Damaged DNA-binding proteins: recognition of N-acetoxy-acetylaminofluorene-induced DNA adducts.

Proteins which bind to the DNA damaged by genotoxic agents can be detected in all living organisms. Damage-recognition proteins are thought to be generally involved in DNA repair mechanisms. On the other hand, the relevance to DNA repair of some other proteins which show elevated affinity to damaged DNA (e.g. HMG-box containing proteins or histone H1) has not been established. Using the electrophoretic mobility-shift assay we have investigated damage-recognition proteins in nuclei from rat hepatocytes. We detected two different protein complexes which preferentially bound the DNA damaged by N-acetoxy-acetylaminofluorene. One of them also recognized the DNA damaged by benzo(a)pyrene diol epoxide (yet with much lower efficiency). The proteins which bind to damaged DNA are permanently present in rat cells and their level does not change after treatment of animals with the carcinogens. Differences in the affinity of the detected damage-recognition proteins to DNA lesion evoked by either carcinogen did not correlate with more efficient removal from hepatic DNA of 2-acetylaminofluorene-induced adducts than benzo(a)pyrene-induced ones.     

DNA ligase activity in carcinogen-treated human fibroblasts

In an enzymological approach to study DNA repair mechanisms induced by carcinogen-treatment of mammalian cells, we have investigated how DNA ligase activity is affected by the treatment with several compounds producing different DNA lesions. Stationary cultures of human fibroblasts were exposed to various doses of carcinogens (UV-light at 254 nm, N-acetoxy-acetyl-aminofluorene, ethyl-methane sulfonate, N-methylnitro-nitrosoguanidine, mitomycin C and 4-nitroquinoline-N-oxide) at different time-intervals before preparing crude cellular extracts and assaying for ligase activity. Results have shown that: 1. UV-irradiation, AAAF, 4NQO or MMC treatment of cells induces a two-fold increase in the ligase activity compared to control cells within 48 hours following the treatment. 2. A partial purification of the enzyme from these cellular crude extracts by sedimentation through sucrose gradients has shown: a. DNA ligase activity from control cells presents a profile composed of two distinct peaks sedimenting respectively at about 4S and 7S; b. the carcinogen treatment of either repair-proficient human fibroblasts or repair-deficient xeroderma pigmentosum cells (complementation group A) seems to induce a specific increase of the 4S-form of DNA ligase.     

Infectivity and reconstitution of TMV RNA modified with N-acetoxy-2-acetylaminofluorene or benzol [a] pyrene 7,8-dihydrodiol 9,10 oxide

TMV RNA was modified by two bulky carcinogens, N-acetoxy-2-acetylamino-fluorene (AAAF) and (+/-)-7beta, 8alpha- dihydroxy-9alpha, 10alpha-epoxy-7,8,9,10-tetrahydrobenzo[alpha]pyrene (BPDE), and the effects of such substituents on biological and physical properties was studied. For both types of modification, the loss of infectivity was directly proportional to the number of chemical modifications indicating that all modifications are lethal. Neither AAAF nor BPDE produced measurable mutations. Reconstitution of modified RNA with TMV protein was partially inhibited, but such inhibition occurred to similar extents with either carcinogen and a varying levels of modification. The data suggest that both types of substitution of TMV RNA generally permit the TMV coat protein to aggregate normally around the RNA, but that AAAF and BPDE may induce some conformational change in the initiation region that inhibits the initiation step.     

Detection of damage-recognition proteins from human lymphocytes

Proteins recognizing and binding to damaged DNA (DDB-proteins) were analyzed in human lymphocytes obtained from healthy donors. Using an electrophoretic mobility shift assay several complexes between nuclear extract proteins and damaged DNA were detected: a complex specific for DNA damaged by N-acetoxy-N-acetylaminofluorene, another complex specific for UV-irradiated DNA, and two complexes specific for DNA damaged by cis-dichlorodiammine platinum. All the detected complexes differed in electrophoretic mobility and possibly contained different proteins. Complexes specific for free DNA ends were also detected in protein extracts from lymphocytes.     

Prior exposure to restraint stress enhances 7,12-dimethylbenz(a)anthracene (DMBA) induced DNA damage in rats

Over the years, several lines of evidence have emerged supporting the role of stress in the development and progression of cancer. Stress can cause an increase in the production of reactive oxygen species (ROS) and decrease in the in vivo antioxidant defense systems. A ROS-induced DNA damage in peripheral lymphocytes, liver and skin cells may be revealed by Comet assay. To test whether DNA is damaged by stress/DMBA/stress and DMBA, rats were exposed to multiple doses of DMBA in the presence and absence of restraint stress, and DNA damage was evaluated. Insignificant differences were detected in all the three cells tested (peripheral lymphocytes, liver and skin cells) between control and stress treatment in terms of frequencies of damaged DNA. The extent of DNA migration was enhanced in DMBA treated rats in a dose dependent manner. Pre-stress DMBA treatment showed still higher frequencies of damage in comparison with control, stress alone or DMBA alone groups. Thus, prior exposure to stress clearly enhanced the DMBA induced DNA damage, especially so in the skin cells (target organ of the carcinogen application) than liver and peripheral lymphocytes as observed on the basis of the extent of DNA migration (tail DNA) during single cell gel electrophoresis.     

Structural evidence on DNA carcinogen interactions: N-acetoxy-N-2acetylaminofluorene binding to DNA

Linear dichroism (LD) gives useful information on the interaction between DNA and the directly acting carcinogen N-acetoxy-N-2-acetylaminofluorene (AAAF). In 50% methanol solvent with low ionic strength only a weak complex (van der Waals) appears. However, above 40° C strand separation takes place and a covalent aminofluorene complex forms. After renaturation a characteristic positive LD.band is observed at 306 nm. The average angular orientation of the longaxis of the fluorene moiety (47° to the local helix axis) is inconsistent with intercalation- It can be explained for instance by a free rotation around a C(DNA)-N (aminofluorene) bond or by a major groove site. The occupation density was 1–2 aminofluorene residues per 100 bases. With native DNA, AAAF slowly forms a covalent complex which has a negative LD at 307 nm. The orientation (70–90° ) is consistent with steric direction by the strand.     

Cellular concentrations of DDB2 regulate dynamic binding of DDB1 at UV-induced DNA damage

Nucleotide excision repair (NER) is the principal pathway for counteracting cytotoxic and mutagenic effects of UV irradiation. To provide insight into the in vivo regulation of the DNA damage recognition step of global genome NER (GG-NER), we constructed cell lines expressing fluorescently tagged damaged DNA binding protein 1 (DDB1). DDB1 is a core subunit of a number of cullin 4-RING ubiquitin ligase complexes. UV-activated DDB1-DDB2-CUL4A-ROC1 ubiquitin ligase participates in the initiation of GG-NER and triggers the UV-dependent degradation of its subunit DDB2. We found that DDB1 rapidly accumulates on DNA damage sites. However, its binding to damaged DNA is not static, since DDB1 constantly dissociates from and binds to DNA lesions. DDB2, but not CUL4A, was indispensable for binding of DDB1 to DNA damage sites. The residence time of DDB1 on the damage site is independent of the main damage-recognizing protein of GG-NER, XPC, as well as of UV-induced proteolysis of DDB2. The amount of DDB1 that is temporally immobilized on damaged DNA critically depends on DDB2 levels in the cell. We propose a model in which UV-dependent degradation of DDB2 is important for the release of DDB1 from continuous association to unrepaired DNA and makes DDB1 available for its other DNA damage response functions.     

Repair of O6-methyl-guanine residues in DNA takes place by a similar mechanism in extracts from hela cells,human liver,and rat liver

Extracts from HeLa S₃ cells, human liver, and rat liver were found to contain an activity that transfers the methyl group from O⁶-methyl-guanine residues in DNA to a cysteine residue of an acceptor protein. The molecular weights of the acceptor proteins in HeLA cells and human liver are 24,000 ± 1,000 and 23,000 ± 1,000. respectively. Assuming that each acceptor molecule is used only once, the average number of acceptor molecules in HeLa cells was calculated to be about 50,000. The extracts also contained 3-methyl-adenine-DNA glycosylase activity and 7-methyl-guanine-DNA glycosylase activity, although the latter activity was not detected in extracts from human liver in our assay system. Thus, the three major alkylation products resulting from the effect of methylating agents, such as N-methyl-N-nitroso urea, can all be repaired in animal cells. Pretreatment of HeLa cells with N-methyl-N′-nitro-N-nitrosoguanidinc (0.1 μg/ml) strongly reduced the capacity of HeLa cell extracts to repair O⁶-methyl-guanine residues, while the activity of three DNA-N-glycosylases was essentially unaltered. This inactivation was not caused by a direct methylation of the enzyme by the carcinogen. The results demonstrate that the mechanism of repair of O⁶-methyl-guaninc residues, in DNA is strikingly similar in E coli and animal cells, including humans.     

Binding of [-14C]aflatoxin B1 to cellular macromolecules in the rat and hamster.

The uptake and binding of ring-labelled [-14C]aflatoxin B1 (AFB1) by rat and hamster liver and kidney has been studied, the former species being extremely sensitive to the carcinogenic action of AFB, whereas the latter is resistant. In contrast to an earlier report (Lijinsky et al, Cancer Res., 30 (1970) 2280-2283, binding of the carcinogen to nucleic acids was far greater than that to protein. Rat liver DNA bound ten times and rRNA twenty times more carcinogen than protein. There were also differences in the amount of carcinogen bound to rat liver nucleic acids compared to those of the hamster, the latter species binding lower amounts of the carcinogen. Rat liver DNA bound four times and rRNA ten times as much AFB1 6 h after carcinogen administration whereas liver protein bound AFB1 was similar for the two species. Not only was there a difference in the amount of AFB1 bound but whereas in the rat, liver nucleic acid bound carcinogen decayed with time, no such fall was seen in the hamster, this remaining at a low level throughout the 48-h time period studied. In contrast, reaction of the carcinogen with kidney macromolecules was similar for the two species. The much higher binding of AFB1 to nucleic acids than to protein might account for the potent carcinogenicity of this compound in the rat, particularly since liver protein binding does not differ between a susceptible and a resistant species. A further important factor in determining carcinogenic sensitivity may be the removal of nucleic acid bound radioactivity with time, a possible repair process.     

Hepatocyte growth factor in ascites from patients with cirrhosis.

Hepatocyte growth factor (HGF) stimulating DNA synthesis of adult rat hepatocytes in primary culture was found in the ascites and plasma from patients with liver cirrhosis, but not in those from patients without cirrhosis. HGF was purified about 400-fold in 10% yield from cirrhotic ascites by ultrafiltration, cation-exchange chromatography on a S-Sepharose column, and affinity chromatography on a heparin-Sepharose CL-6B column. The partially purified factor was a heat- and acid-labile cationic protein with a molecular weight of 100,000-150,000. Its effect was half-maximal at 3.8 micrograms/ml, and was additive with those of insulin and epidermal growth factor. HGF in ascites from patients with cirrhosis had the same properties as HGF purified and characterized from rat platelets. These findings suggest that HGF is secreted into the ascites from the plasma or liver of patients with cirrhosis and may increase in the plasma with the development of hepatic impairment and act in repair of the damaged liver of patients with chronic liver disease.     

Recognition of cisplatin-DNA interstrand cross-links by replication protein A

Replication protein A (RPA) is a heterotrimeric protein that is required for DNA replication and most DNA repair pathways. RPA has previously been shown to play a role in recognizing and binding damaged DNA during nucleotide excision repair (NER). RPA has also been suggested to play a role in psoralen DNA interstrand cross-link (ICL) repair, but a clear biochemical activity has yet to be identified in the ICL DNA repair pathways. Using HeLa cell extracts and DNA affinity chromatography, we demonstrate that RPA is preferentially retained on a cisplatin interstrand cross-link (ICL) DNA column compared with undamaged DNA. The retention of RPA on cisplatin intrastrand and ICL containing DNA affinity columns is comparable. In vitro electrophoretic mobility shift assays (EMSAs) using synthetic DNA substrates and purified RPA demonstrate higher affinity for cisplatin ICL DNA binding compared with undamaged DNA. The enhanced binding of RPA to the cisplatin ICL is dependent on the DNA length. As the DNA flanking the cisplatin ICL is increased from 7 to 21 bases, preferential RPA binding is observed. Fluorescence anisotropy reveals greater than 200-fold higher affinity to a cisplatin ICL containing 42-mer DNA compared with an undamaged DNA and a 3-4-fold higher affinity when compared with a cisplatin intrastrand damaged DNA. As the DNA length and stringency of the binding reaction increase, greater preferential binding of RPA to cisplatin ICL DNA is observed. These data are consistent with a role for RPA in the initial recognition and initiation of cisplatin ICL DNA repair.     

Persistent and heritable structural damage induced in heterochromatic DNA from rat liver by N-nitrosodimethylamine

Analysis, by benzoylated DEAE-cellulose chromatography, has been made of structural change in eu- and heterochromatic DNA from rat liver following administration of the carcinogen N-nitrosodimethylamine (10 mg/kg body weight). Either hepatic DNA was prelabeled with [3H]thymidine administered 2-3 weeks before injection of the carcinogen or the labeled precursor was given during regenerative hyperplasia in rats treated earlier with N-nitrosodimethylamine. Following phenol extraction of either whole liver homogenate or nuclease-fractionated eu- and heterochromatin, carcinogen-modified DNA was examined by stepwise or caffeine gradient elution from benzoylated DEAE-cellulose. In whole DNA, nitrosamine-induced single-stranded character was maximal 4-24 h after treatment, declining rapidly thereafter; gradient elution of these DNA preparations also provided short-term evidence of structural change. Following incubation of purified nuclei with micrococcal nuclease, 10-12% of labeled DNA was solubilized (eu-chromatin) by 1.0 unit of micrococcal nuclease (5 mg of DNA)-1 mL-1 after 9 min. In prelabeled animals, administration of N-nitrosodimethylamine caused a marked fall in the specific radioactivity of solubilized DNA, while that of sedimenting DNA was not affected. Caffeine gradient chromatography suggested short-term nitrosamine-induced structural change in euchromatic DNA, while increased binding of heterochromatic DNA was evident for up to 3 months after carcinogen treatment. Preparations of newly synthesized heterochromatic DNA from animals subjected to hepatectomy up to 2 months after carcinogen treatment provided evidence of heritable structural damage. Carcinogen-induced binding of heterochromatic DNA to benzoylated DEAE-cellulose was indicative of specific structural lesions whose affinity equalled that of single-stranded DNA up to 1.0 kilobase in length.(ABSTRACT TRUNCATED AT 250 WORDS)     

DNA-binding studies with 6BT and 5I: implications for DNA-binding/carcinogenicity and DNA-binding/mutagenicity correlations

The divergent activities of a reported carcinogen/noncarcinogen pair of monoazo dyes related to the hepatocarcinogen Butter Yellow (DAB) are currently under investigation in our laboratories. As part of these studies we have determined (a) target organ distribution after oral dosing to rats and (b) covalent binding of 14C-labelled compound to DNA. In DNA-binding studies, 3 rat liver-metabolising systems were employed: in vivo (whole liver), isolated intact hepatocytes, and liver subcellular fractions. Distribution studies revealed that comparable levels of both compounds were detected in the liver at similar times after dosing, and these in vivo tissue concentrations were used for in vitro DNA-binding studies. At this 'in vivo equivalent dose', the carcinogen was consistently bound to DNA more effectively, and the difference (ratio of DNA binding) between the 2 compounds was far greater in vivo. In subsequent studies, covalent DNA binding to bacterial (Salmonella) DNA was assessed at the in vivo equivalent dose. In contrast to the afore-mentioned findings in mammalian systems, the carcinogen was bound less effectively to DNA, and gave fewer revertant counts/plate when the 2 compounds were bound to an equivalent extent. These data are discussed in view of their implications for DNA-binding/carcinogenicity correlations, and with respect to the relationship between DNA binding and mutagenicity in the Salmonella assay.     

Calpain inhibition by peptide epoxides.

The protein activator of phosphorylated branched-chain 2-oxo acid dehydrogenase complex was purified greater than 1000-fold from extracts of rat liver mitochondria; the specific activity was greater than 1000 units/mg of protein (1 unit gives half-maximum re-activation of 10 munits of phosphorylated complex). Sodium dodecyl sulphate/polyacrylamide-gel electrophoresis gave two bands (Mr 47700 and 35300) indistinguishable from the alpha- and beta-subunits of the branched-chain dehydrogenase component of the complex. On gel filtration (Sephacryl S-300), apparent Mr was 190000. This and other evidence suggests that activator protein is free branched-chain dehydrogenase; this conclusion is provisional until identical amino acid composition of the subunits has been demonstrated. Activator protein (i.e. free branched-chain dehydrogenase) was inhibited (up to 30%) by NaF, whereas branched-chain complex was not inhibited. There was no convincing evidence for interconvertible active and inactive forms of activator protein in rat liver mitochondria. Activator protein was detected in mitochondria from liver (ox, rabbit and rat) and kidney (ox and rat), but not in rat heart or skeletal-muscle mitochondria. In rat liver mitochondrial extracts, branched-chain complex sedimented with the mitochondrial membranes, whereas activator protein remained in the supernatant. Activator protein re-activated phosphorylated (inactive) particulate complex from rat liver mitochondria, but it did not activate dephosphorylated complex. Liver and kidney, but not muscle, mitochondria apparently contain surplus free branched-chain dehydrogenase, which is bound by the complex with lower affinity than is the branched-chain dehydrogenase intrinsic to the complex. It is suggested that this functions as a buffering mechanism to maintain branched-chain complex activity in liver and kidney mitochondria.     

The TGGCA-binding protein: a eukaryotic nuclear protein recognizing a symmetrical sequence on double-stranded linear DNA.

Low salt extracts of chicken oviduct nuclei contain a DNA binding protein with high affinity for specific DNA sequences in the flanking regions of the chicken lysozyme gene. Two of the three binding sites found within a total of 11 kb upstream from the promoter are located only 92 bp apart from each other. Upon comparison of the DNA binding sites, the symmetrical consensus sequence 5'- TGGCANNNTGCCA -3' can be deduced as the protein recognition site. This sequence is the central part of 23 to 25 base pairs protected by the DNA binding protein from DNAase I digestion. A homologous binding activity can be detected in nuclei from several chicken tissues and from mouse liver.     

The giant (gt) mutants of Drosophila melanogaster alter DNA metabolism

Summary Abnormalities in DNA metabolism have been found in third-instar females of Drosophila melanogaster that are heteroallelic or homoallelic for X-chromosomal giant (gt) mutations. Analysis of DNA metabolism in larval brain ganglia was carried out using alkaline sucrose gradient centrifugation, incorporation assays and a neutral filter elution assay. These analyses show that gt stocks synthesize DNA of a reduced molecular weight, have an unusually high frequency of spontaneous single and doublestrand breaks, and exhibit a reduction in the normal inhibition of DNA synthesis following treatment with UV and the carcinogen AAAF. These phenomena are not associated with a defect in the repair of X-ray induced DNA breaks nor are they accompanied by any alterations in chromosome stability. Analysis of homozygous 1(2)gl larvae also reveal that these phenomena are specific to the gt locus and are thus not attributable solely to an extended developmental program. These findings strengthen the suggestion that the genetic instability associated with gt is related to perturbations in chromosome metabolism (Green 1982).Abbreviations used UV ultraviolet radiation-principal wavelength 313 nm - AAAF N-acetoxy-2-acetylaminofluorene     

Damaged DNA-binding protein DDB stimulates the excision of cyclobutane pyrimidine dimers in vitro in concert with XPA and replication protein A

Human cells contain a protein that binds to UV-irradiated DNA with high affinity. This protein, damaged DNA-binding protein (DDB), is a heterodimer of two polypeptides, p127 and p48. Recent in vivo studies suggested that DDB is involved in global genome repair of cyclobutane pyrimidine dimers (CPDs), but the mechanism remains unclear. Here, we show that in vitro DDB directly stimulates the excision of CPDs but not (6-4)photoproducts. The excision activity of cell-free extracts from Chinese hamster AA8 cell line that lacks DDB activity was increased 3-4-fold by recombinant DDB heterodimer but not p127 subunit alone. Moreover, the addition of XPA or XPA + replication protein A (RPA), which themselves enhanced excision, also enhanced the excision in the presence of DDB. DDB was found to elevate the binding of XPA to damaged DNA and to make a complex with damaged DNA and XPA or XPA + RPA as judged by both electrophoretic mobility shift assays and DNase I protection assays. These results suggest that DDB assists in the recognition of CPDs by core NER factors, possibly through the efficient recruitment of XPA or XPA.RPA, and thus stimulates the excision reaction of CPDs.     

Replication of hepatic DNA in rats treated with dimethylnitrosamine.

Replication of DNA containing unrepaired lesions such as depurinated sites, single-strand breaks or methylated bases such as O-6 and N-7 methylguanine was studied in the rat liver. Rat liver DNA was damaged by administering 10 mug dimethylnitrosamine (DMN)/g body wt i.p. 4 h prior to partial hepatectomy. The analysis of DNA on alkaline sucrose gradient revealed considerable damage to the parental strand at the time of and 48 h subsequent to partial hepatectomy. During this time interval, the synthesis of new strands was studied using labeled thymidine. In the control liver, radioactivity in DNA appeared as small fragments at 15 and 30 min following the administration of labeled thymidine which became bigger within 4 h. In the carcinogen-treated livers, the newly made DNA remained as small fragments for longer periods of time. Sometime between 4 and 24 h these became bigger in size than the parental damaged template DNA. Thus, with a delay, the newly made strands became eventually bigger, in spite of the fact that the parental template DNA strand was damaged. Such replication of DNA with unrepaired lesions (miscoding and/or non-coding) offers a mechanism by which the original damage to DNA caused by the carcinogen can be permanently imprinted on the newly made cell, a phenomenon that could account for the initiation of carcinogenesis under certain circumstances.