducts in aquatic organisms exposed to environmental carcinogens. However, the following factors need to be taken into consideration during the data interpretation: (1) species-specific, naturally occurring DNA modifications (or I-compounds) are found in aquatic organisms at levels which are highly season-dependent; and (2) many aquatic organisms, particularly lower invertebrates, cannot form DNA adducts from common pollutants such as polycyclic aromatic hydrocarbons (PAHs). The level of natural adducts is especially high in lower invertebrates, such as sponges and sea-urchins during their reproductive phase in the spring time (March/April): in subsequent months adducts were either undetectable or present at only trace levels. These invertebrates do not metabolize PAHs such as benzo[a]pyrene but readily biotransform aromatic amines such as 2-acetylaminofluorene to DNA-reactive forms. Pollution-related DNA adducts have been found in fish living in highly polluted rivers and marine sites and in carp exposed to an artificial Diesel-2/crude oil slick. In certain fish (English sole, brown bullheads, etc.) living in polluted environments, the formation of pollution-related DNA adducts has been correlated with an increased incidence of tumours. It is concluded that, while DNA adducts detected in aquatic organisms can be used for biomonitoring and detecting pollutants, there are several confounding factors that should be taken into consideration before one attempts to determine the type and concentration of carcinogenic pollutants present in aquatic environments.

Animals↗

Effect of in vitro DNA methylation on beta-globin gene expression.

When the human beta-globin gene was methylated at every cytosine residue and was inserted into mouse fibroblasts by DNA-mediated gene transfer, the transcription of the gene was strongly inhibited. This methylation also prevented expression and induction of the gene in mouse erythroleukemia cells. By using partially methylated hybrid molecules, it was shown that methylation-sensitive negative regulatory elements are located in both the 5' and 3' ends of the beta-globin gene but not in the 90-base-pair region usually associated with promoter activity. To further investigate the role of DNA methylation in the regulation of the beta-globin gene, 50-base-pair poly(dG-dC) tracts were introduced into various sites in a mouse-human hybrid gene, and these inserts were methylated by means of the Hha I methylase. Heavy methylation of these artificially added sites had no effect on either transcription initiation or elongation, suggesting that DNA modification operates through fixed endogenous sites in the gene domain.

Animals↗

[Genomic variability of sugar beet morphogenic and non-morphogenic callus].

Cytogenetic characters and the level of DNA methylation were studied in sugarbeet callus cultures with different morphogenic potential which were obtained from the same leaf explant. It was shown that non-morphogenic callus in comparison with the morphogenic one was characterized by the higher level of cell ploidy and of the frequency of chromosome structural rearrangements even at the early stages of cultivation. Overspiralization of chromosomes and formation of condensed chromatin were observed in polyploid cells of non-morphogenic callus. At the same time cytosine hypermethylation occurs in site-specific CpCpGpG-sequences of DNA indicating the possible role of this DNA modification in the processes of genome rearrangements.

Beta vulgaris↗

Programmable enzymes for targeted gene insertion.

Genome editing technologies have advanced from nuclease-based reagents that generate programmed DNA double-strand breaks, which can cause deleterious effects, to next-generation reagents that perform controlled DNA modification through double-strand break-independent mechanisms, such as base editing and prime editing. Although these approaches enable precise small-scale sequence changes, methods for programmable insertion of large DNA cargos have been limited. The ability to write entire genes or large regions into the genome could transform the treatment of genetically heterogeneous disorders, for which numerous pathogenic variants underlie a common disease and mutation-specific editing strategies are impractical. Recent advances in computational genome mining have accelerated the discovery of naturally occurring enzymes with novel biochemical and functional properties, including recombinases and transposases capable of large-scale modifications. Moreover, directed evolution, rational engineering and expanded homologue discovery are enabling the repurposing and optimization of these systems for genome engineering. Here we review recent technology development efforts that harness diverse enzymes for kilobase-scale genome engineering, with a particular focus on CRISPR-associated transposase systems.

Journal Article↗

DNA damage induced by peroxynitrite: subsequent biological effects.

Nitric oxide (NO) and superoxide rapidly react to yield peroxynitrite. Peroxynitrite is a potent oxidant which reacts with proteins, lipids, and DNA. The present paper overviews the various DNA modifications induced by exposure to peroxynitrite or NO and superoxide concurrently, with special reference to the formation of 8-nitroguanine and 8-oxoguanine as well as the induction of DNA single strand breakage. In addition, we review the secondary processes that may follow the process of DNA damage, such as activation of the nuclear enzyme, poly(ADP-ribose) synthetase, apoptosis, and carcinogenesis.

Animals↗

Induction and processing of promutagenic O4-ethylthymine lesion in specific gene segments of plasmid DNA.

High affinity antibodies were used for the quantitative assessment of the miscoding O4-ethylthymine (O4-EtThy) base lesion in nanogram amounts of membrane transblotted restriction fragments of ENU treated DNA. The polyclonal antibody (TB3) specifically recognized attomoles of the alkylation adducts in modified DNA with no cross-reactivity to an excess of unmodified DNA. The sensitivity of the immuno-quantitative method was determined to be in the range of 76 attomoles to 2.43 fmol, corresponding to 0.24 x 10(-7) to 7.9 x 10(-7) adducts per nucleotide in plasmid DNA. Modification levels in ras and tk genes were estimated as 0.025 and 0.014 adducts respectively. Specific antibody binding was proportional to the dose of ENU and size of the DNA fragments. In differentially ethylated ras gene, the amount of O4-EtThy was quantified as 0.026, 0.08 and 0.13 adducts per gene fragment. A DNA concentration dependent antibody binding was observed with large (23.13 and 9.41 kb) and smaller (2.02 kb) fragments of HindIII digested ENU treated phage lambda DNA. To monitor the repair of O4-EtThy lesions in specific segments, damage was assessed in sequences of plasmid DNA established in various Escherichia coli strains. The loss of antibody binding to O4-EtThy adducts in ethylated DNA fragments of 6.4 kb ras gene and 3.6 kb tk gene occurred with an approximate t1/2 of 45 and 35 min, respectively, in the repair proficient wild type E. coli. On the contrary, no repair was seen in the alkyltransferase deficient double mutant ada-ogt- strain. The results specifically demonstrate the sensitivity of the immunological technique and the unique ability of the O4-EtThy specific antibodies to scan this promutagenic base lesion and its repair in very small amounts of selected gene segments in DNA.

Alkylation↗

Properties of Bacillus subtilis 168 derivatives freed of their natural prophages.

An isogenic set of Bacillus subtilis 168 strains which are non-inducible for prophage PBSX and are cured of prophage SP beta has been constructed. By utilizing these strains, prophage SP beta has been shown to control the inducible DNA modification system which exists in this bacterium. However, neither the PBSX nor the SP beta prophages alter the ability of the bacterium to undergo genetic recombination, to repair damaged DNA or to sporulate. Prophageless B. subtilis would be a useful host for the phi 3T cloning vector, because of the absence of vector--prophage interactions.

Bacillus subtilis↗

32P-post-labeling analysis of DNA adduct formation by antitumor drug nitracrine (Ledakrin) and other nitroacridines in different biological systems.

A 32P-post-labeling method has been employed to detect DNA adducts formed by derivatives of nitro-9-aminoacridine in both cellular and non-cellular systems. The treatment of HeLa S3 cells in culture or Ehrlich ascites tumor cells in vivo with nitracrine and two other antitumor 1-nitro-9-aminoacridines, denoted C-857 and C-1006, resulted in covalent binding of these compounds to cellular DNA. Each derivative studied gave rise to a distinct pattern of adduct spots and the similarity of the respective adduct profiles was noted for the both cellular models. Calf thymus DNA samples modified in vitro with nitracrine and C-857 in the presence of either rat hepatic microsomal fraction or dithiothreitol yielded chromatographic profiles resembling those obtained in the cellular systems, suggesting similarity in the DNA adduct structures. There were also neither qualitative nor quantitative differences in calf thymus DNA modification by these two 1-nitro derivatives between aerobic and anaerobic conditions, thus the reduction of a nitro group seems not to be the only determinant of covalent binding to DNA in vitro. No DNA adduct formation was detected in the cellular systems used with 2-nitro and 4-nitro isomers of nitracrine that are devoid of cytotoxic activity, which provides further evidence that both covalent binding and DNA crosslinking, but not intercalation, are responsible for cytotoxic and antitumor properties of 1-nitro-9-aminoacridines.

Aminoacridines↗

Genetic diversity at the FMR1 locus in Mexican population.

BACKGROUND: Fragile X syndrome is the most frequent cause of inherited mental retardation; it is caused by expansion of CGG repeats in the first exon of the FMR1 gene. Number of CGG repeats varies between 6 and 50 triplets in normal individuals and the most common alleles have 29 or 30 repeats. Allelic patterns in the global population are similar; however, some reports show statistical differences among several populations. Distribution of allelic frequencies for FMR1 locus has not been reported in Mexican population. METHODS: Determination of the CGG repeat number was achieved by polymerase chain reaction (PCR) on modified DNA from 129 unrelated Mexican mestizos (46 FRAXA-negative males with mental retardation and 83 healthy individuals). DNA modification by sodium bisulfite achieves conversion of unmethylated cytosine residues to uracil, which allows efficient amplification by single PCR. Methylation status of FMR1 region for each individual was also established. DNA sequencing of a number of amplified samples was realized to validate the procedure. RESULTS: Molecular analysis of the FMR1 gene showed 23 different alleles. Statistical comparison of allelic length between healthy and affected individuals does not show significant differences. Trinucleotide repeat number varied from 16-40, with modal number of 32 (27.58%), second peak at 30 (25.28%), and minor peak at 34 (10.34%). Together, allelic distribution in the Mexican sample differs significantly from those reported for Caucasian, Chinese, African, Indonesian, Brazilian, Chilean, and Mixtec populations. An excess of large alleles (> or =34 repeats) was evident. CONCLUSIONS: Allele distribution in FMR1 gene from Mexican mestizos is different from that of other reported populations around the world. This unusual modal pattern probably is related to the particular ethnic background of the Mexican population. On the other hand, PCR on modified DNA is a valuable and efficient method for determination of CGG repetitive sequences in FMR1 gene.

Alleles↗

Transformation with DNA from 5-azacytidine-reactivated X chromosomes.

It has been shown that 5-azacytidine (5-Aza-Cyd) can reactivate genes on the inactive human X chromosome. It is assumed that the 5-Aza-Cyd acts by causing demethylation of the DNA at specific sites, but this cannot be demonstrated directly without a cloned probe. Instead, we have utilized the technique of DNA-mediated transformation to show that the 5-Aza-Cyd-induced reactivation occurs at the DNA level. DNAs from various mouse-human or hamster-human hybrid cell lines, deficient for mouse or hamster hypoxanthine phosphoribosyltransferase (HPRT, EC 2.4.2.8) and varying in whether they contained either an active or inactive human X chromosome, were used in transformation of HPRT- cells. DNA from the active human X chromosome-containing cell lines yielded HPRT+ transformants, whereas DNA from the inactive X chromosome-containing cells lines did not. The inactive X chromosomal DNA was able to transform thymidine kinase-deficient mouse cells, indicating that the DNA solution was normal. These results confirm that inactivation of the X chromosome involves a DNA modification. Furthermore, DNAs from three cell lines with a 5-Aza-Cyd-reactivated X chromosome also transform HPRT- cells, demonstrating that the 5-Aza-Cyd has altered the DNA structure and supporting the idea that methylation plays a role in X chromosome inactivation.

Animals↗

Molecular aspects of antitumor effects of a new platinum(IV) drug.

The new platinum(IV) complex cis,trans,cis-[PtCl(2)(CH(3)COO)(2)-(NH(3))(1-adamantylamine)] [adamplatin(IV)] seems promising for the perspective application in therapy of corresponding tumors. It is therefore of great interest to understand details of mechanisms underlying its biological efficacy. Cellular uptake of the drug, alterations in the target DNA induced by platinum drugs along with processing of platinum-induced damage to DNA and drug inactivation by sulfur-containing compounds belong to major pharmacological factors affecting antitumor effects of platinum compounds. We examined in the present work the significance of these factors in the mechanism of antitumor effects of adamplatin(IV) and compared the results with those of the parallel studies performed with "conventional" cisplatin. The results show that deactivation of adamplatin(IV) by sulfur-containing compounds (such as glutathione or metallothioneins) is likely to play a less significant role in the mechanism of resistance of tumor cells to adamplatin(IV) in contrast to the role of these reactions in the effects of cisplatin. Moreover, the treatment of tumor cells with adamplatin(IV) does not result in DNA modifications that would be markedly different from those produced by cisplatin. In contrast, the effects of other factors, such as enhanced accumulation of the drug in cells, strong inhibition of DNA polymerization by these adducts, lowered DNA repair, and DNA-protein cross-linking are different from the effects of these factors in the mechanism underlying activity of cisplatin. Hence, the differences between effects of adamplatin(IV) and cisplatin observed in the present work on molecular level may help understand the unique activity of adamplatin(IV).

Adamantane↗

Cytosolic ribosomal mutations that abolish accumulation of circular intron in the mitochondria without preventing senescence of Podospora anserina.

The filamentous fungus Podospora anserina presents a degeneration syndrome called Senescence associated with mitochondrial DNA modifications. We show that mutations affecting the two different and interacting cytosolic ribosomal proteins (S7 and S19) systematically and specifically prevent the accumulation of senDNA alpha (a circular double-stranded DNA plasmid derived from the first intron of the mitochondrial cox1 gene or intron alpha) without abolishing Senescence nor affecting the accumulation of other usually observed mitochondrial DNA rearrangements. One of the mutant proteins is homologous to the Escherichia coli S4 and Saccharomyces cerevisiae S13 ribosomal proteins, known to be involved in accuracy control of cytosolic translation. The lack of accumulation of senDNA alpha seems to result from a nontrivial ribosomal alteration unrelated to accuracy control, indicating that S7 and S19 proteins have an additional function. The results strongly suggest that modified expression of nucleus-encoded proteins contributes to Senescence in P. anserina. These data do not fit well with some current models, which propose that intron alpha plays the role of the cytoplasmic and infectious Determinant of Senescence that was defined in early studies.

Amino Acid Sequence↗

Alteration of apparent restriction endonuclease recognition specificities by DNA methylases.

An in vitro method of altering the apparent cleavage specificities of restriction endonucleases was developed using DNA modification methylases. This method was used to reduce the number of cleavage sites for 34 restriction endonucleases. In particular, single-site cleavages were achieved for Nhe I in Adeno-2 DNA and for Acc I and Hinc II in pBR322 DNA by specifically methylating all but one recognition sequence.

Base Composition↗

Mitochondrial DNA alterations as a source of human disorders.

The mitochondrial genome has an underdeveloped "DNA repair repertoire" compared with the nuclear genome, making the mitochondrial DNA more susceptible to mutations by endogenous factors such as defects of the mitochondrial polymerase itself, and by exogenous factors such as radiation and UV light. Increased sensitivity to mutagenic factors may account for the mitochondrial DNA polymorphism within ethnic groups and the mitochondrial diseases associated with all mitochondrial DNA mutations, including DNA depletion. The presence in highly developed organisms of a DNA repair repertoire less organized in the mitochondria than in the nuclei might be a source of biologic dysfunction relevant also to aging and cell death. Uncorrected mitochondrial DNA modifications may determine lethal and severe diseases or asymptomatic biochemical dysfunctions. Considering the long life span and the complex metabolism of highly developed cells, the tendency to produce and accumulate mitochondrial DNA mutations may assume a pathogenetic role with aging.

Aging↗

DNA methylation changes at human Th2 cytokine genes coincide with DNase I hypersensitive site formation during CD4(+) T cell differentiation.

The differentiation of naive CD4(+) T lymphocytes into Th1 and Th2 lineages generates either cellular or humoral immune responses. Th2 cells express the cytokines IL-4, -5, and -13, which are implicated in asthma and atopy. Much has been published about the regulation of murine Th2 cytokine expression, but studies in human primary T cells are less common. We have developed a method for differentiating human CD45RA(+) (naive) T cells into Th1 and Th2 populations that display distinct cytokine expression profiles. We examined both CpG methylation, using bisulfite DNA modification and sequencing, and chromatin structure around the IL-4 and IL-13 genes before and after human T cell differentiation and in normal human skin fibroblasts. In naive cells, the DNA was predominantly methylated. After Th2 differentiation, DNase I hypersensitive sites (DHS) appeared at IL-4 and IL-13 and CpG demethylation occurred only around the Th2-specific DHS. Both DHS and CpG demethylation coincided with consensus binding sites for the Th2-specific transcription factor GATA-3. Although fibroblasts, like naive and Th1 cells, did not express IL-4 or IL-13, DHS and unmethylated CpG sites that were distinct from the Th2-specific sites were observed, suggesting that chromatin structure in this cluster not only varies in T cells according to IL-4/IL-13 expression but is also tissue specific.

Base Sequence↗