Cellular localization of the apurinic/apyrimidinic endodeoxyribonucleases in rat liver

Purification and some properties of apurinic/apyrimidinic DNA endonucleases in rat liver

1. Three kinds of apurinic/apyrimidinic (AP) DNA endonucleases, APcI, APcII, APcIII were purified from rat liver chromatin. 2. Molecular weights of APcI, APcII and APcIII were 30,000, 42,000 and 13,000 Da, which have isoelectric points of 7.2, 6.3 and 6.2, respectively. 3. Mg2+ was essential for the activities of these 3 enzymes, and sulfhydryl compounds (beta-mercaptoethanol) had a stimulatory effect on the enzyme activities while N-ethylmaleimide and HgCl2 inhibited the enzyme activity. 4. Km values of APcI, APcII and APcIII for AP site of DNA were 0.53, 0.27 and 0.36 microM, respectively, and AMP was the most potent inhibitor to these three enzymes among nucleotides tested.

Condensation and precipitation of chromatin by multivalent cations

The condensation and the precipitation of rat liver chromatin upon addition of spermine4+, spermidine3+, hexamminecobalt(III)3+ and Mg2+ cations have been studied using solubility, fluorescence, circular dichroism, melting curves, electric dichroism and spermidine binding measurements, made on both soluble and precipitated complexes. The soluble complexes obtained with tetra- and trivalent cations were depleted from all histones and enriched in other proteins, particularly high mobility group proteins 1 and 2, which brings about an important enhancement of tryptophan fluorescence without modification of its two lifetimes 5.1 and 1.2 ns. In the precipitates the non-histone proteins are eliminated. Under precipitation by Mg2+ ions, the distribution of proteins remains practically unchanged. The electric dichroism and the melting curves indicate that the soluble complexes between polyamines and chromatin undergo important condensation and, at high ratios of cation over phosphate, are constituted by heterogeneous assemblies of non-histone proteins and DNA. On the contrary, the insoluble complexes seem to retain the main features of original chromatin. Precipitation by Mg2+ ions reveal much less drastic changes than those produced by polyamines. Precipitation by spermidine occurs when one cation is bound per eight nucleotides, which in addition to the histone positive charges brings about a complete neutralization of chromatin phosphates.

The enzymology of apurinic/apyrimidinic endonucleases

Studies on the enzymology of apurinic/apyrimidinic (AP) endonucleases from procaryotic and eucaryotic organisms are reviewed. Emphasis will be placed on the enzymes from Escherichia coli from which a considerable portion of our knowledge has been derived. Recent studies on similar enzymes from eucaryotes will be discussed as well. In addition, we will discuss the chemical and physical properties of AP sites and review studies on peptides and acridine derivatives which incise DNA at AP sites.

The rat-liver microsomal AP endonuclease. The endoplasmic reticulum is presented as a net thrown into the cytosol to capture newly synthesized karyophilic proteins

Although most of the rat-liver AP (apurinic/apyrimidinic) endonuclease is in chromatin, some activity is found in microsomes. A quantitative assay of the microsomal AP endonuclease is described. The enzyme is a peripheral membrane protein that is located on the outside surface of microsomes. All the binding sites on the microsomes appear to have the same affinity for the AP endonuclease, suggesting the presence of receptors for the enzyme. The AP endonuclease is displaced from its membrane attachment by submicromolar concentrations of the karyophilic signal of SV-40 T antigen. The AP endonuclease receptors are likely to be on the cytosolic side of the endoplasmic reticulum. It is suggested that binding of the protein to these receptors might be the first step of the transport mechanism that enables the AP endonuclease to penetrate into the nucleus. The same mechanism utilizing the same receptors might be used by other karyophilic proteins, including SV-40 T antigen.

Antibody to a human DNA repair protein allows for cloning of a Drosophila cDNA that encodes an apurinic endonuclease

The cDNA of a Drosophila DNA repair gene, AP3, was cloned by screening an embryonic lambda gt11 expression library with an antibody that was originally prepared against a purified human apurinic-apyrimidinic (AP) endonuclease. The 1.2-kilobase (kb) AP3 cDNA mapped to a region on the third chromosome where a number of mutagen-sensitive alleles were located. The cDNA clone yielded an in vitro translation product of 35,000 daltons, in agreement with the predicted size of the translation product of the only open reading frame of AP3, and identical to the molecular size of an AP endonuclease activity recovered following sodium dodecyl sulfate-polyacrylamide gel electrophoresis of Drosophila extracts. The C-terminal portion of the predicted protein contained regions of presumptive DNA-binding domains, while the DNA sequence at the amino end of AP3 showed similarity to the Escherichia coli recA gene. AP3 is expressed as an abundant 1.3-kb mRNA that is detected throughout the life cycle of Drosophila melanogaster. Another 3.5-kb mRNA also hybridized to the AP3 cDNA, but this species was restricted to the early stages of development.

Antibody to a human DNA repair protein allows for cloning of a Drosophila cDNA that encodes an apurinic endonuclease

The cDNA of a Drosophila DNA repair gene, AP3, was cloned by screening an embryonic lambda gt11 expression library with an antibody that was originally prepared against a purified human apurinic-apyrimidinic (AP) endonuclease. The 1.2-kilobase (kb) AP3 cDNA mapped to a region on the third chromosome where a number of mutagen-sensitive alleles were located. The cDNA clone yielded an in vitro translation product of 35,000 daltons, in agreement with the predicted size of the translation product of the only open reading frame of AP3, and identical to the molecular size of an AP endonuclease activity recovered following sodium dodecyl sulfate-polyacrylamide gel electrophoresis of Drosophila extracts. The C-terminal portion of the predicted protein contained regions of presumptive DNA-binding domains, while the DNA sequence at the amino end of AP3 showed similarity to the Escherichia coli recA gene. AP3 is expressed as an abundant 1.3-kb mRNA that is detected throughout the life cycle of Drosophila melanogaster. Another 3.5-kb mRNA also hybridized to the AP3 cDNA, but this species was restricted to the early stages of development.

Possible roles of beta-elimination and delta-elimination reactions in the repair of DNA containing AP (apurinic/apyrimidinic) sites in mammalian cells

Histones and polyamines nick the phosphodiester bond 3' to AP (apurinic/apyrimidinic) sites in DNA by inducing a beta-elimination reaction, which can be followed by delta-elimination. These beta- and delta-elimination reactions might be important for the repair of AP sites in chromatin DNA in either of two ways. In one pathway, after the phosphodiester bond 5' to the AP site has been hydrolysed with an AP endonuclease, the 5'-terminal base-free sugar 5'-phosphate is released by beta-elimination. The one-nucleotide gap limited by 3'-OH and 5'-phosphate ends is then closed by DNA polymerase-beta and DNA ligase. We have shown in vitro that such a repair is possible. In the other pathway, the nicking 3' to the AP site by beta-elimination occurs first. We have shown that the 3'-terminal base-free sugar so produced cannot be released by the chromatin AP endonuclease from rat liver. But it can be released by delta-elimination, leaving a gap limited by 3'-phosphate and 5'-phosphate. After conversion of the 3'-phosphate into a 3'-OH group by the chromatin 3'-phosphatase, there will be the same one-nucleotide gap, limited by 3'-OH and 5'-phosphate, as that formed by the successive actions of the AP endonuclease and the beta-elimination catalyst in the first pathway.

Action of phenobarbital given to rats together with diethylnitrosamine on the O6-ethylguanine content of liver DNA

When rats are fed diethylnitrosamine (10 mg/kg/day), no O6-ethylguanine is found in liver DNA after 2 weeks, but a considerable amount accumulates after 4 weeks. On the other hand, a 2-week feeding of diethylnitrosamine is not sufficient to induce liver cancers, whereas a 4-week treatment leads to hepatocarcinomas in 50% of the animals. Administration of phenobarbital (75 mg/kg/day) together with diethylnitrosamine during 4 weeks prevents the formation of liver cancers. It also prevents accumulation of O6-ethylguanine in liver DNA. Phenobarbital does not change the amount of O6-ethylguanine repair activity present in liver chromatin after 2 or 4 weeks of treatment with diethylnitrosamine. It is thus concluded that, by inducing the development of the endoplasmic reticulum, phenobarbital decreases the equilibrium concentration of the ultimate carcinogen derived from this indirect alkylating agent.

Further purification and characterization of the DNA 3'-phosphatase from rat-liver chromatin which is also a polynucleotide 5'-hydroxyl kinase

The DNA 3'-phosphatase activity of rat-liver chromatin has been purified. A DNA 5'-hydroxyl kinase activity comigrates at each step of purification. Both enzymes have the same molecular mass (79 kDa) and the same isoelectric point (8.6). It thus seems that the two activities are born by the same protein just as with the phage T4 enzyme which is, at the same time, a 5'-hydroxyl kinase and a 3'-phosphatase. An additional argument is that ATP, which does not influence the rate of the 3'-phosphatase reaction but which is a cosubstrate of the 5'-hydroxyl kinase, protects the 3'-phosphatase activity against thermal denaturation and trypsin digestion. The two active sites must, however, be largely independent within a common support: the thermal denaturation and trypsin inactivation rates are very different for the two activities; increasing the ionic strength activates the kinase and inhibits the phosphatase; polyvalent anions inhibit the phosphatase and have little effect on the kinase. The two active sites might belong to different domains of the protein; they could not however be separated by a partial trypsin digestion. The rates of 3'-dephosphorylation and 5'-phosphorylation by the chromatin enzyme are the same in native and denatured DNA. The 3'-phosphatase has no action on 3'-monodeoxynucleotide, but it hydrolyzes the 3'-phosphate in dinucleotides. The Km of the 3'-phosphatase is 0.548 microM. The Km (5'-OH) and Km (ATP) of the 5'-hydroxyl kinase are about 3.9 microM and 0.69 microM respectively. The chromatin enzyme is unable to hydrolyze 3'-phosphoglycolate ends in DNA.

Studies on the distribution of O6-methylguanine-DNA methyltransferase in rat

O6-Methylguanine-DNA methyltransferase, a DNA repair enzyme which transfers the methyl group of O6-methylguanine residue to a cysteinyl residue in the methyltransferase itself, was examined in rat organs by quantifying the S-methylcysteine formed in the methyl acceptor protein. Among the various organs examined, the spleen exhibited the highest enzyme specific activity followed by the thymus, liver, lung and testis. Brain had the lowest activity. The patterns of subcellular distribution of the methyltransferase in spleen and liver were different: while 75-80% of the activity was present in the nuclear fraction of the spleen, 54% of the activity in the liver was found in the nuclei and 35% in the cytosolic fraction. Forty-five and thirty-five percent of the total nuclear enzyme activity could be extracted with 1 M and 2 M NaCl solutions, respectively, indicating that the repair enzyme is not tightly bound to the nuclear matrix. When isolated nuclei were incubated with [methyl-3H]DNA substrate and subsequently fractionated into histone and non-histone protein fractions, over 90% of the radioactivity was coeluted on a Bio-Rex 70 column with the non-histone fraction and only a negligible amount of radioactivity was found to be associated with the histone fraction. The molecular mass of the [methyl-3H]methyltransferase in the non-histone fraction was determined to be 23,000, and its pI value was found to be 6.6 by two-dimensional polyacrylamide gel electrophoresis.

Deoxyribonuclease IV from rat liver chromatin and the excision of apurinic sites from depurinated DNA

Deoxyribonuclease IV, a 5'-3' exonuclease degrading double-stranded DNA from intra-strand nicks, has been purified from the chromatin of rat liver cells. The enzyme, which has an Mr of 58000, excises the apurinic (AP) sites from a depurinated DNA nicked 5' to these AP sites with the chromatin AP endonuclease. The excision is not the result of hydrolysis of the phosphodiester bond 3' to the AP sites since the excision product does not behave as deoxyribose 5-phosphate but as its 2,3-unsaturated derivative. This result suggests that, to remove the AP sites from the DNA nicked by an AP endonuclease, the chromatin deoxyribonuclease IV rather acts as a catalyst of beta-elimination.

Apurinic endonuclease activity remains constant during early Drosophila development

An endonuclease activity that acts on alkali-labile lesions in x-irradiated PM2 DNA and recognizes apurinic lesions in heat/acid treated DNA has been partially purified from Drosophila melanogaster embryos and its specific activity monitored throughout early development. The enzyme activity also showed a low level of activity on UV-irradiated DNA. The saturation kinetics observed with both x-irradiated and apurinic PM2 DNA substrates were similar. The endonuclease activity exhibited a broad pH optimum between pH 6 and 8.5 and was almost completely inhibited by 100 mM NaCl, 0.1 mM EDTA, 2 mM CaCl2 and 10 mM NEM. The reaction was not completely dependent on the presence of Mg++cation, but optimum activity was obtained at a concentration of 0.1 mM; concentrations greater than 1 mM Mg++ were inhibitory. The specific activity of the apurinic endonuclease, partially purified from several stages of embryonic and early larval development, remained the same. Unfertilized eggs exhibited a reduced level of this presumptive repair activity.

Properties of the chromatin repair activity against O6-ethylguanine lesions in DNA. Mechanism of the reaction

Chromatin proteins from rat liver contain a repair activity that removes O6-ethylguanine from ethylnitrosourea-treated DNA. This activity does not depend on divalent cations and works in the presence of EDTA, but does depend on the presence of free thiol groups. Thus, it is destroyed by N-ethylmaleimide and is protected by dithiothreitol. The repair activity on single-stranded DNA is only 20% of what it is on double-stranded DNA; its half-life at 35 degrees C is 55 min, but DNA, ethylated or not, affords some protection. The repair reaction is a transethylation from O6-ethylguanine in DNA onto two different cysteine residues contained in acceptor proteins. The reaction can be followed by monitoring the appearance of ethylated proteins or by disappearance of O6-ethylguanine from DNA.

Repair of O6-ethylguanine DNA lesions in isolated cell nuclei. Presence of the activity in the chromatin proteins

Cell nuclei prepared from rat liver were alkylated in vitro with ethylnitrosourea; the nuclear DNA was found to lose O6-ethylguanine and 7-ethylguanine during a subsequent incubation at 37 degrees C. The rate of O6-ethylguanine loss is comparable to that observed in vivo, indicating that no cytoplasmic component is needed for the repair; no free O6-ethylguanine was found in the incubation medium of the ethylated nuclei. The rate of 7-ethylguanine loss is higher than the spontaneous depurination in vitro and an amount of free 7-ethylguanine equivalent to that lost by the nuclear DNA was found in the incubation medium; these results suggest that this DNA lesion is excised by a DNA glycosylase. The proteins of the chromatin prepared from the isolated nuclei induced the disappearance of O6-ethylguanine from an added ethylated DNA. No free O6-ethylguanine was released indicating that the repair is not catalyzed by a DNA glycosylase; no oligonucleotides enriched in O6-ethylguanine were released either, indicating that the disappearance of O6-ethylguanine from DNA is not the result of the cooperative action of a specific endonuclease and an exonuclease. Activities capable of removing O6-ethylguanine from DNA were found in other cell compartments; most of it, however, is in the nucleus where the main location is chromatin. A pretreatment of the rats with daily low doses of diethylnitrosamine during 3 or 4 weeks increased 2-3-times the repair activity of the chromatin proteins.

Intracellular localization of rat-liver uracil-DNA glycosylase. Purification and properties of the chromatin enzyme

Most of the uracil-DNA glycosylase of the rat liver cell is located in chromatin; there is, however, some activity in the nuclear sap and in the cytoplasm. The chromatin uracil-DNA glycosylase has been purified; the preparation is devoid of endonuclease and exonuclease activities; the enzyme does not need divalent cations, has a broad optimum pH around 8, is strongly inhibited by increasing ionic strength and free uracil. The apparent Km is independent of the strandedness of the DNA substrate containing uracil, but V is slightly higher with the single-stranded substrate. The frequency of uracil substitution in the double-stranded DNA influences the kinetic parameters: a higher frequency increases both Km and V. The inhibitory effects of NaCl and free uracil are greater when the substrate is double-stranded rather than single-stranded. It is speculated that, acting either on the DNA or on the enzyme, both oppose the opening of the double helix necessary for the formation of the enzyme-substrate complex. The increased reaction rate with a higher frequency of uracil residues in double-stranded DNA is interpreted as a tendency for the repair enzyme to work in a processive way. It is supposed that processivity also occurs with single-stranded DNA and that it is opposed by both NaCl and free uracil, explaining a greater inhibition when the single-stranded substrate has a higher uracil content.

Alteration in the nucleosome and chromatin structures upon interaction with platinum coordination complexes

The interaction of various platinum coordination complexes with nucleosomes and chromatin has been investigated by ultraviolet absorption spectrophotometry, circular and electric linear dichroism, and thermal denaturation, at low binding ratios (r less than 0.1-0.2). The general trend of the changes in these physicochemical properties is similar to that observed for the DNA-platinum complexes, which indicates that the same binding sites are involved in the platinum interaction with DNA and with its nucleoprotein complex. The cis-bidentate ligands, cis-dichlorodiammine, diaminocyclohexane and ethylenediamine platinum(II), showed a distinct behavior, with a more important destabilization of the DNA structure in the nucleoprotein than the trans-bidentate ligand, trans-dichlorodiammine-Pt(II), and monodentate ligand, diethylenetriamine-Pt(II). The drastic decrease of the negative electric dichroism in the 260 nm absorption band of the bases, observed with the five ligands, indicates a profound alteration of the DNA arrangement in chromatin and nucleosomes, attributed to a condensation of its superhelical structure. Some differences with previous observations on DNA complexes with the same platinum compounds indicate the possible formation of protein-DNA crosslinks in chromatin and nucleosomes. These could have some importance for the biological effects.

The apurinic/apyrimidinic endodeoxyribonuclease of rat-liver chromatin

The extract from rat liver chromatin contains two apurinic/apyrimidinic (AP) endodeoxyribonucleases named 0.2 M and 0.3 M isozymes according to the phosphate concentration necessary to elute them from an hydroxyapatite column. The 0.3 M isozyme is the main and perhaps the only chromatin AP endodeoxyribonuclease in the living cell. This 0.3 M isozyme was purified by successive chromatographies on hydroxyapatite, phosphocellulose, heparin-Sepharose and alkylated-depurinated DNA-cellulose. It has a molecular weight of approximately 39000; its optimum pH is around 8.0; it needs Mg2+ or Mn2+ to be active and the optimum concentration for Mg2+ is between 5 mM and 10 mM. The 0.3 M isozyme has no action on intact DNA strands or on alkylated sites; it cuts the phosphodiester bridge which is the immediate neighbour of the AP site on its 5' side leaving 3'-hydroxyl and 5'-phosphate ends. It has no associated exonuclease activity. To hydrolyze the phosphoester bond near the AP site, the enzyme makes a close contact with three base residues in the large groove of the DNA molecule.

Unscheduled DNA synthesis and elimination of DNA damage in liver cells of gamma-irradiated senescent mice

The level of 'spontaneous' and gamma-radiation-induced DNA synthesis which is not inhibited with hydroxyurea (unscheduled synthesis) is considerably lower in hepatocytes of 18-22-month-old mice than that of 1.5-2-month-old mice. The dose-dependent increase (10-300 Gy) of unscheduled DNA synthesis (UDS) in hepatocytes of senescent mice is higher than in young animals. The elimination of damage in DNA of gamma-irradiated hepatocytes (100 Gy) was examined by using an enzyme system (M. luteus extract and DNA-polymerase I of E. coli). It was found that the rate of elimination of the DNA damage in hepatocytes of 20-month-old mice is lower than that of 2-month-old mice although the activities of DNA-polymerase beta and apurinic endonuclease remain equal in the liver of both senescent and young mice. However, the nucleoids from gamma-irradiated liver nuclei of 2-month-old mice are relaxed to a greater extent (as judged by the criterion of ethidium-binding capacity) than those of 20-month-old mice. The results suggest that there are limitations in the functioning of repair enzymes and in their access to damaged DNA sites in the chromatin of senescent mouse liver cells.

Repair of AP sites in DNA

Escherichia coli endonuclease VI is a deoxyribonuclease specific for AP (apurinic or apyrimidinic) sites; it cleaves the phosphodiester bond immediately neighbouring the AP site on its 5' side leaving 3'-hydroxyl and 5'-phosphate ends. DNA with AP sites can be repaired in vitro with endonuclease VI, DNA polymerase I and ligase; the repair mechanism is described. E. coli has other AP endonucleases; some of them are not specific for AP sites and some of them cut 3' to the AP sites. Most of the rat liver AP endonuclease activity is in chromatin. Some is however found in other cell compartments and it has been speculated that these enzymes might be precursors of the chromatin enzyme. The chromatin AP endonuclease is specific for AP sites; it cuts 5' to the AP site. DNA with AP sites can be repaired in vitro with enzymes purified from chromatin; AP endonuclease, 5'-3 exonuclease, DNA polymerase beta and ligase.

Repair of O6-ethylguanine in DNA by a chromatin fraction from rat liver: transfer of the ethyl group to an acceptor protein

Incubation of O6-[3H]ethylguanine-containing DNA with a rat liver chromatin fraction resulted in a decrease in the O6-ethylguanine content of the DNA. Analysis of the products of this reaction showed that the ethyl group had been transferred from the O6-ethylguanine to a protein acceptor. When the incubation mixture was separated on a cesium chloride gradient, the radioactivity removed from O6-ethylguanine appeared in a low-density band. This material has been isolated and subjected to trypsin digestion and high-pressure liquid chromatography analysis; it was sensitive to trypsin and the digest contained new high-pressure liquid chromatography peaks characteristic of oligopeptides. Radioactive peaks from the trypsin digestion have been digested further to the amino acid level and have been shown to contain S-[3H]ethylcysteine. Thus, we conclude that the repair activity in rat liver chromatin removes the ethyl group from O6-ethylguanine and transfers it to a cysteine moiety contained in an acceptor protein.

Localization of the phosphoester bond hydrolyzed by the major apurinic/apyrmidinic endodeoxyribonuclease from rat-liver chromatin

The major apurinic/apyrimidinic (AP) endodeoxyribonuclease from rat liver chromatin, an enzyme specific for AP sites in DNA, cleaves the phosphodiester bridge which is the immediate neighbour of the AP site on its 5' side leaving 3'-hydroxyl and 5'-phosphate ends. In contrast with Escherichia coli endonuclease VI, this chromatin enzyme is inactive on reduced AP sites.

Fanconi's anemia: anomaly of enzyme passage through the nuclear membrane? Anomalous intracellular distribution of topoisomerase activity in placental extracts in a case of Fanconi's anemia

In cells of Fanconi's anemia (FA) spontaneous breakage of chromosomes was first recognized by Schroeder et al. (1964). Sensitivity to bivalent alkylants has been found to be a constant feature, whereas low levels of several repair-related enzymes have been described in different FA cell lines. In a family with known FA, during a further pregnancy the prenatal diagnosis of the disease was made by cytogenetic analysis of amniotic cells. After birth the fresh placenta was extracted for further enzymologic analysis. An unusual distribution of DNA topoisomerase activity was noted: high in the cytoplasm and only a little activity in the nuclear sap. This contrasts with findings in normal placentae. Since amniotic cells, lymphocytes, and fibroblasts of this child exhibited both high spontaneous breakage of chromosomes and sensitivity to the bivalent alkylant, diepoxybutane, a correlation between the findings on cytogenetic and enzymologic levels is assumed. Whereas in other published cases, a true reduction of activities of enzymes involved in DNA replication and repair has been found, the present results suggest the interpretation that in our patient the genetic anomaly does not affect the level of synthesis of the enzyme itself, but the passage of the enzyme from the place of synthesis (the cytoplasm) to the substrate (inside the nucleus). A genetic anomaly of the nuclear membrane might be a possible explanation, or alternatively, a structural mutation of the enzyme at a site not affecting the catalytic activity, but affecting the membrane passage or intranuclear accumulation. Meanwhile, placentae of two other cases gave similar results, thus supporting our findings.

Purification and properties of the major apurinic/apyrimidinic endodeoxyribonuclease of rat-liver chromatin

Two nucleases active on alkylated-depurinated DNA have been extracted from rat liver chromatin with 1 M KCl. The major enzyme was purified to near homogeneity; it has a molecular weight of 12 500 (although some dimerization might occur), needs Mg2+ or Mn2+ for activity. The endonuclease activity is specific for apurinic/apyrimidinic sites in DNA; the enzyme has no associated exonuclease activity.