An altered apurinic DNA endonuclease activity in group A and group D xeroderma pigmentosum fibroblasts

Xeroderma pigmentosum patients from Germany: repair capacity of 45 XP fibroblast strains of the Mannheim XP Collection as measured by colony-forming ability and unscheduled DNA synthesis following treatment with methyl methanesulfonate and N-methyl-N-nitrosourea

A total of 45 XP fibroblast strains from the Mannheim XP Collection (representatives of XP complementation groups A, C, D, E, F or G, I, and XP variants) were investigated for colony-forming ability (term: D0) after treatment with up to ten doses of the methylating carcinogen MeSO2OMe. As controls 16 fibroblast strains from normal donors were used. Except for 4 XP strains (1 from group C and 3 from group D) which, however, were borderline cases, none of the remaining 41 XP strains was found to be more sensitive than normal controls. This held true within the limits of an experimental accuracy (experimental variability of D0 values) of +/- 7%. When weighted means were calculated for XP complementation groups and compared with that of normal donors at a significance level of 5%, no significant difference was detected. In contrast, after exposure of 6 XP group D strains to MeNOUr, a weighted mean D0 value was obtained which was significantly decreased by 27%. Unscheduled DNA synthesis (term: G0 which serves as a measure of excision repair) after exposure to MeNOUr was quantitatively the same (experimental variability: +/- 8%) both in the group of normal strains and in most of the XP complementation groups. Exceptions were group E and group F (or G) which had higher, and group I which had lower repair. Analogous G0 values measured after exposure to MeSO2OMe (experimental variability: +/- 13%), however, differed from that of the control strains: they were lower in XP complementation groups A, D, E, F (or G), and I. However, groups A, E, F (or G), and I including only 3 individual strains or less may be considered to be possibly ill-represented. Yet, group D including 11 XP strains did show reduction of the mean G0 value by 35%. From this it is concluded that there are repair defects in XP group D strains with regard to MeSO2OMe-induced adducts. These defects seem to be small.

Efficient breakage of DNA apurinic sites by the indoleamine related 9-amino-ellipticine

The aromatic amine, 9-NH2-ellipticine, is a synthetic DNA intercalating derivative of the antitumor agent ellipticine, which breaks circular DNA containing apurinic sites. This breakage is inhibited when the apurinic (AP) sites are reduced. The concentration of 9-NH2-ellipticine required to get a significant effect (0.1 microM) is the lowest known among chemicals which induce the same breakage reaction. Comparison with the action of structurally related amines shows that the amino-indole structure is specific for AP sites. The ability of ellipticine derivatives to induce breakage in DNA containing apurinic sites is related to the nucleophile substituent in position 9. Two ellipticine derivatives with known antitumor activity, BD 40 and 9-OH-ellipticine, were able to break purified DNA at apurinic sites.

Ionic inhibition of formation of RecA nucleoprotein networks blocks homologous pairing

Conditions that favor the complete coating of single-stranded DNA by RecA protein promote the association of these presynaptic filaments with naked double-stranded DNA to form large nucleoprotein networks before homologous pairing occurs. These RecA nucleoprotein networks sequester virtually all of the DNA in the reaction mixture. Conditions that are suboptimal for the formation of the RecA presynaptic filament rendered both the formation of RecA-DNA networks and the subsequent formation of joint molecules sensitive to inhibition by excess ATP or by pyrophosphate when these were added during synapsis. The rate of homologous pairing was directly related to the degree of inhibition of network formation. Various multivalent cations added during synapsis restored both the formation of networks and the pairing of homologous molecules. These observations support the view that the nucleoprotein network is a synaptic intermediate by means of which RecA protein facilitates the conjunction of DNA molecules and the subsequent processive search for homology. Inhibition by multivalent anions and restoration by multivalent cations suggests in addition, that negative charge repulsion inhibits the binding of naked duplex DNA to presynaptic filaments.

Kinetics of homologous pairing promoted by RecA protein: effects of ends and internal sites in DNA

When recA protein was preincubated with single-stranded DNA in the presence of an ATP-regenerating system prior to the addition of homologous duplex DNA, a slow presynaptic step was eliminated, and the subsequent homologous pairing was revealed as a reaction whose rate exceeds by 1 or 2 orders of magnitude the calculated rate of spontaneous renaturation in 0.15 M NaCl at Tm -25 degrees C. The pairing reaction displayed saturation kinetics with respect to both single-stranded and double-stranded DNA, indicating the existence of a rate-limiting enzyme-substrate complex. The signal observed in the assay of the pairing reaction was due to pairing at free homologous ends of the duplex DNA, as well as pairing in the middle of the duplex molecule, away from a free end. The apparent rate of pairing of circular single strands with linear duplex DNA was equal to the sum of the rates of pairing at sites located at either end of the duplex DNA or at interior sites, but the apparent rates attributable to ends were greater, and nicks also stimulated the apparent rate.

Hydroxymethyluracil DNA glycosylase in mammalian cells

An activity has been purified 350-fold from extracts of mouse plasmacytoma cells that forms 5-hydroxymethyluracil (alpha-hydroxythymine) and apyrimidinic sites with phage SPO1 DNA, which contains this base in place of thymine. This DNA glycosylase presumably functions to eliminate hydroxymethyluracil, a major thymine-derived DNA lesion produced by ionizing radiation and oxidative damage. The enzyme has no cofactor requirement and is active in EDTA. Neither intermediate formation nor hydrolysis of hydroxymethyl-deoxyuridine or hydroxymethyldeoxyuridine monophosphate was detected. The enzyme does not cleave apyrimidinic sites in DNA. It does release uracil from the uracil-containing DNA of phage PBS2, but this activity is less than 2% of the predominant uracil DNA glycosylase activity of the cell, which is separated by phosphocellulose chromatography. The major uracil DNA glycosylase does not release hydroxymethyluracil from SPO1 DNA. The hydroxymethyluracil glycosylase is also separated upon phosphocelluose chromatography from a thymine glycol DNA glycosylase activity that is accompanied by an apyrimidinic endonuclease activity.

Mechanism of the concerted action of recA protein and helix-destabilizing proteins in homologous recombination

Secondary structure in single-stranded DNA impedes the presynaptic association of recA protein and consequently blocks the formation of joint molecules as evidenced by effects of temperature, nucleotide sequence, and ionic conditions. Escherichia coli single-strand-binding protein eliminates sequence-specific "cold spots" by removing folds even from sites of strong secondary structure. Thus, destabilization of secondary structure in single-stranded DNA is critical for the action of recA protein, whereas specific interactions directly between helix-destabilizing proteins and recA protein are unimportant.

A DNA-recombinogenic activity in human cells

A DNA recombining protein has been partly purified from cell lines derived from patients suffering from the hereditary disease, Bloom's syndrome. The protein induces the formation of displacement loops in phi X174 RFI DNA molecules after the addition of single-stranded DNA fragments. A filter binding method and electron microscopy were used to determine the reaction. The recombinogenic protein is dependent on divalent cations and ATP for activity.

Repair of psoralen adducts in human DNA: differences among xeroderma pigmentosum complementation groups

Angelicin and 5-methylangelicin formed photoadducts in DNA after illumination with 360-nm radiation that were excised rapidly from normal cells; 80-90% of the initial angelicin adducts and 65% of the initial 5-methylangelicin adducts were excised within 24 h. Xeroderma pigmentosum group A cells excised about 20% of the angelicin adducts, group D cells excised 55-60%, and group E, 80%. This extent of excision resembles that reported for pyrimidine dimers in these complementation groups, except for group D. Repair of psoralen adducts may not, therefore, be identical in every respect to repair of pyrimidine dimers. Group D cells seem exceptionally able to repair angelicin adducts in comparison to their repair of pyrimidine dimers, suggesting that these cells lack a gene product that is required to a greater extent for the repair of pyrimidine dimers than for the repair of angelicin adducts.

Isolation of uvrA mutation on a multicopy plasmid: preliminary characterization of the mutant protein

A new uvrA mutation (uvrA276) has been isolated on a multicopy plasmid and shown to reside within the region of the uvrA gene defined by the KpnI to SalI endonuclease sites. The protein produced by the uvrA276 mutant gene is identical in size to the wild-type protein and binds to single-stranded DNA under the same conditions as the wild-type protein. However, extracts prepared from strains containing this mutant are deficient at incision of DNA that has been irradiated with UV light.

Stable low molecular weight DNA in xeroderma pigmentosum cells

Xeroderma pigmentosum (XP) cells from several complementation groups contained more low molecular weight DNA upon alkaline sucrose gradient centrifugation than did other human cells examined. Under conditions in which only 5% of the DNA in normal cells sedimented at 16 S or less, 20% of the DNA in XP cells from complementation group A sedimented at 16 S or less. Because cells were layered directly onto the gradients for lysing of cells and denaturing of the DNA, it appears that this low molecular weight material is due to naturally existing gaps or alkali-sensitive sites, or both, in the cellular DNA. The increase in low molecular weight DNA seen in XP complementation group A cells also is seen in complementation groups C, D, and E. When prelabeled cells were incubated for increasing times after removal of the radioactive label, the amount of low molecular weight material remained constant over a 3-hr period. The introduction of the DNA-damaging agent, bleomycin, to prelabeled XP cells produced a surprising effect. The normal response of human cells to bleomycin is an increase in low molecular weight DNA, dependent on the dose of the drug and time of treatment. In XP cells the reverse was observed. That is, the low molecular weight DNA observed in untreated XP cells disappeared upon addition of the drug. The process responsible for the unusual response of XP cells to bleomycin is unknown, but these results are compatible with an inducible repair process.

Cell lines from xeroderma pigmentosum complementation group A lack a single-stranded-DNA-binding activity

Human fibroblasts and HeLa cells contain two major DNA-binding activities for superhelical DNA, which can be separated by phosphocellulose chromatography. The DNA-binding activity which elutes first from the column coelutes with and is probably identical to a single-stranded-DNA-binding activity. The second activity has been characterized previously. It binds preferentially to super-helical DNA containing DNA damage, but does not bind to single-stranded DNA. Five cell lines derived from patients with the repair-deficiency syndrome xeroderma pigmentosum (XP) were analyzed for the presence of these binding activities. Four of the cell lines were from the A-complementation group and one was from the D-complementation group of XP. The binding activity with preference for damaged DNA was present in all cell lines. The single-stranded-DNA-binding activity was present in the XP-D cell line but was absent or reduced in all of the four XP-A cell lines tested.

Base excision repair in the thermophile Thermus sp. strain X-1

The thermophile Thermus sp. strain X-1, grown at 70 degrees C, contains uracil-DNA glycosylase and apurinic endonuclease activities, both of which are known to have roles in the repair of DNA damaged by heat. Both of these activities have temperature optima of about 70 degrees C. However, neither of these activities is present in quantities significantly greater than that found in Escherichia coli grown at 37 degrees C. Therefore, it appears that thermophilic organisms may not contain greatly elevated levels of the enzymes thought to be involved in the repair of DNA damaged by heat.

A DNA-binding protein from Ustilago maydis prefers duplex DNA without chain interruptions

Using a nitrocellulose filter binding assay, we have partially purified a protein from mitotic cells of Ustilago maydis that binds preferentially to covalently closed circular duplex DNA. DNA containing single- or double-strand breaks is bound poorly by the protein. Once formed, the DNA-protein complex is stable, resisting dissociation in high salt. However, when a DNA strand is broken, the complex appears to dissociate. The protein binds equally well to form I DNA of phi X174 or the plasmid pBR322, but has a higher affinity for a hybrid plasmid containing a cloned region of Drosophila melanogaster satellite DNA.

Studies on the inhibition of repair of ultraviolet- and methyl methanesulfonate-induced damage in the DNA of human fibroblasts by novobiocin

The antibiotic novobiocin is shown to alter the sedimentation properties of human cellular DNA in alkaline sucrose. This alteration is at least partially due to increased DNA-protein binding in the cell in the presence of novobiocin. Pyrimidine dimer analysis and repair replication studies support previous reports that novobiocin inhibits repair of UV damage in human cells but we find this block to be shortlived. It is also shown that novobiocin is ineffective at blocking "long-patch" repair induced by methyl methanesulfonate as measured both by CsCl density centrifugation and the ara-C inhibition technique. However, the accumulation of breaks in MMS-treated cellular DNA in the presence of novobiocin suggests that some "short-patch" alkylation repair may be inhibited by the antibiotic. These findings are discussed in light of the proposal that novobiocin may inhibit a DNA gyrase-like activity in human as in bacterial cells.

Apurinic endonuclease from Drosophila melanogaster: reduced enzymatic activity in excision-deficient mutants of the mei-9 and mus(2)201 Loci

An endonuclease activity, which is specific for partially depurinated PM2 DNA, has been assayed in extracts prepared from cultured cells and larval brain ganglia of Drosophila melanogaster. Activity detected in repair-proficient cells is stimulated by Mg++ and is inhibited by EDTA. Extracts prepared from established cell cultures of the excision-deficient strain mei-9a and from larval brain ganglia derived from y mei-9a, mei-9L1, sn3 mei-9D2 and sn3 mei-9D4 are partially deficient in this activity. At least one allele of a second excision-deficient strain, cn mus (2)201D1, also shows reduced AP-endonuclease activity in ganglia extracts.

5,6-Saturated thymine lesions in DNA: production by ultraviolet light or hydrogen peroxide

Thymine analogs with saturated 5-6 bonds are important types of DNA damage that are recognized by the DNA N-glycosylase activity of E. coli endonuclease III. Seeking agents which could preferentially form 5,6-hydrated thymine residues in duplex DNA both in vivo and in vitro, we exposed purified duplex DNA to 325- or 313-nm light; however, after such exposure pyrimidine dimers greatly predominated over 5,6-hydrated thymine. Hydrogen peroxide, on the other hand, formed significant numbers of endonuclease III-sensitive sites in vitro which were not apurinic/apyrimidinic lesions and thus were likely to be 5,6-hydrated thymines.

Purification and properties of an endonuclease from the mitochondrion of Saccharomyces cerevisiae

An endonuclease, which is found only in the mitochondrion of the yeast Saccharomyces cerevisiae, has been purified. The protein has a sedimentation coefficient of 6.3 S, equivalent to a molecular weight of 105,000. The enzyme is active at pH 7.6, when it degrades single-stranded DNA about 10-times faster than double-stranded DNA, but at pH 5.4 only double-stranded DNA is degraded. In both cases the enzyme acts endonucleolytically, breaking a single phosphodiester bond at a random location within the DNA substrate. Mn2+ or Mg2+ are required for activity; Ca2+ and Zn2+ are ineffective cofactors. Enzyme activity at pH 7.6 is severely inhibited by low concentrations of NaCl or KCl, while activity at pH 5.4 is unaffected by salt. Ethidium bromide inhibits both the DNase activity at pH 5.4 and the activity with single-stranded DNA at pH 7.6, but has no effect on the DNase activity with double-stranded DNA at pH 7.6.

Selective inhibition by harmane of the apurinic apyrimidinic endonuclease activity of phage T4-induced UV endonuclease

1-Methyl-9H-pyrido-[3,4-b]indole (harmane) inhibits the apurinic/apyrimidinic (AP) endonuclease activity of the UV endonuclease induced by phage T4, whereas it stimulates the pyrimidine dimer-DNA glycosylase activity of that enzyme. E. coli endonuclease IV, E. coli endonuclease VI (the AP endonuclease activity associated with E. coli exonuclease III), and E. coli uracil-DNA glycosylase were not inhibited by harmane. Human fibroblast AP endonucleases I and II also were only slightly inhibited. Therefore, harmane is neither a general inhibitor of AP endonucleases, nor a general inhibitor of Class I AP endonucleases which incise DNA on the 3'-side of AP sites. However, E. coli endonuclease III and its associated dihydroxythymine-DNA glycosylase activity were both inhibited by harmane. This observation suggests that harmane may inhibit only AP endonucleases which have associated glycosylase activities.

Evidence that the UV endonuclease activity induced by bacteriophage T4 contains both pyrimidine dimer-DNA glycosylase and apyrimidinic/apurinic endonuclease activities in the enzyme molecule

We performed experiments to determine whether the phage T4-induced UV endonuclease activity is a single protein containing both pyrimidine dimer-DNA glycosylase and apyrimidinic endonuclease activities. The UV endonuclease activity is induced by the denV gene and codes for the glycosylase activity. We obtained several kinds of evidence that the protein containing the glycosylase activity also contains the apyrimidinic endonuclease activity. After chromatography on DEAE-cellulose, the two activities copurified during phosphocellulose chromatography and Sephadex G-100 chromatography, with a constant ratio of activities across the activity peaks. On Sephadex G-100 columns the molecular weights of the two activities agreed within 2,500 or less. When an extract of cells infected with the T4 V1 mutant was purified in exactly the same way as an extract of cells infected with T4 V1+, neither glycosylase nor apyrimidinic endonuclease activity was detected in the normal elution position of the T4 UV endonuclease activity. The glycosylase and apyrimidinic endonuclease activities were induced with similar kinetics, which were characteristic of immediate early rather than delayed early enzymes. This correlated well with the presumed major role of these activities in repairing thymine dimers in parental DNA before DNA replication begins. Finally, glycosylase and apyrimidinic endonuclease activities were lost in parallel during incubation of the enzyme at 46 degree C. Our results indicated that both of these enzyme activities are contained in the same enzyme molecule and, probably, in the same polypeptide.

Heat-labile glucose-6-phosphate dehydrogenase in cultured fibroblasts from patients with De Sanctis-Cacchione Syndrome

The normal senescent fibroblasts in culture accumulate a significantly high proportion of altered enzymes, and the alterations are considered to be the manifestation of ageing in molecular terms. To detect the possible molecular alterations in patients with De Sanctis-Cacchione syndrome, the severest form of xeroderma pigmentosum, in which repair processes to UV light-damaged DNA are defective and the neurologic abnormalities are considered to reflect accelerated ageing, we studied the heat stability of glucose-6-phosphate dehydrogenase (G6PD) in crude extracts of cultured skin fibroblasts. Three patients with the syndrome were the center of our investigation. Even at early passage in culture the heat-labile portion of G6PD was increased in the cells from patients in comparison to normal controls. The life span of the cells in culture from patients was not reduced below normal age-matched controls, and no appreciable senescent appearance was observed. The increase in the heat-labile portion of G6PD from cells of DeSanctis-Cacchione syndrome patients to reflect that defective repair of DNA damage occurs, rather than being a direct result of ageing of cultured cells.

Apurinic DNA endonucleases from Drosophila melanogaster embryos

Apurinic DNA endonuclease activity from Drosophila melanogaster embryos was resolved into two separable forms by phosphocellulose chromatography, one which flowed through the column (Fraction I) and the other which was retained and eluted at approximately 200 mM potassium phosphate (Fraction II). Both fractions, purified further by glycerol gradient sedimentation, were found to introduce nicks into DNA that were specific for and equal in number to the alkali-labile sites in depurinated DNA. They had similar apparent Km values for apurinic sites (0.7 nM apurinic sites for Fraction I and 0.8 nM for Fraction II), but differed with respect to optimal pH, Mg++ requirement and sensitivity to EDTA.

Partial purification and properties of an exonuclease inhibitor induced by bacteriophage Mu-1

From an induced lysogen of bacteriophage Mu-1, we partially purified a substance of high molecular weight that blocks the action of several exonucleases on double-stranded DNA. The presence of the inhibitor in cell-free extracts is dependent on induction of a Mu prophage. The Mu-related inhibitor acts by binding to double-stranded DNA rather than by interacting with the DNase. The inhibitor protects linear duplex DNA of Mu, P22, and phi X174am3 from exonucleolytic degradation by recBC DNase and lambda exonuclease. Single-stranded DNA, however, is not protected by the inhibitor from degradation by either recBC DNase or exonuclease I. The inhibitor preparation contains a protein that binds to linear duplex DNA, but not to circular duplex DNA; ends are required for binding to occur. Single-stranded DNA is not a substrate for the binding protein. These and other results suggest that the binding protein and the inhibitor are the same activity.

Interaction of the chick oviduct progesterone receptor with deoxyribonucleic acid

The purified DNA binding component (receptor A) of the chick oviduct progesterone receptor has been analyzed for its ability to bind to the cloned ovalbumin gene and to plasmid DNA of various structural compositions. The rapid equilibrium filter adsorption assay of Riggs et al. [Riggs, A. D., Suzuki, H., & Bourgeois, S. (1970) J. Mol. Biol. 48, 67] has been used to demonstrate high affinity binding of the protein to DNA (Kdiss = 10(-10) M at 50 mM KCl, pH 7.2). Studies of association rates are consistent with equilibrium measurements (t 1/2 = 40-80 min). Association of purified receptor with DNA and the kinetics of the interaction have been verified independently by velocity sedimentation techniques. Direct binding assays were performed with the ovalbumin structural gene (cDNA), the entire natural ovalbumin gene containing seven intervening sequences, and various ovalbumin gene fragments coding for the 5' end of the nuclear precursor RNA, intron-exon junctions, and the 3'-noncoding region of the gene. No DNA-sequence specificity was identified for the binding of the receptor protein to any region of ovalbumin gene DNA. In contrast, the structural integrity of the DNA template greatly affected receptor binding. The poorest affinity was to supercoiled DNA and to blunt end, linear duplex gene fragments. The receptor bound saturably to DNA containing limited nicks but became nonsaturable as nicks were increased. Binding of the protein to double-stranded DNA increased susceptibility of the DNA to digestion by the enzyme S1, a single strand specific nuclease. On the basis of preferential receptor binding to single-stranded DNA, a possible mechanism involving DNA helix destabilization is discussed.

Synthesis by DNA polymerase I on bleomycin-treated deoxyribonucleic acid: a requirement for exonuclease III

phi X174 RFI DNA treated with bleomycin (BLM) under conditions permitting nicking does not serve as a template-primer for Escherichia coli DNA polymerase I. Purified exonuclease III from E. coli and extracts from wild-type E. coli strains are able to convert the BLM-treated DNA to suitable template-primer, but extracts from exonuclease III deficient strains are not. Brief digestion by exonuclease III is enough to create the template-primer, suggesting that the exonuclease III is converting the BLM-treated DNA by a modification of 3' termini. The exonucleolytic rather than the phosphatase activity of exonuclease III appears to be involved in the conversion. Comparative studies with micrococcal nuclease indicate that BLM-created nicks do not have a simple 3'-P structure. Bacterial alkaline phosphatase does not convert BLM-treated DNA to template-primer. The endonuclease VI activity associated with exonuclease III does not incise DNA treated with BLM under conditions not allowing nicking, in contrast to DNA with apurinic sites made by acid treatment, arguing that conversion does not require the endonuclease VI action on uncleaved sites.

Repair of Bleomycin-damaged DNA by human fibroblasts

The ability of human fibroblasts to repair bleomycin-damaged DNA was examined in vivo. Repair of the specific lesions caused by bleomycin (BLM) was investigated in normal cell strains as well as those isolated from patients with apparent DNA repair defects. The diseases ataxia telangiectasia (AT), Bloom syndrome (BS), Cockayne syndrome (CS), Fanconi anemia (FA), and xeroderma pigmentosum (XP) were those selected for study. The method used for studying the repair of DNA after BLM exposure was alkaline sucrose gradient centrifugation. After exposure to BLM, a fall in the molecular weight of DNA was observed, and after drug removal the DNA reformed rapidly to high molecular weight. The fall in molecular weight upon exposure to BLM was observed in all cells examined with the exception of some XP strains. Prelabeled cells from some XP complementation groups were found to have a higher percentage of low molecular weight DNA on alkaline gradients than did normal cells. This prelabeled low molecular weight DNA disappeared upon exposure to BLM.