Nuclear endo-exonuclease of Neurospora crassa. Evidence for a role in DNA repair

Mitochondrial Endonuclease G function in apoptosis and mtDNA metabolism: a historical perspective

All mitochondria contain a single, major Mg2+-dependent nuclease capable of extensively degrading DNA and RNA in vitro. This nuclease activity and its gene now go by the name Endonuclease G. For many years, however, a number of different names for this mitochondrial nuclease have been used. This can lead to great deal of confusion for anyone searching the literature. The name Endonuclease G had originally been assigned to an endonuclease activity identified in nuclear extracts of chicken erythrocytes that was found to specifically nick within guanine (G) tracts in DNA in vitro. Subsequent studies however, established that this Endonuclease G activity was identical to the well known, major endonuclease activity isolated from mitochondria of several species. In addition, studies of the mammalian mitochondrial endonuclease showed that the endonuclease is not restricted to only attacking guanine tracts, although it does so avidly. The enzyme is also capable of avidly nicking within cytosine tracts, and at a large variety of sites, that fragments duplex DNA extensively. Despite this, the name Endonuclease G persists. One purpose of this review is to summarize the history of Endonuclease G that spans some 40 years, and review what we have learned about the enzyme's biochemical and biologic properties. Endonuclease G likely serves a role in repair and/or degradation of damaged mtDNA in vivo. Recently, genetic and biochemical evidence has emerged that Endonuclease G is released from the inter membrane space during early stages of programmed cell death, and translocates to the nucleus where it presumably facilitates degradation of chromatin. This exciting new potential role for the enzyme in apoptotic cell death will be discussed.

Incision at nucleotide insertions/deletions and base pair mismatches by the SP nuclease of spinach

Spinach leaves contain a highly active nuclease called SP. The purified enzyme incises single-stranded DNA, RNA, and double-stranded DNA that has been destabilized by A-T-rich regions and DNA lesions [Strickland et al. (1991) Biochemistry 30, 9749-9756]. This broad range of activity has suggested that SP may be similar to a family of nucleases represented by S1, P1, and the mung bean nuclease. However, unlike these single-stranded nucleases that require acidic pH and low ionic strength conditions, SP has a neutral pH optimum and is active over a wide range of salt concentrations. We have extended these findings and showed that an outstanding substrate for SP is a mismatched DNA duplex. For base-substitution mismatches, SP incises at all mismatches except those containing a guanine residue. SP also cuts at insertion/deletions of one or more nucleotides. Where the extrahelical DNA loop contains one nucleotide, the preference of extrahelical nucleotide is A >> T approximately C but undetectable at G. The inability of SP to cut at guanine residues and the favoring of A-T-rich regions distinguish SP from the CEL I family of neutral pH mismatch endonucleases recently discovered in celery and other plants [Oleykowski et al. (1998) Nucleic Acids Res. 26, 4597-4602]. SP, like CEL I, does not turn over after incision at a mismatched site in vitro. Similar to CEL I, the presence of a DNA polymerase or a DNA ligase allows SP to turn over and stimulate its activity in vitro by about 20-fold. The possibility that the SP nuclease may be a natural variant of the CEL I family of mismatch endonucleases is discussed.

Identification and characterization of an endo/exonuclease in Pneumocystis carinii that is inhibited by dicationic diarylfurans with efficacy against Pneumocystis pneumonia

Dicationic diarylfurans and dicationic carbazoles are under development as therapeutic agents against opportunistic infections. While their ability to bind to the minor groove of DNA has been established, the complete mechanism of action has not. We demonstrate here that an effective diarylfuran, 2,5-bis[4-(N-isopropylguanyl)phenyl]furan, inhibits an endo/exonuclease activity present in Pneumocystis carinii, Cryptococcus neoformans, Candida albicans, and Saccharomyces cerevisiae. This activity was purified from the particulate fraction of P. carinii. The enzyme requires Mg++ or Mn++, and shows preferences for single-over double stranded DNA and for AT-rich over GC-rich domains. A panel of 12 dicationic diarylfurans and eight dicationic carbazoles, previously synthesized, were evaluated for inhibition of the purified nuclease and for efficacy against Pneumocystis pneumonia in rats. Among the diarylfurans, potency of nuclease inhibition, in vivo antimicrobial activity, and DNA binding strength were all strongly correlated (p < 0.001). These findings suggest that one target for antimicrobial action of the diarylfurans may be a nucleolytic or other event requiring unpairing of DNA strands. Dicationic carbazoles which were strong nuclease inhibitors all displayed anti-Pneumocystis activity in vivo, but there were also noninhibitory carbazoles with in vivo efficacy.

A new meiotic endonuclease from Coprinus meiocytes

Two different types of Coprinus meiotic nuclease have been previously reported by the authors which are believed to be involved in meiotic chromosome recombination [1,2]. A third meiotic endonuclease was purified from the cap tissues of the basidiocarp of Coprinus cinereus. The enzyme is a 60 kDa molecule composed of a monopolypeptide as revealed by SDS-PAGE and FPLC-Sephacryl S-300 gel filtration. The enzyme belongs to a type of endonuclease which can preferentially digest single-stranded DNA and requires divalent cations as a co-factor, most commonly Mg2+ ions. In the presence of this co-factor, the enzyme converts the supercoiled plasmid DNA (form I) to both the relaxed form (form II) and the linear form (form III). Ca2+ ions can also function as a co-factor, though, in this case, not only is form I plasmid converted to form II, but a few ladder bands between form I and form II are also produced. The Ca2+ ion effect as a cofactor can be prevented with ATP. Immunohistochemical observation shows that the enzyme is distributed in the surface of the gills, which contain the meiotic tissues. These characteristics clearly differ from those of the meiotic nucleases reported previously.

Endo-exonuclease of human leukaemic cells: evidence for a role in apoptosis

Inactive forms of endo-exonuclease, activated in vitro by treatment with trypsin, have been identified in human leukaemic CEM and MOLT-4 cells. They comprise over 95% of the total single-strand DNase activity in nuclei and are mainly bound to chromatin and the nuclear matrix. The activated enzyme had Mg2+(Mn2+)-dependent, Ca(2+)-stimulated activities with single- and double-strand DNAs and RNA (polyriboadenylic acid) and other properties characteristic of endo-exonucleases previously described. At least twice as much inactive endo-exonuclease has also been localised in extranuclear compartments of CEM and MOLT-4 cells, 85% bound to the membranes of the endoplasmic reticulum and 15% free in the cytosol. The soluble cytosolic trypsin-activatable endo-exonuclease was immunoprecipitated by antibodies raised independently to both Neurospora and monkey CV-1 cell endo-exonucleases. The free and bound enzymes of both nuclear and extranuclear compartments also cross-reacted on immunoblots with the antibody raised to Neurospora endo-exonuclease to reveal multiple polypeptides ranging in size from 18 to 145 kDa, many of which exhibited activity on DNA gels. The major species bound to the chromatin/matrix were in the 55–63 kDa range. Limited proteolysis of the large polypeptides to those of 18 to 46 kDa accompanied spontaneous chromatin DNA fragmentation to form DNA “ladders' in an isolated nuclei/cytosol system. When the leukaemic cells were treated in culture with either etoposide or podophyllotoxin to induce apoptosis, the largest polypeptides disappeared and smaller endo-exonuclease-related polypeptides of 18 to 46 kDa were detected in the nuclear extracts. The appearance of these polypeptides also correlated with extensive chromatin DNA fragmentation. In addition, there were correlations between the depletion of the major 55–63 kDa species bound to the membranes of the endoplasmic reticulum, depletion of the extranuclear trypsin-activatable activity and the onset and extent of chromatin DNA fragmentation in both cell lines. The extranuclear 55–63 kDa species may be precursors of the chromatin/matrix bound endo-exonuclease. The results indicate that endo-exonuclease plays a role in chromatin DNA degradation in mammalian cells during apoptosis.

Involvement of DNase II in nuclear degeneration during lens cell differentiation

The characterization of DNase II and DNase I activity was undertaken to discriminate their different roles in physiological nuclear degradation during lens fiber cell differentiation. The activity of both nucleases determined in a new assay allows to discriminate DNase II from DNase I in the same extract. In fibers, both types of nuclease activities are found and appear higher than in epithelial cells. Specific polyclonal antibodies directed against these two nucleases reveal by Western blot analysis the presence of various DNase isoforms. DNase II like-nuclease, present in fibers, is represented by three major bands (60,23, and 18 kDa), which are not detected, at least for two of them (60 and 23 kDa), in epithelial cells. DNase I like-nuclease pattern in fiber cells shows a single 32-kDa band, while several bands can be detected in epithelial cells. Immunocytochemistry studies show both nucleases present in lens cell sections. DNase II is, as usual, in cytoplasm of epithelial cells, but it appears strikingly concentrated in the nuclei of fibers. DNase I is always concentrated in nuclei of epithelial and fiber cells. DNA degradation observed in agarose gels shows that DNase II-activating medium cleaves the DNA from fiber cells more efficiently than DNase I-activating buffer. In addition, DNase II antibody is able to prevent this degradation. These results suggest a specific involvement of DNase II in nuclear degradation during lens cell differentiation.

Apoptosis overview emphasizing the role of oxidative stress, DNA damage and signal-transduction pathways

Apoptosis (programmed cell death) is a central protective response to excess oxidative damage (especially DNA damage), and is also essential to embryogenesis, morphogenesis and normal immune function. An understanding of the cellular events leading to apoptosis is important for the design of new chemotherapeutic agents directed against the types of leukemias and lymphomas that are resistant to currently used chemotherapeutic protocols. We present here a review of the characteristic features of apoptosis, the cell types and situations in which it occurs, the types of oxidative stress that induce apoptosis, the signal-transduction pathways that either induce or prevent apoptosis, the biologic significance of apoptosis, the role of apoptosis in cancer, and an evaluation of the methodologies used to identify apoptotic cells. Two accompanying articles, demonstrating classic apoptosis and non-classic apoptosis in the same Epstein-Barr virus-transformed lymphoid cell line, are used to illustrate the value of employing multiple criteria to determine the type of cell death occurring in a given experimental system. Aspects of apoptosis and programmed cell death that are not covered in this review include histochemistry, details of cell deletion processes in the sculpting of tissues and organs in embryogenesis and morphogenesis, and the specific pathways leading to apoptosis in specific cell types. The readers should refer to the excellent books and reviews on the morphology, biochemistry and molecular biology of apoptosis already published on these topics. Emphasis is placed, in this review, on a proposed common pathway of apoptosis that may be relevant to all cell types.

Endo-exonucleases: enzymes involved in DNA repair and cell death?

Endo-exonucleases from E. coli to man, although very different proteins, are multifunctional enzymes with similar enzymatic activities. They probably have two common but opposing biological roles. On the one hand, they promote survival of the organism by acting in recombination and recombinational DNA repair to diversify and help preserve the genome intact. On the other hand, they degrade the genomic DNA when it is damaged beyond repair. This ensures elimination of heavily mutagenized cells from the population.

Activity gel and activity blotting methods for detecting DNA-modifying (repair) enzymes

Zymographical methods (activity gel, overlay gel, activity blot and activity blotting) for detecting DNA-modifying (repair) enzymes are reviewed. Emphasis is put on the novel activity blotting method in which DNA repair enzymes electrophoresed on a gel are blotted and detected on a damaged DNA-fixed nylon membrane. Its practical procedures, including a non-radioactive detection procedure, and representative results are also described.

Utilization of the specific-locus assay in the ad-3 region of two-component heterokaryons of Neurospora for risk assessment of environmental chemicals

The utilization of the specific-locus assay in the ad-3 region of two-component heterokaryons of Neurospora crassa is compared with that of other eukaryotic assay systems for the evaluation of the mutagenic effects of environmental chemicals. In contrast to other in vitro specific-locus assays, the Neurospora assay can detect mutations not only at the ad-3A and ad-3B loci but also recessive lethal mutations elsewhere in the genome. Mutational damage in this system can be characterized readily by means of classical genetic techniques involving heterokaryon tests to determine genotype, and allelic complementation among ad-3BR mutations. The percentages of ad-3BR mutations showing allelic complementation with polarized or nonpolarized complementation patterns provide a presumptive identification of the genetic alterations at the molecular level in individual mutants. Dikaryon and trikaryon tests (using 3 strains carrying multilocus deletion mutations as tester strains) distinguish ad-3 mutations resulting from gene/point mutation, multilocus deletion mutation, and various types of multiple-locus mutation. The array of ad-3 mutations recovered from forward-mutation experiments can be expressed in terms of Mutational Spectra, which make it possible to make comparisons of mutational types between different doses of the same mutagen, different mutagens, or the effects of the same mutagen on different strains. Another important feature of this specific-locus assay system is that the effects of mutagens can be studied in both DNA excision repair-proficient (H-12) and -deficient (H-59) two-component heterokaryons to evaluate both quantitative and qualitative differences between the spectra of induced ad-3 mutations. The utilization of this assay on large numbers of environmental chemicals has shown that some chemicals produce predominantly, or exclusively, gene/point mutations, whereas other agents produce both gene/point mutations and multilocus deletion mutations in H-12. When the mutagenic effects of the same chemicals were compared in H-12 and H-59, marked differences between forward-mutation frequencies and Mutational Spectra of ad-3 mutations were detected.

The split-end model for homologous recombination at double-strand breaks and at Chi

In recent years two different styles of model for homologous recombination have been discussed, depending on whether or not the recombination event occurs in the vicinity of a double-strand break in DNA. The models of Holliday and Meselson and Radding exemplify those that do not involve a break whereas the model of Szostak et al is taken as an example of those that do. Recent advances in understanding a prototypic recombination system thought to promote exchange distant from DNA ends, at Chi sites, suggest a mechanism of initiation neither like Holliday/Meselson-Radding nor like Szostak et al. In those models, only one strand of DNA may invade a homologous DNA molecule. We propose a model for Chi in which exonuclease degrades DNA from a double-strand break to the Chi site; the exonuclease is converted into a helicase upon interaction with Chi; unwinding produces a recombinagenic split-end, and both 3'- and 5'-ending strands at the split-end are capable of invading a homologue. Different genetic consequences are proposed to result from invasion by each. We review evidence supporting the split-end model and suggest its application in at least some cases previously considered to proceed via the Meselson/Radding model and by the double-strand-break repair model of Szostak et al.

Detection of possible DNA repair enzymes on sodium dodecyl sulfate-polyacrylamide gels by protein blotting to damaged DNA-fixed membranes

A novel method for detecting possible DNA repair enzymes on sodium dodecyl sulfate-polyacrylamide gels by blotting them onto a damaged DNA-fixed membrane is presented. To prepare the membrane, highly polymerized calf thymus DNA immobilized on a nylon membrane is damaged chemically. Enzymes, either homogeneous or crude, that are possibly involved in the priming step of DNA repair are fractionated by SDS-polyacrylamide gel electrophoresis (SDS-PAGE) and are renatured to active form by incubating the gel in an appropriate buffer. The renatured enzyme is then blotted onto the damaged DNA-fixed membrane, a process during which incision and/or excision are introduced to the damaged DNA by the enzymes. The incision and/or excision provide priming sites for repair DNA synthesis in the subsequent step in which the membrane is incubated with DNA polymerase in the presence of alpha-32P-labeled substrate. The site of substrate incorporation on the membrane reflecting the molecular weight of the repair enzyme is finally visualized by autoradiography. The present technique is established using Escherichia coli exonuclease III and a DNA-fixed membrane treated with bleomycin or acid-depurinated. By application of this method, a priming factor (an exonuclease) involved in the initiation of bleomycin-induced DNA repair is detected in the extract of mouse ascites sarcoma cells, and thus the molecular weight of the enzyme is estimated. Some apurinic/apyrimidinic endonucleases of mammals are also detected by the present procedure.

Neurospora endo-exonuclease is immunochemically related to the recC gene product of Escherichia coli

Immunochemical cross-reaction between the endo-exonuclease of Neurospora crassa, an enzyme previously implicated in recombination and recombinational DNA repair, and the recC-encoded polypeptide of Escherichia coli has been detected by immunoblotting extracts of strains of E. coli having a deletion that includes the recBCD genes but carrying multicopy plasmids bearing all three of the recBCD genes or only one or two of these genes. It was predicted that homology would also be found at the amino acid sequence level between the recC polypeptide and both nuclear and mitochondrial endo-exonucleases of Saccharomyces cerevisiae, which cross-react with antibodies raised to the N. crassa endo-exonuclease. Since the gene for the S. cerevisiae mitochondrial enzyme, NUC1, has been cloned and sequenced and the predicted amino acid sequence is known, this sequence was aligned with the predicted amino acid sequence of the recC polypeptide. Extensive homology was found by aligning 306 of the 329 amino acids of the yeast mitochondrial nuclease sequence with the carboxy-terminal one-quarter of the amino acid sequence of the recC polypeptide.

Lens fiber differentiation correlated with activation of two different DNAases in lens embryonic cells

In order to identify the different DNAases present in the lens differentiating tissue, we have used an assay which reveals their activity directly on DNA-containing gels after SDS polyacrylamide gel electrophoresis. DNAase renaturation from nuclear embryonic lens extracts does not occur after separation in 0.1% SDS polyacrylamide gel electrophoresis in contrast to that observed with purified micrococcal nuclease. When the SDS concentration in the running buffer and separating gel is decreased to 0.075%, renaturation of lens DNAase and enzyme activities are observed. Isoelectrofocusing was carried out in a polyacrylamide gel which was overlaid with an agarose gel containing DNA, permitting the visualization of the pI of DNAase activity. The presence of several DNAase isoenzymes was demonstrated in 11-day embryonic lenses. In epithelial lens nuclei, high molecular weight (MW) isoenzymes with basic pI were predominant. In post-mitotic fiber lens nuclei, two lower MW isoenzymes with acidic pI were detected as well as high MW activity with a basic pI.

A single, phosphate-repressible deoxyribonuclease, DNase A, secreted in Aspergillus nidulans

High levels of nuclease activities were identified in filtrates of Aspergillus cultures after growth in low-but not in high-phosphate media. Deoxyribonuclease activities, characterized extensively by column chromatography, showed a coincident single peak for ss- and ds-DNase which was distinct from the peak for RNase. Both ss-DNase and ds-DNase are endonucleolytic and showed the highest activity in the presence of Ca2+ and Mn2+ (at pH 8.0). They also showed identical heat sensitivities suggesting that a single, phosphate-repressible DNase was secreted. This enzyme, therefore, corresponds to the well-characterized extracellular DNase A of Neurospora. However, the Aspergillus DNase A did not cross-react with antisera to secreted Neurospora nucleases and showed different chromatographic properties, and active peptides of different sizes were visualized on DNA activity gels. The increasing derepression of Aspergillus DNase A by decreasing phosphate levels was similar to that of secreted alkaline phosphatase and these increases were both abolished by the regulatory mutant palcA.

Sensitivity to bleomycin and hydrogen peroxide of DNA repair-defective mutants in Neurospora crassa

Mutations were induced in Neurospora which cause increased sensitivity to MMS (methyl methane-sulfonate) and other mutagens. Genetic analysis of such mus demonstrated that some of them defined new DNA repair genes (mus-21, and mus-27 to mus-30), while others represented new alleles in previously known genes. To characterize them further, and especially to identify rec- types which have not yet been found in this species, many MMS-sensitive strains were tested for cross-sensitivities to bleomycin (BLM) and to hydrogen peroxide (H2O2) to which some rec- of other species are hypersensitive. In Neurospora, many of the MMS-sensitive mutants were found to be cross-sensitive to BLM and frequently these were also hypersensitive to ionizing radiation. Bleomycin sensitivity was demonstrated for all alleles of 10 different genes, 4 of them new ones, with mus-27 being the most sensitive of the latter (resembling uvs-6; Koga and Schroeder, 1987, Mutation Res., 183, 139). In contrast, very few of the MMS-sensitive mutants were hypersensitive to H2O2 and, in general, results of H2O2 tests were variable and differences between strains small. However, consistent deviations from wild type were observed in a few cases (most clearly for mus-9 and mus-11) when results from treatments of germinating conidia were compared with those of non-growing ones.

Inducible responses to DNA damaging or stress inducing agents in Neurospora crassa

Two-dimensional polyacrylamide gel electrophoresis has been used to analyze proteins from wild type and mutagen sensitive mutants of Neurospora crassa under constitutive conditions and after treatment with mutagens and other stress inducing agents. Several proteins have been detected that are either induced or show changes in electrophoretic mobility in response to UV irradiation, 4-NQO, X-ray, paraquat and heat shock. Ten proteins were found to respond to more than one of the stress inducing agents, demonstrating a complex pattern of polypeptide inductions. The significance of these findings and the possible effects of some of these proteins on the DNA repair process and stress management are discussed.