Enzymatic repair of DNA

A critical spotlight on the paradigms of FFPE-DNA sequencing

In the late 19th century, formalin fixation with paraffin-embedding (FFPE) of tissues was developed as a fixation and conservation method and is still used to this day in routine clinical and pathological practice. The implementation of state-of-the-art nucleic acid sequencing technologies has sparked much interest for using historical FFPE samples stored in biobanks as they hold promise in extracting new information from these valuable samples. However, formalin fixation chemically modifies DNA, which potentially leads to incorrect sequences or misinterpretations in downstream processing and data analysis. Many publications have concentrated on one type of DNA damage, but few have addressed the complete spectrum of FFPE-DNA damage. Here, we review mitigation strategies in (I) pre-analytical sample quality control, (II) DNA repair treatments, (III) analytical sample preparation and (IV) bioinformatic analysis of FFPE-DNA. We then provide recommendations that are tested and illustrated with DNA from 13-year-old liver specimens, one FFPE preserved and one fresh frozen, applying target-enriched sequencing. Thus, we show how DNA damage can be compensated, even when using low quantities (50 ng) of fragmented FFPE-DNA (DNA integrity number 2.0) that cannot be amplified well (Q129 bp/Q41 bp = 5%). Finally, we provide a checklist called 'ERROR-FFPE-DNA' that summarises recommendations for the minimal information in publications required for assessing fitness-for-purpose and inter-study comparison when using FFPE samples.

Homologous recombination rescues ssDNA gaps generated by nucleotide excision repair and reduced translesion DNA synthesis in yeast G2 cells

Repair of DNA bulky lesions often involves multiple repair pathways such as nucleotide-excision repair, translesion DNA synthesis (TLS), and homologous recombination (HR). Although there is considerable information about individual pathways, little is known about the complex interactions or extent to which damage in single strands, such as the damage generated by UV, can result in double-strand breaks (DSBs) and/or generate HR. We investigated the consequences of UV-induced lesions in nonreplicating G2 cells of budding yeast. In contrast to WT cells, there was a dramatic increase in ssDNA gaps for cells deficient in the TLS polymerases η (Rad30) and ζ (Rev3). Surprisingly, repair in TLS-deficient G2 cells required HR repair genes RAD51 and RAD52, directly revealing a redundancy of TLS and HR functions in repair of ssDNAs. Using a physical assay that detects recombination between circular sister chromatids within a few hours after UV, we show an approximate three-fold increase in recombinants in the TLS mutants over that in WT cells. The recombination, which required RAD51 and RAD52, does not appear to be caused by DSBs, because a dose of ionizing radiation producing 20 times more DSBs was much less efficient than UV in producing recombinants. Thus, in addition to revealing TLS and HR functional redundancy, we establish that UV-induced recombination in TLS mutants is not attributable to DSBs. These findings suggest that ssDNA that might originate during the repair of closely opposed lesions or of ssDNA-containing lesions or from uncoupled replication may drive recombination directly in various species, including humans.

Complexing properties of nucleic-acid constituents adenine and guanine complexes

Cobalt, nickel and copper complexes of adenine and guanine, as nucleic-acid constituents, were prepared. The adenine and guanine complexes are of tetrahedral and octahedral geometries, respectively. All are of high spin nature. The nickel complexes are of 2:1 metal:ligand ratio with Ni...Ni direct interaction in the guanine complex. The coordination bonds of adenine metal complexes are calculated and follow the order: Cu(II)-adenine < Ni(II)-adenine < Co(I)-adenine. The Cu(II)-adenine complex is the stronger following the softness of the copper, while that of guanine is less covalent. The copper complexes are with stronger axial field. The differential thermal analysis (DTA) and TGA of the complexes pointed to their stability. The mechanism of the thermal decomposition is detected. The thermodynamic parameters of the dissociation steps are evaluated. The complexes are of semi-conducting behaviour for their technical applications. Empirical equations are deduced between the electrical conducting and the energy of activation of the complexes.

New applications of bacterial systems to problems in toxicology

Bacterial systems have long been of use in toxicology. In addition to providing general models of enzymes and paradigms for biochemistry and molecular biology, they have been adapted to practical genotoxicity assays. More recently, bacteria also have been used in the production of mammalian enzymes of relevance to toxicology. Escherichia coli has been used to express cytochrome P450, NADPH-cytochrome P450 reductase, flavin-containing monooxygenase, glutathione S-transferase, quinone reductase, sulfotransferase, N-acetyltransferase, UDP-glucuronosyl transferase, and epoxide hydrolase enzymes from humans and experimental animals. The expressed enzymes have been utilized in a variety of settings, including coupling with bacterial genotoxicity assays. Another approach has involved expression of mammalian enzymes directly in bacteria for use in genotoxicity systems. Particularly with Salmonella typhimurium. Applications include both the reversion mutagenesis assay and a system using a chimera with an SOS-response indicator and a reporter.

Rat DNA polymerase beta gene can join in excision repair of Escherichia coli

Though DNA polymerase I (poll) of Escherichia (E.) coli is understood to play a role in repair synthesis of excision repair, it is still obscure whether DNA polymerase beta (pol beta) plays a similar role in eukaryotic cells. To estimate the role of pol beta in excision repair processes, we inserted the rat pol beta gene into several mutant E. coli defective in a diverse set of enzymatic activities of poll. UV resistance was seen only when the 5'----3' exonuclease (exo) activity of poll molecules remained. Therefore it is suggested that 5'----3' exo activity as well as pol beta activity are essential for repair synthesis of excision repair in eukaryotic cells.

The development of ideas about the effect of DNA repair on the induction of gene mutations and chromosomal aberrations by radiation and by chemicals

An historical overview is given of the development of ideas about chromosomal and DNA repair as they relate to the induction of mutations, chromosomal aberrations, and sister-chromatid exchanges by radiations and chemicals. The genetic and molecular bases of the various repair pathways are reviewed whenever possible. Work on both prokaryotes and eukaryotes is included. Mention is made, when deemed appropriate, of major developments in other areas that served as essential background for the repair work, but no attempt is made to cover these background developments in any detail. Near the end, a brief review is given of factors affecting polymerase fidelity. The history is subdivided into approximately 10-year intervals. For the most part, references are to reviews and symposia in which the ideas of the time were brought together. The implications of these findings for some practical problems in genetic toxicology and for our understanding of the maintenance of the genome are discussed at the end.

Pyrimidine dimer dependent cleavage of single-stranded DNA by T4 UV endonuclease

T4 UV endonuclease cleaves double- and single-stranded DNA with equal specificity for photo-pyrimidine dimers. Thus, the enzyme can be used for mapping and quantifying pyrimidine dimers in single-stranded DNA as well as in double-stranded DNA. Mapping of pyrimidine dimers shows that rates of UV-dimerization are not only affected by 5', 3' adjacent bases, but also by position within pyrimidine tracts. Di-pyrimidines at 3' ends of tracts are more photoreactive than those at 5' ends.

Adaptation-like response to the chemical induction of sister chromatid exchanges in human lymphocytes

Experiments have been performed to determine whether human lymphocytes in primary cultures can show an "adaptive" response to the induction of cellular lesions (manifested as a production of sister chromatid exchanges, SCEs) as previously found in bacteria and established human and mammalian cell lines. Human lymphocytes were pretreated with various subtoxic concentrations (5-50 ng/ml) of N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) once every 6h for 72 h, and subsequently challenged by a high dose (4 micrograms/ml) of MNNG. The lymphocytes in MNNG-challenged cultures had the lowest frequency of SCEs when pretreated with 10 ng/ml MNNG. Further cross-resistance study revealed that repeated pretreatments of lymphocytes with 10 ng/ml MNNG for 72 h can render the cells resistant to the induction of SCEs by the following challenge with a high dose of MNNG, but not of mitomycin C or ethyl nitrosourea. The data also suggest variations in the degree of the adaptation-like response among individuals.

Single-strand breakage of DNA in UV-irradiated uvrA, uvrB, and uvrC mutants of Escherichia coli

We transduced the uvrA6, uvrB5, uvrC34, and uvrC56 markers from the original mutagenized strains into an HF4714 background. Although in the original mutagenized strains uvrA6 cells are more UV sensitive than uvrB5 and uvrC34 cells, in the new background no significant difference in UV sensitivity is observed among uvrA6, uvrB5, and uvrC34 cells. No DNA single-strand breaks are detected in UV-irradiated uvrA6 or uvrB5 cells, whereas in contrast a significant number of single-strand breaks are detected in both UV-irradiated uvrC34 and uvrC56 cells. The number of single-strand breaks in these cells reaches a plateau at 20-J/m2 irradiation. Since these single-strand breaks can be detected by both alkaline sucrose and neutral formamide-sucrose gradient sedimentation, we concluded that the single-strand breaks observed in UV-irradiated uvrC cells are due to phosphodiester bond interruptions in DNA and are not due to apurinic/apyrimidinic sites.

Inhibition of DNA repair by trifluoperazine

We examined the possible role of calmodulin in the excision repair of ultraviolet light-induced pyrimidine dimers in damaged DNA by means of specialized assay systems. These assays included bromodeoxyuridine photolysis, dimer chromatography and cytosine arabinoside incorporation in conjunction with hydroxyurea. The calmodulin antagonist, trifluoperazine, and the calcium-chelating agent, EGTA, were employed to ascertain what affect calmodulin played in the repair process. Normal human fibroblast cells were used in all studies described in this report. After exposure to 10 J/m2 of 254 nm light, we observed a decrease of about 30% in the number of single-strand breaks produced in the presence of 25 microM trifluoperazine (1.9 vs. 3.3) in controls although the numbers of bases re-inserted in the repaired regions were similar (64 vs. 72). Measurement of thymine-containing dimers remaining throughout a 24 h time period indicated a 30% difference in the excision of dimers when tested with either EGTA or trifluoperazine. We also observed a significant decrease in the number of cytosine arabinoside arrested repair sites in the presence of either EGTA or trifluoperazine. The results are discussed with relation to the possibility of calmodulin altering the initial incision by repair endonuclease.

A quantitative analysis of the cytotoxic action of chemical mutagens

A quantitative hypothesis is developed to explain the cytotoxic action of chemical mutagens on eukaryotic cells. The hypothesis forms an extrapolation of previously developed concepts used to explain the effect of ionizing radiation and the cytotoxic action of UV light. The crucial potentially lethal lesion is assumed to be a DNA double-strand lesion which may be an interstrand cross-link or a pair of DNA single-strand alkylations, for example. The effect of repair processes is included in the analytical equation derived to describe cell survival. The analysis of several sets of cell survival data for different chemical mutagens is used to demonstrate the applicability of the hypothesis. The logical extension of the hypothesis permits a division of chemical mutagens into 4 separate classes on the basis of the mechanisms proposed for the cytotoxic activity, and the relative importance of the risk associated with low-level exposure to each class is discussed. The hypothesis is amenable to further experimental verification.

Host cell reactivation capacity of different strains of E. coli B resistant or sensitive to ozone

Host cell reactivation capacity for ozonated or irradiated phage was determined for different strains of E. coli either more sensitive or resistant to ozone than the wild type strain. The results suggest that the ozr gene product could be involved in the same repair pathway for ozone-induced lesions on DNA as the polA gene. The possible involvement of a specific endonuclease for these lesions is also considered.

Removal of UV light-induced pyrimidine-pyrimidone(6-4) products from Escherichia coli DNA requires the uvrA, uvrB, and urvC gene products

Ultraviolet light induces the formation of cyclobutane pyrimidine dimers and pyrimidine- pyrimidone (6-4) photoproducts in cellular DNA. In Escherichia coli, the uvrA, uvrB, and uvrC genes are necessary for excision of cyclobutane dimers. To determine whether the uvrABC gene products are required for (6-4) product removal from DNA, a sensitive HPLC assay was developed that allows the separation and quantitation of both types of photoproducts. Both the T T cyclobutane dimer and the T-C(6-4) product were completely removed from the DNA after 2 hr of repair in a wild-type strain. Both products were also removed in the wild-type strain in the presence of chloramphenicol, an inhibitor of protein synthesis. No decrease in the amount of either T T cyclobutane dimer or of T-C(6-4) products was observed in strains that were deficient in any one of the three uvr gene products under similar conditions. We conclude the uvrABC enzyme complex is required for excision of (6-4) photoproducts from E. coli DNA.

Rapid inactivation of Ca2+, Mg2+-dependent endonuclease of rat liver nuclei after cycloheximide treatment

Ca2+, Mg2+ dependent endonuclease activity of isolated nuclei from rat liver disappeared completely within one to two hours after intraperitoneal administration of inhibitors of eukaryotic protein synthesis such as cycloheximide or puromycin. Actinomycin D, on the other hand, revealed no inhibition of the endonuclease activity, but even reversed the effect of cycloheximide by simultaneous addition.

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.

Excision repair participates in the Weigle reactivation of ultraviolet light-irradiated phi X174 double-stranded DNA

The efficiency of Weigle reactivation of ultraviolet light-irradiated single and double-stranded phi X174 DNA by wild-type and excision repair-defective E. coli hosts was determined. After limited exposure to ultraviolet light, the efficiency of Weigle reactivation by an ultraviolet light-irradiated wild-type host was greater for double-stranded phi X174 DNA than for its single-stranded counterpart. However, the efficiency of inducible recovery of the double-stranded DNA molecule decreased as its exposure to ultraviolet light increased until it became constant at a value 1.5 times less than that for single-stranded form of phi X174 DNA. The efficiency of Weigle reactivation of the single-stranded DNA molecule by the same host, however, was independent of the dose to the DNA, as were the efficiencies of reactivation for both forms of phi X174 DNA by ultraviolet light-irradiated excision repair-deficient hosts. In excision repair-defective hosts the efficiency of Weigle reactivation of double-stranded phi X174 DNA was also 1.5 times less than that for the single-stranded molecule. These results suggest that the Weigle reactivation of double-stranded phi X174 DNA is mediated in part by an excision repair process, and that this component of Weigle reactivation eventually can be saturated by ultraviolet light-induced DNA damage leaving other repair processes, such as trans-damage synthesis, responsible for the remaining inducible reactivation.

International Commission for Protection Against Environmental Mutagens and Carcinogens. Dosimetry of genotoxic agents and dose-response relationships of their effects

Dose-response relationships and determination of dose of mutagens and carcinogens are summarized and discussed on the basis of conceptual and kinetic aspects. Different dose definitions may be referred to steps in the chain of events from exposure (or emission) to observed effects. A system is applied to show the influence of various processes on the kinetics of the transfers between consecutive steps. The same system illustrates processes influenced by protraction and fractionation of dose, synergists, comutagens/cocarcinogens, heritable factors, etc. The response at a given dose is expected to depend on the product of consecutive transfer functions. An application of general rules of chemical kinetics shows that when a chemical is introduced at a sufficiently low level, all processes affecting the transfers and therefore the transfer functions themselves become first-order, provided the induction status of enzymes and the cell-division rate remain constant. Under the same conditions, dose-response relationships are expected to be linear, i.e. without "safe" thresholds. However, present knowledge of the kinetics of repair at low levels of DNA damage and of the kinetics of induction of repair functions is not enough complete to be decisive. These considerations and the fact that observed dose-response data in some cases indicate the existence of thresholds but in others appear able to reject the threshold hypothesis lead to the conclusion that, generally, dose-response curves are most probably linear down to dose zero. However, certain mutagens/carcinogens give rise to lesions repaired so effectively that quasi-thresholds appear in certain subpopulations or organs.

Repair resynthesis in Escherichia coli mutants deficient in single-stranded DNA-binding protein

A series of Escherichia coli strains deficient in single-stranded DNA-binding protein (SSB) and DNA polymerase I was constructed in order to analyze the effects of these mutations on DNA repair resynthesis after UV-irradiation. Since SSB has been suggested to play a role in protecting single-stranded regions which may transiently exist during excision repair and since long single-stranded regions are believed to occur frequently as repair intermediates in strains deficient in DNA polymerase I, studies of repair resynthesis and strand rejoining were performed on strains containing both the ssb-1 and polA1 mutations. Repair resynthesis appears to be slightly decreased in the ssb-1 strain at 42 degrees C relative to the wild-type; however, this effect is not enhanced in a polA1 derivative of this strain. After UV-irradiation, the single-strand molecular weight of the DNA of an ssb-1 strain decreases and fails to recover to normal size. These results are discussed in the context of long patch repair as an inducible component of repair resynthesis and of the protection of intermediates in the excision repair process by SSB. A direct role for SSB in repair resynthesis involving modulation of the proteins involved in this mode of DNA synthesis (particularly stimulation of DNA polymerase II) is not supported by our findings.

Inactivation, mutation induction and repair in Bacillus subtilis spores irradiated with heavy ions

Studies on the response of bacterial spores to accelerated heavy ions (HZE particles) help in understanding problems of space radiobiology and exobiology. Layers of spores of Bacillus subtilis strains, differing in repair capabilities, were irradiated with accelerated boron, carbon and neon ions of linear energy transfer (LET) values up to 14000 MeV cm2/g. Inactivation as measured by loss of colony forming ability and induction of mutations as measured by reversion to histidine prototrophy and resistance to 150 micrograms/ml sodium azide were tested, as well as the influence of repair processes on these effects. For inactivation, the cross-sectional values sigma plotted as a function of LET follow a saturation curve. The plateau, which is reached around a LET of 2000 MeV cm2/g, occurs at 2.5 x 10(-9) cm2, a value in good agreement with the dimensions of the spore protoplast. Lethal damage produced at LET values < 2000 MeV cm2/g is reparable. Recombination repair is more effective than excision repair. At higher LET values, lethal damage could not be reconstituted by the repair mechanisms studied. In addition, at these high LET values, the frequency of induced mutations was drastically decreased. The data support the assumption of at least two qualitatively different types of lesion, depending on the LET of the affecting heavy ion.

An analysis of the repair processes in ultraviolet-irradiated Micrococcus luteus using purified ultraviolet-endonuclease

The measurement of the frequency of endonucleolytic incisions in ultraviolet-irradiated DNA serves as the test for the presence of pyrimidine dimers. In accordance with this approach, the lysates of three Micrococcus luteus strains containing radioactively labeled chromosomes were treated with purified M. luteus ultraviolet-endonuclease to trace segregation of dimers amongst parental and newly synthesized DNA and their removal during postreplication and excision DNA repair. A considerable proportion of the dimers in all strains tested proved to be insensitive to the action of exogenous incising enzyme. The use of chloramphenicol as an inhibitor of postirradiation protein synthesis in combination which ultraviolet-endonuclease treatment of DNA allowed to reveal at least two alternative pathways of postreplication repair: constitutively active recombinational pathway and inducible nonrecombinational one.

Molecular structure of uvrC gene of Escherichia coli: identification of DNA sequences required for transcription of the uvrC gene

We have carried out experiments to identify the regulatory regions of the uvrC gene of Escherichia coli. A uvrC+ plasmid, pUV7, containing the intact transcriptional unit for the uvrC gene, was used to subclone either the structural gene or combinations of the structural gene and 5'-flanking sequences. The plasmids so constructed were tested for ability to restore UV-resistant phenotype to uvrC- cells as an indication of expression of the uvrC gene. The chromosomal DNA in plasmid pUV7 was probed for strong binding with E. coli RNA polymerase in an attempt to identify a restriction fragment which bears the regulatory sequences for the uvrC transcriptional unit. The results indicate that DNA sequences at least 0.9 Kb upstream from the structural gene, but not the 5'-proximal sequences, regulate expression of the uvrC gene. Analysis of protein synthesis encoded by plasmid pUV7 and its derivatives suggest that there may be another gene that lies between the promoter and the uvrC gene and codes for a 27,000-Mr protein. The relation of this gene to uvrC function is not clear.

Effect of bacterial host repair systems on the viability of hydroxylamine and methyl methanesulfonate treated T4 and lambda bacteriophages

Survival of HA1 or MMS-treated T4 and lambda phages was estimated in bacterial cells differing in their ability to repair DNA. It has been found that the mismatch repair system of the bacterial host, which involves mutS mutR MutL uvrE and dam loci, does not excise, or does so to only a limited extent, the nonpaired bases from DNA of HA or MMS-treated phages. Mutation in polA, both in the polymerase as well as in the 5' leads to 3' exonuclease activity, have a small effect on survival of HA-treated phages, whereas mutation in the polymerase activity has a pronounced effect on survival of MMS-treated phages. There was a difference in the effect of polA mutations on survival of MMS-treated T4 and lambda phages; the survival of the former was less affected than the latter. Induction of SOS response has no effect on repair of HA and MMS-treated phages. Pretreatment of bacterial host (including the ada- mutant) with low doses of alkylating agents increases the survival of MMS (but not HA)-treated phages; pretreatment of bacteria with HA has no effect on survival of HA-treated phages. Three lines of evidence: the different inactivation rates of MMS-treated T4 and lambda phages, variation in the effect of polA mutations on survival of T4 and lambda phages, and a different level of adaptive response in ada- cells towards of MMS-treated T4 and lambda phages, suggest that the patterns of DNA methylation in T4 and lambda phages are different.

Photodynamic effects of dyes on bacteria. V. Mutagenesis by acridine orange and 460-nm or 500-nm light in strains of Escherichia coli that differ in repair capability

With acridine orange (AO) and monochromatic 460-nm light, the mutation rate of the wild-type strain of Escherichia coli (WP2) was 3-fold higher than that of the endonuclease-deficient strain WP2 (uvrA). In addition, the mutation rates of the recombination-deficient strains WP10 (recA) and Bs-1 (uvrB lexA) were also about 3-fold less than that of wild-type strain. This observation is in striking contrast to the earlier results with AO and 500-nm light in which strains WP10 and Bs-1 yielded mutation rates that were 12-fold and 5-fold greater, respectively, than the wild-type response. The relatively large decrease in mutation rate when the uvrA endonuclease was absent together with structural considerations in the binding of AO to DNA lead us to propose that the major lesions leading to mutations produced by 460-nm light in the presence of AO may be true DNa single-strand breaks and occur before DNA replication.

Characterization of long patch excision repair of DNA in ultraviolet-irradiated Escherichia coli: an inducible function under rec-lex control

Excision repair in ultraviolet-irradiated wild-type Escherichia coli produces a bimodal distribution of repair patch sizes in the DNA. Approximately 99% of the repair events result in short patches of 20-30 nucleotides produced by a constitutive repair system. The remaining 1% result in patches which are at least 1,500 nucleotides in length. This long patch repair is shown to be a damage-inducible process under control of the rec-lex regulatory circuit. The kinetics of the two processes differ; short patch synthesis begins immediately after irradiation and is virtually completed prior to synthesis of the majority of the long patches. Long patch repair synthesis is a linear function of UV dose up to a plateau at 60 J/m2, and hence each long patch event is the consequence of a single UV-induced lesion. Long patch repair does not appear to be necessarily error-prone, since no alteration in repair synthesis occurs as a result of a mutation umuC- which renders cells nonmutable by UV. Evidence is presented suggesting that DNA polymerase I is responsible for both long and short patch synthesis in wild type cells under inducing conditions. In the absence of polymerase I the constitutive patch size averages 80-90 nucleotides, and this distribution is unchanged by induction.

Purification and properties of a new DNase activity from KB cells

A deoxyribonuclease activity with specificity towards single-stranded DNA has been purified approximately four hundred-fold from KB cells, by chromatography on DEAE-cellulose, phosphocellulose and hydroxylapatite. The last step of the purification results in separation of the enzyme from a DNase activity which has been described previously (Wang, E.C., Furth, J.J. and Rose, J.A., (1978) Biochemistry 17: 544-549). The properties of the new DNase activity are significantly different from those of the enzymes which have previously been identified in these cells. The activity sediments at approximately 7.5S in a glycerol gradient. The DNase activity is optimal at pHs between 6.0 and 6.5. It cleaves DNA endonucleolytically and hydrolyzes single-stranded DNA at about 11 times the rate of double-stranded DNA and at twice the rate of Poly (dA). The activity is moderately sensitive to inhibition by N-ethylmaleimide and is inhibited 80% by 50 mM NaCl. It is stimulated twenty-fold by Mn++ at an optimal concentration of approximately 0.7 mM. It is stimulated by a lesser extent by Mg++, but not by Ca++.

Weigle reactivation of the single-stranded DNA phage f1

The survival of ultraviolet light (UV) damaged single-stranded DNA bacteriophage f1 is increased when the Escherichia coli host is irradiated with UV prior to infection. This repair, called Weigle reactivation, is multiplicity independent and is absent in recA and in lexA mutants. The function of the recA-lexA repair system needed is repair and not recombination, as demonstrated by the absence of Weigle reactivation in mutants that are recombination proficient but defective in repair of double-stranded DNA. Weigle reactivation of f1 requires high levels of the recA protein, and in addition activation of recA or another protein. This activation can be produced by UV irradiation, or by the tif-1 allele of recA together with the spr allele of lexA. Mutagenesis of f1 has the same requirements as W-reactivation, and in addition requires UV irradiation of the phage.

Excision repair and patch size in UV-irradiated bacteriophage T4

We determined the average size of excision repair patches in repair of UV lesions in bacteriophage T4 by measuring the photolysis of bromodeoxyuridine incorporated during repair. The average patch was small, approximately four nucleotides long. In control experiments with the denV1 excision-deficient mutant, we encountered an artifact, a protein(s) which remained bound to phenol-extracted DNA and prevented nicking by the UV-specific endonucleases of Micrococcus luteus and bacteriophage T4.

A UV-sensitive human clonal cell line, RSa, which has low repair activity

The repair activity of a human transformed cell line, RSa, which was found to be highly sensitive to the lethal effects of 254 nm far-ultraviolet radiation, was compared with that of HeLa cells by evaluating the range of UV-induced incorporation of [methyl-3H]thymidine ([3H]dThd) or 5-[6-3H]bromodeoxyuridine ([3H]BrdUrd) into deoxyribonucleic acid. Direct scintillation counting was used for measuring the extent of unscheduled DNA synthesis (UDS) in UV-irradiated cells, which were treated with hydroxyurea or with arginine deprivation. More quantitative measurements were made by using the density labeling and equilibrium centrifugation method for assaying repair replication. All the amounts of UDS and repair replication in RSa cells were markedly below those in HeLa cells. The possible relationships of the low repair activity to abnormally high UV sensitivity in RSa cells are discussed.

Analysis of resynthesis tracts in repaired Escherichia coli deoxyribonucleic acid

Excision repair of ultraviolet radiation-induced damage in a wild-type strain of Escherichia coli has been examined, using two methods for characterizing the resynthesis step of the repair process. Comparison of data obtained after both isopycnic analysis of repaired deoxyribonucleic acid and sedimentation velocity analysis of deoxyribonucleic acid after selective photolysis of bromouracil-containing repaired regions has shown that the repaired deoxyribonucleic acid molecules contain a semicontinuous distribution of sizes of repair tracts. Further analysis of our data suggests two major classes of repair patches, one abut 20 to 40 nucleotides in length, and the other containing 1,600 to 2,000 nucleotides. Under the conditions employed, approximately 2 to 10% of the fully repaired regions are long repair patches.

Poly(adenosine diphosphoribose) synthesis in ultraviolet-irradiated xeroderma pigmentosum cells reconstituted with Micrococcus luteus UV endonuclease

Synthesis of DNA and poly(adenosine diphosphoribose) [poly(ADPR)] was examined in permeabilized xeroderma pigmentosum lymphoblasts (XP3BE) before and after UV irradiation and in the presence and absence of Micrococcus luteus UV endonuclease. M. luteus UV endonuclease had no effect on the level of DNA or poly(ADPR) synthesis in control, unirradiated cells. UV irradiation caused a decrease in replicative DNA synthesis without any significant change in poly(ADPR) synthesis. In UV-irradiated cells treated with M. luteus UV endonuclease, DNA synthesis was restored to a level slightly greater than in the unirradiated control cells, and poly(ADPR) synthesis increased by 2- to 4-fold. Time--course studies showed that the UV endonuclease dependent poly(ADPR) synthesis preceded the endonuclease-dependent DNA synthesis. Inhibition of endonuclease-dependent poly(ADPR) synthesis with 3-aminobenzamide, 5-methylnicotinamide, or theophylline produced a partial inhibition of the endonuclease-dependent DNA synthesis. Conversely, inhibition of the endonuclease-dependent DNA synthesis with dideoxythymidine triphosphate, phosphonoacetic acid, or aphidicolin had no effect on the endonuclease-dependent poly(ADPR) synthesis. These studies show that stimulation of poly(ADPR) synthesis in UV-irradiated cells occurs subsequent to the DNA strand breaks created by the specific action of the UV endonuclease on UV-irradiated DNA. The effect of the inhibitors of poly(ADPR) synthesis in UV-irradiated cells indicates that the endonuclease-stimulated DNA synthesis is dependent in part on the prior synthesis of poly(ADPR).

A new procedure for the simultaneous large-scale purification of bacteriophage-T4-induced polynucleotide kinase, DNA ligase, RNA ligase and DNA polymerase

A procedure for simultaneous large-scale purification of the bacteriophage-T4-induced polynucleotide kinase, DNA ligase, RNA ligase and DNA polymerase has been developed. The method involves bacterial cell disruption by sonication, fractionation of cell extract with polymin P, salt elution from the polymin pellets, ammonium sulfate precipitation, and subsequent column chromatography purification of the enzymes. To enrich the enzyme content highly in the initial source non-permissive Escherichia coli B-23 cells infected with T4 amN82 phage were used. The procedure described is rapid, reproducible, high in yield, and able to handle preparations using from 1 g to 200 g cell paste. It can be easily scaled up. The method results in large amounts of the enzymes with very high specific activities, good stability essential lacking exonuclease and endonuclease contamination. The final enzyme preparations were efficiently used in DNA sequencing and in multiple experiments on construction of various recombinant DNAs for cloning and expression in vivo.

Postreplication repair of deoxyribonucleic acid and daughter strand exchange in uvr- mutants of Bacillus subtilis

The fate of pyrimidine dimers in deoxyribonucleic acid (DNA) newly synthesized by Bacillus subtilis after ultraviolet irradiation was monitored by use of a damage-specific endonuclease that introduces single-strand breaks adjacent to nearly all of the dimer sites. Two Uvr- strains, one defective in the initiation of dimer excision and the other defective in a function required for efficient dimer excision, were found to be similar to their wild-type parent in the kinetics and extent of converting low-molecular-weight DNA newly synthesized after ultraviolet irradiation to high molecular weight. In the Uvr- strains large molecules of newly synthesized DNA remained susceptible to nicking by the damage-specific endonuclease even after extended incubation in growth medium, whereas the enzyme-sensitive sites were rapidly removed from both preexisting and newly synthesized DNA in Uvr+ cells. Our results support the hypothesis that postreplication repair in bacteria includes recombination between dimer-containing parental DNA strands and newly synthesized strands.

DNA polymerase III-dependent repair synthesis in response to bleomycin in toluene-treated Escherichia coli

Bleomycin (BLM) is an antitumor drug which interacts with and damages DNA. We have reported a repair response dependent on DNA polymerase I in toluene-treated Escherichia coli. We report here that DNA polymerase III can also catalyze a repair response in toluene-treated E. coli following exposure to BLM. Polymerase III-mediated synthesis differs because it is ATP-dependent, whereas polymerase I-mediated repair synthesis is not. Polymerase III repair synthesis is independent of replicative synthesis, as demonstrated in a polA-, dnaBts strain, or use of Novobiocin to inhibit replication, and replication persists in the presence of repair synthesis. It appears that ATP-dependent repair synthesis in response to BLM is also present in polA+ strains. Repair synthesis does not require the uvrA gene product.

An endonuclease from yeast mitochondrial fractions

A membrane-bound endonuclease has been isolated from mitochondrial fractions of Saccharomyces cerevisiae. The enzyme is present in a stable complex and has an approximate molecular weight of 14 000. It requires Mg2+ or Mn2+ for activity, and has an optimum pH of 7.0. Its activity with native DNA is five times less than with denatured DNA in 0.05 M KCl and is very low in 0.2 M KCl. The activity with RNA is 40% of that with denatured DNA; the two substrates are competitive. Its mode of action is endonucleolitic, cuts both strands of native lambda DNA at the same or nearby sites. After mild digestion of DNA, analysis of 5'-end groups of the digestion products indicated a marked preference for deoxythymidylic and deoxyguanilic acid residues as the site of enzymatic cleavage. After exhaustive digestion of DNA, mononucleotides (2.4%), dinucleotides (70.5%) and trinucleotides (27%) ending in 5'-phosphate are produced.

Formation and excision of nitrofuran-DNA adducts in Escherichia coli

When Escherichia coli were incubated with the strong mutagen 2[14C]2-amino-4-(5-nitro-2 furyl)-thiazole (ANFT) radioactivity became tightly and presumably covalently bound to DNA. Hydrolysis of the DNA with nucleases yielded low molecular weight radioactive material. The bound radioactivity was associated with at least two functionally and chemically distinct adducts. One of these was rapidly removed in uvr+ E. coli while the other was more persistent. Analysis of enzymatic hydrolysates on a Dowex AG 50W-X4 column showed that the 'excisable adducts' were chromatographically different from most of the persistent ones. ANFT caused daughter-strand gaps when the DNA of treated cells was replicated, provided this DNA contained excisable adducts. In situations where removal of these adducts was complete no gaps were found in newly synthesized DNA. 3-[14C]2-(2-furyl)-3-(5-nitro-2-furyl) acrylamide (AF2) (another strongly mutagenic nitrofuran) became bound to the DNA of E. coli WP2 uvrA to a slightly greater extent than did [14C]ANFT. In contrast, [14C]nitrofurazone (the semicarbazide of 5-nitro-2-furaldehyde) a much weaker mutagen, gave considerably less binding. With AF2 and ANFT there was roughly the same relation between the amount of adduct formed and the subsequent yield of daughter strand gaps when the DNA replicated while with nitrofurazone the yield of gaps per adduct was somewhat lower. Incubation in vitro of [14C]ANFT with DNA in the presence of an E. coli nitrofuran reductase preparation also resulted in the binding of 14C to DNA.