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PubMed1989

Cloning, characterization and heterologous expression of the SmaI restriction-modification system.

The genes coding for the class-II Serratia marcescens restriction-modification system have been cloned and expressed in E. coli. Recombinant clones, restricted incoming phage only poorly; the recombinant plasmids, however, became fully modified in vivo, i.e. completely resistant against digestion with R.SmaI. The determined nucleotide sequence of the cloned system revealed three open reading frames with lengths of 252 bp, 741 bp, and 876 bp. Through various deletion experiments and an insertion-mutation experiment the 876 bp open reading frame could be assigned to the SmaI DNA modification enzyme and the 741 bp open reading frame to the SmaI restriction endonuclease. Mapping of the transcription start sites of the genes revealed that the SmaI endonuclease is transcribed as polycistronic mRNA together with a 252 bp long preceding open reading frame of unknown function. No homology was found when comparing the amino acid sequence of M.SmaI with the published sequences of m5C-specific DNA modification methyltransferases. On the other hand, a stretch of 14 amino acids in the C-proximal region of M.SmaI shows a significant homology to the C-proximal amino acid sequences of the N6A-methyltransferases M.HinfI and M.DpnIIA and the N4C-methyltransferase M.PvuII.

Amino Acid Sequence↗
PubMed1993

Copper ion-mediated modification of bases in DNA in vitro by benzoyl peroxide.

The mouse skin tumor promoter benzoyl peroxide (BzPO), in conjunction with Cu(I), causes promutagenic damage in DNA. Because free radical intermediates are produced by the reaction of BzPO with Cu(I), we sought to determine whether BzPO plus Cu(I) caused DNA base damage typical of that caused by the hydroxyl radical. A broad range of modified DNA bases were measured by GC-MS with selected-ion monitoring after exposure of purified plasmid pCMV beta gal DNA to BzPO +/- Cu(I). Exposure to BzPO/Cu(I) caused up to 20-fold increases in the levels of adenine-derived modified bases, up to 4-fold increases in guanine- and cytosine-derived modified bases, and only a < 2-fold increase in thymine-derived modified bases. The guanine-derived modified base 8-hydroxyguanine was elevated to the highest net amount, approximately 160 molecules/10(5) DNA bases. Exposure to BzPO alone or Cu(I) alone induced only minor (< < 2-fold) DNA base modification. Also, benzoic acid, the major non-radical metabolite of BzPO, or BzPO plus Fe(II) were ineffective at inducing DNA base modification. The hydroxyl radical scavenger dimethyl sulfoxide inhibited BzPO/Cu(I)-induced base modification by 10-50%. These data suggest that the reaction of BzPO with Cu(I) generates hydroxyl radical or a similarly reactive intermediate which causes DNA base damage. This damage may be responsible for BzPO/Cu(I)-mediated mutagenesis.

Adenine↗
PubMed1989

Immunocytochemical analysis of O6-alkylguanine shows tissue specific formation in and removal from esophageal and liver DNA in rats treated with methylbenzylnitrosamine, dimethylnitrosamine, diethylnitrosamine and ethylnitrosourea.

The formation and repair of carcinogen-DNA adducts in esophagus and liver of rats treated with a single i.p. dose of methylbenzylnitrosamine (MBN), dimethylnitrosamine (DMN), diethylnitrosamine (DEN) or ethylnitrosourea (ENU) has been studied using peroxidase immunocytochemistry to visualize O6-alkylguanine in DNA of individual cells. After MBN O6-methylguanine (O6-MeG) specific nuclear staining was only present in the target tissue for tumor induction, the esophageal epithelium. Part of the adducts persisted for at least 72 h. No O6-MeG could be detected in liver. DEN, a carcinogen in liver and esophagus, led to DNA modification of esophageal epithelial cells, and liver parenchymal and non-parenchymal (Kupffer and sinusoidal) cells of the centrilobular area. O6-EtG was removed within 72 h from both liver cell populations. A similar distribution of adduct (O6-MeG) formation was observed in liver after the hepatocarcinogen DMN, but this nitrosamine did not detectably modify esophageal cells. O6-MeG persisted in Kupffer and especially sinusoidal lining cells of liver, consistent with the induction of sarcomas by DMN. The relatively unspecific, directly alkylating carcinogen ENU modified DNA of all cell types to a similar extent. A qualitative correlation was obtained between the tissue specific ability to induce tumors and the formation of O6-alkylguanine (O6-alkylG). Our experiments support the hypothesis that DNA modification is necessary for the initiation of carcinogenesis by chemical carcinogens, and that a low capacity to repair promutagenic lesions, like O6-alkylG, potentiates this process.

Animals↗
PubMed2001

Cell degeneration in the model system Podospora anserina.

Podospora anserina is a filamentous fungus used in many studies of fundamental cell biology, including cell ageing. In this organism, ageing is defined as a diminution of cell ability to proliferate and/or differentiate. This may or may not culminate with cell death. Two different ageing processes are intensively studied. The 'Senescence' phenomenon is present in all wild-type strains, results in cell death and is caused by a yet undefined cytoplasmic and infectious element. It is associated with extensive mitochondrial DNA modifications. Longevity of the strains is controlled by a highly complex network of genes. Among these, those involved in cytosolic translation and respiratory metabolism are of special importance. The 'Crippled Growth' phenomenon is present only in strains with elevated translational accuracy. It does not result in cell death but in a severe impairment of cell growth, an acceleration of Senescence and a diminution of differentiation potencies. No mitochondrial DNA modification is associated with Crippled Growth. Another cytoplasmic and infectious element with peculiar properties, C, is causally involved in the set up of this cell degeneration. The study of P. anserina degenerative processes provides a conceptual framework to understand ageing in more complex organisms. Especially, it emphasises the complex control exerted by genes on longevity, the multiplicity of degenerative processes that may occur to cells with identical genotype and the potential role of non-conventional infectious elements in cell ageing.

Animals↗
PubMed2005

Visible light (>395 nm) causes micronuclei formation in mammalian cells without generation of cyclobutane pyrimidine dimers.

Solar radiation gives rise to DNA damage in mammalian cells not only directly by excitation of DNA, which generates predominantly pyrimidine dimers, but also indirectly by the excitation of endogenous photosensitizers, which causes oxidative DNA modifications. The latter mechanism has a low quantum yield, but it is the only one proceeding in the visible range of the spectrum. To investigate its relevance for the genotoxicity of sunlight, we have analysed the generation of micronuclei associated with the induction of oxidative DNA damage by visible light in melanoma cells and primary human skin fibroblasts. Similar yields of light-induced oxidative DNA base modifications sensitive to the repair glycosylase Fpg (7,8-dihydro-8-oxoguanine and other oxidative purine modifications) were observed in the normal fibroblasts and the malignant melanoma cells of the same donor. When irradiations were carried out at intervals to compensate for a photodecomposition of the endogenous chromophore, a significant generation of micronuclei was observed in both cell types. Cyclobutane pyrimidine dimers could be excluded to be responsible for the micronuclei induction at wavelengths >395 nm. Experiments with a cut-off filter indicate that the ratio of pyrimidine dimers and Fpg-sensitive oxidative modifications in irradiated cells not only reflects the relative contributions of direct and indirect mechanisms, but is also similar to the ratio by which the two mechanisms contribute to the generation of the micronuclei. The results suggest that indirectly generated oxidative DNA modifications can contribute significantly to the adverse effects of sunlight.

Animals↗
PubMed1987

DNA base modification: ionized base pairs and mutagenesis.

The nature of hydrogen bonding between normal and modified bases has been re-examined. It is proposed that hydrogen-bonding schemes may involve tautomeric, ionized or conformational forms (syn, anti and wobble). Several important cases are presented or reviewed in which physical evidence indicates the existence of ionized base pairs. When thermodynamic values determined in aqueous solution under physiological conditions are considered, it can be argued that base ionization will contribute substantially to the stability of many biologically relevant base pairs containing modified bases. A significant incidence of ionized bases in DNA may have important kinetic ramifications for the further chemical reactivity of both the modified base and its cross-strand pairing partner. Moreover, DNA structure at and surrounding ionized base pairs may be altered. For this reason, the model presented in this study should be useful as DNA-sequence analysis becomes more commonly applied to the study of mutagenesis.

Base Composition↗
PubMed2000

Epigenetic properties of fumonisin B(1): cell cycle arrest and DNA base modification in C6 glioma cells.

Fumonisin B(1) produced by the fungus Fusarium moniliforme is a member of a new class of sphinganine analogue mycotoxins that occur widely in the food chain. Epidemiological studies associate FB(1) with human oesophageal cancer in China and South Africa. FB(1) also causes acute pulmonary edema in pigs and equine leucoencephalomalacia. This disease is thought to be a consequence of inhibition by FB(1) of cellular ceramide synthesis in cells. To investigate further on this pathogenesis, the effect of FB(1) was studied on cell viability (3 to 54 microM of FB(1)), protein (2.5 to 20 microM of FB(1)) and DNA syntheses (2.5 to 50 microM of FB(1)), and cellular cycle (3 to 18 microM of FB(1)) of rat C6 glioma cells after 24 h incubation. The results of the viability test show that FB(1) induces 10 +/- 2% and 47 +/- 4% cell death with, respectively, 3 and 54 microM, in C6 cells. This cytotoxicity induced by FB(1) was efficiently prevented when the cells were preincubated 24 h with vitamin E (25 microM). FB(1) displays epigenetic properties since it induced hypermethylation of the DNA (9-18 microM). Inhibition of protein synthesis was observed with FB(1) with an IC(50) of 6 microM showing that C6 glioma cells are very sensitive to FB(1); however, the synthesis of DNA was only slightly inhibited, up to 20 microM of FB1. The flow cytometry showed that the number of cells in phase S decreased significantly as compared to the control p = 0.01 from 18. 7 +/- 2.5% to 8.1 +/- 1.1% for 9 microM FB(1). The number of cells in phase G(2)/M increased significantly as compared to the control (p </= 0.05) from 45.7 +/- 0.4% to 54.8 +/- 1.1% for 9 microM FB(1), whereas no change occurs in the number of cells in the phase G(0)/G(1). These results show that cytotoxic concentrations of FB(1) induce cellular cycle arrest in phase G(2)/M in rat C6 glioma cells possibly in relation with genotoxic events.

Animals↗
PubMed2007

Deficiency of the Cockayne syndrome B (CSB) gene aggravates the genomic instability caused by endogenous oxidative DNA base damage in mice.

The Cockayne syndrome B protein (CSB) has long been known to be involved in the repair of DNA modifications that block the RNA polymerase in transcribed DNA sequences (transcription-coupled repair). Recent evidence suggests that it also has a more general role in the repair of oxidative DNA base modifications such as 7,8-dihydro-8-oxo-2'-deoxyguanosine (8-oxoG). In mammalian cells, 8-oxoG is a substrate of the repair glycosylase OGG1. Mice without this enzyme accumulate 8-oxoG in the genome and have elevated spontaneous mutation rates. To elucidate the role of CSB in the prevention of mutations by oxidative DNA base damage, we have generated mice that are deficient in Csb or Ogg1 or both genes and carry a non-transcribed bacterial lacI gene for mutation analysis (Big Blue mice). Our results indicate that the overall spontaneous mutation frequencies in the livers of Csb(m/m)/Ogg1-/- -mice are elevated not only compared with heterozygous control mice (factor 3.3), but also with Ogg1-/- -animals (factor 1.6). Sequence analysis revealed that the additional mutations caused by CSB deficiency in an Ogg1-/- background are mostly G:C to T:A transversions and small deletions. For all mouse strains, the background levels of oxidative purine modifications in the livers correlate linearly with the numbers of G:C to T:A transversions observed. The data indicate that CSB is involved in the inhibition of mutations caused by spontaneous oxidative DNA base damage in a non-transcribed gene.

Animals↗
PubMed1987

Hydrogen peroxide formation and DNA base modification by tumor promoter-activated polymorphonuclear leukocytes.

This report shows that generation of hydrogen peroxide (H2O2) by human polymorphonuclear leukocytes (PMNs) activated with tumor promoters of varying potency as first and second stage promoters correlates well with activities of these promoters in vivo. Those tested were 12-O-tetradecanoylphorbol-13-acetate (TPA), a complete promoter, 12-O-retinoylphorbol-13-acetate (RPA), a synthetic TPA derivative almost devoid of first stage activity in some strains of mice, and mezerein (Mez), a potent second stage and much weaker first stage promoter. Mez-stimulated PMNs produced up to four times less H2O2, whereas RPA-stimulated PMNs produced up to 10 times less H2O2 than TPA-activated cells when used at concentrations between 0.5 and 15 nM to activate 7.5-8.5 X 10(4) PMNs/ml. Phorbol, a non-promoter, was totally inactive in this assay. Furthermore, the tumor promoter-activated PMNs caused formation of 5-hydroxymethyl-2'-deoxyuridine (HMdU) and thymidine glycol (dTG) in DNA co-incubated with those cells. The amounts of modified thymidines formed, particularly of HMdU, correlated well with first stage tumor promoting efficacy and with the amount of H2O2 that was generated by promoter activated PMNs. In comparison with TPA, Mez- or RPA-stimulated PMNs induced formation of 25 or 70% less H2O2 and 30 or 75% less HMdU, respectively, under conditions favoring HMdU formation. Thus, formation of either H2O2 by tumor promoter-stimulated phagocytes or HMdU in DNA exposed to those activated cells may serve as a measure of potency as a first stage tumor promoter. Formation of modified bases such as HMdU in DNA might constitute the genetic change imparted by the first stage tumor promoters.

DNA↗
PubMed2006

Safety and efficacy of ultraviolet-a light-activated gene transduction for gene therapy of articular cartilage defects.

BACKGROUND: Gene therapies for articular cartilage defects are limited by the absence of an in vivo delivery system that can mediate site-specific transduction restricted to within the margins of the defect during routine arthroscopy. We have proposed the use of ultraviolet light to stimulate gene expression following infection by recombinant adeno-associated virus (rAAV). However, research has demonstrated that short-wavelength ultraviolet light (ultraviolet C), while effective, is neither safe nor practical for this purpose. We evaluated the safety and efficacy of long-wavelength ultraviolet light (ultraviolet A) from a laser to induce light-activated gene transduction in articular chondrocytes in vitro and in vivo. METHODS: The effects of ultraviolet A from a 325-nm helium-cadmium laser, delivered through a fiberoptic cable, on cytotoxicity, mutagenesis, intracellular reactive oxygen species, and light-activated gene transduction of human articular chondrocytes were evaluated in dose-response experiments of primary cultures. Cytotoxicity was determined by trypan blue exclusion. The presence of pyrimidine dimers in purified genomic DNA was determined by enzyme-linked immunosorbent assays. Intracellular reactive oxygen species levels were determined by flow cytometry at one hour and twenty-four hours. In vitro light-activated gene transduction with rAAV vectors expressing the green fluorescent protein (eGFP) or beta-galactosidase (LacZ) was determined by fluorescence microscopy and bioluminescence assays, respectively. In vivo light-activated gene transduction was quantified by stereotactic immunohistochemistry for beta-galactosidase in rabbit articular cartilage defects in the patellar groove that had been irradiated with +/-6000 J/m2 of ultraviolet A one week after direct injection of 10(7) transducing units of rAAV-eGFP. RESULTS: Ultraviolet A failed to induce significant cytotoxicity at all fluencies below 6000 J/m2. Dose-dependent cytotoxicity was observed at greater fluencies. In contrast to ultraviolet C, which induced significant (p < 0.05) pyrimidine dimer formation at all fluencies in a dose-dependent manner, ultraviolet A failed to induce DNA modifications. Conversely, ultraviolet C proved to be a poor inducer of intracellular reactive oxygen species, while ultraviolet A immediately induced high levels of intracellular reactive oxygen species, which were completely resolved twenty-four hours later. Ultraviolet A demonstrated significant light-activated gene transduction effects in vitro, which were dose-dependent (p < 0.05). In vivo, ultraviolet A mediated a tenfold increase in transduction in which 40.8% of the superficial chondrocytes adjacent to the defect stained positive for green fluorescent protein compared with 5.2% in the knees treated with no ultraviolet A (p < 0.006). CONCLUSIONS: These results provide what we believe is the first formal demonstration of an agent that can induce rAAV transduction in the complete absence of cytotoxicity and DNA modification. They also suggest that the mechanism by which long-wavelength ultraviolet light mediates site-specific gene expression is by means of the induction of intracellular reactive oxygen species. Finally, laser-derived ultraviolet A can be readily transferred through a fiberoptic cable to mediate light-activated gene transduction in vivo.

Cartilage, Articular↗
PubMed2006

Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis.

Cytosine methylation is important for transposon silencing and epigenetic regulation of endogenous genes, although the extent to which this DNA modification functions to regulate the genome is still unknown. Here we report the first comprehensive DNA methylation map of an entire genome, at 35 base pair resolution, using the flowering plant Arabidopsis thaliana as a model. We find that pericentromeric heterochromatin, repetitive sequences, and regions producing small interfering RNAs are heavily methylated. Unexpectedly, over one-third of expressed genes contain methylation within transcribed regions, whereas only approximately 5% of genes show methylation within promoter regions. Interestingly, genes methylated in transcribed regions are highly expressed and constitutively active, whereas promoter-methylated genes show a greater degree of tissue-specific expression. Whole-genome tiling-array transcriptional profiling of DNA methyltransferase null mutants identified hundreds of genes and intergenic noncoding RNAs with altered expression levels, many of which may be epigenetically controlled by DNA methylation.

Arabidopsis↗
PubMed1995

Structural modification of DNA by a DNA-binding motif SPKK: detection of changes in base-pair hydrogen bonding and base stacking by UV resonance Raman spectroscopy.

Interactions of a DNA-binding motif SPKK with polynucleotides have been investigated by uv resonance Raman spectroscopy. Analysis of the Raman spectra has shown that the tetrapeptide SPKK weakens the adenine-thymine base-pair hydrogen bonding in poly(dA-dT).poly(dA-dT) and reduces the adenine-adenine base stacking interactions in poly(dA).poly(dT), both effects being indicative of destabilization of the DNA double helical structure. On the other hand, poly(dG-dC).poly(dG-dC) and poly(dG).poly(dC) do not show any structural change in the presence of SPKK. The present observations confirm that the SPKK motif, which is frequently found in histone H1 proteins, specifically binds to A/T-rich regions of DNA and loosens the DNA double-helical structure. One of the roles of the SPKK motifs in histones may be to increase DNA flexibility so that DNA can wrap around core histones and be assembled into chromosomes more easily.

Amino Acid Sequence↗
PubMed1993

Telomeres and their possible role in chromosome stabilization.

The evidence to date generally supports the hypothesis that telomere capping makes chromosome fragments refractory to subsequent rejoining events, but this control may be somewhat relaxed after chromosome breakage. Cell survival requires that the fragments rejoin before metaphase. Unprotected ends such as those produced by DNA damage are subject to degradation, presumably by endogenous cellular exo- and endonucleases. Telomere repeat sequences may be added to broken chromosome ends to protect the ends from further degradation. That telomeric DNA does not always prevent rejoining raises interesting questions as to what constitutes capping, and how rapidly it occurs after DNA damage in relation to chromosome break rejoining. The prevention of degradation and control of rejoining may be mediated by telomere-specific binding proteins, especially the telomere terminal binding protein [Gualberto et al., 1992; Longtine et al., 1989; Price, 1990; Price and Cech, 1989]. Some of these proteins may be involved in scavenging telomeric DNA when the cell senses that chromosomal breaks have occurred. This mechanism is consistent with the observations of Murnane and Yu [1993], who found that a plasmid with telomere sequences was stably integrated in vivo into a chromosome terminal breakpoint lacking telomere repeats. It is also consistent with the high frequency of interstitial telomere sequences observed in normal cells; a history of DNA damage and repair may be recorded by these sequences (Ijdo et al., 1991]. Although chromosome break rejoining is an efficient process in eukaryotic cells, some breaks are never rejoined and can result in terminal deletions and chromatid and isochromatid deletions at metaphase. It is unclear why these breaks are not rejoined, but it may be due to one or more of the following: 1) chance: broken chromosomes are separated, do not approach sufficiently close to one another, and are consequently physically unable to rejoin; 2) a large number of added telomere repeat sequences indicating to the cell that the chromosome has an authentic telomere; 3) some other DNA modification event that protects DNA ends from degradation, e.g., folding back of DNA ends to form a hairpin, as has been implicated in VDJ recombination [Lieber, 1993].

Animals↗
PubMed2005

PARP-1-dependent 3-nitrotyrosine protein modification after DNA damage.

3-nitrotyrosine (NO2-Tyr) is thought to be a specific marker of cell injury during oxidative damage. We have evaluated the role of poly(ADP-ribose)polymerase-1 (PARP-1) in protein nitration after treatment of immortalized fibroblasts parp-1+/+ and parp-1-/- with the alkylating agent 2'-methyl-2'-nitroso-urea (MNU). Both cell lines showed increased iNOS expression following MNU treatment in parallel with a selective induction of tyrosine nitration of different proteins. PARP-1 deficient cells displayed a delayed iNOS accumulation, reduced number of nitrated proteins, and a lower global nitrotyrosine "footprint." We have identified the mitochondrial compartment as the major site of oxidative stress during DNA damage, being MnSOD one of the NO2-Tyr-modified proteins, but not in parp-1-/- cells. These results suggest that NO-derived injury can be modulated by proteins involved in the response to genotoxic damage, such as PARP-1, and may account for the limited oxidative injury in parp-1 knockout mice during carcinogenesis and inflammation.

Animals↗
PubMed2004

Development of a system for integrative and stable transformation of the zygomycete Rhizopus oryzae by Agrobacterium-mediated DNA transfer.

Two transformation systems, based on the use of CaCl(2)/PEG and Agrobacterium tumefaciens, respectively, were developed for the zygomycete Rhizopus oryzae. Irrespective of the selection marker used, a pyr4 marker derived from R. niveus or a dominant amdS(+) marker from Aspergillus nidulans, and irrespective of the configuration of the transforming DNA (linear or circular), the transformants obtained with the CaCl(2)/PEG transformation method were found to carry multiple copies of tandemly linked vector molecules, which failed to integrate into the genomic DNA. Furthermore, these transformants displayed low mitotic stability. In contrast, transformants obtained by Agrobacterium-mediated transformation were mitotically stable, even under non-selective conditions. Detailed analysis of these transformants revealed that the transforming DNA had integrated into the genome of R. oryzae at a single locus in independently obtained transformants. In addition, truncation of the transforming DNA was observed, resulting in the integration of the R. niveus pyr4 marker gene, but not the second gene located on the transferred DNA. Modification of the transforming DNA, resulting in partial resistance to restriction enzyme digestion, was observed in transformants obtained with the CaCl(2)/PEG transformation method, suggesting that a specific genome defence mechanism may exist in R. oryzae. It is likely that the unique mechanism used by A. tumefaciens to deliver its transferred DNA to its hosts facilitates bypass of the host defence mechanisms, thus allowing the DNA to integrate into the chromosomal genome.

Chromosomal Instability↗
PubMed1977

The photodynamic modification of DNA by hematoporphyrin.

Illumination (white light: 300-750 nm) of DNA in the presence of hematoporphyrin (less than or equal to 5-10 (-4) M) results in selective degradation of the guanine moiety. DNA so illuminated exhibits physical chemical properties (lowered sedimentation coefficients, lower temperatures of helix-coil transitions, increased buoyant density values) consistent with single-chain scissions (and the generation of single-stranded regions) which presumably are secondary to the photodegradation of the guanine residue. Illumination of DNA in the presence of low levels of hematoporphyrin (greater than or equal to 2.5 - 10 (-4) M) results in a biopolymer exhibiting all of the physical properties described above with the exception of a lowered sedimentation coefficient; on the contrary such DNA is aggregated. Of the four usual deoxynucleosides irradiated in the presence of hematoporphyrin, only deoxyguanosine is destroyed.

Binding Sites↗