The determination of the nature of the interaction of neutral Mn2+-dependent DNAse with DNA by immunoelectron microscopy

The interaction of neutral DNAase with native and denatured DNA was shown by immunoelectron microscopy method with the help of colloidal gold. The neutral DNAase of the rat liver nuclear chromatin is absorbed both to denatured DNA, in which the denatured regions are arranged at 5'-3' ends, and to DNA in which these regions are distributed along the whole molecule.     

Ultrastructural localization of neutral DNAse in hepatocytes by immune electron microscopy using colloidal gold

A method for obtaining of the colloidal gold with particles 20 nm in diameter is described. The use of conjugate of colloidal gold-specific antibodies to the neutral DNAase is shown to determine the DNAase localization on ultrathin epontic sections of rat liver fixed by glutaraldehyde. The conditions of fixation, filling and immune reactions are described. The neutral DNAase has been found to localize mainly in heterochromatin.     

Some aspects of the desoxyribonuclease activities of animal tissues

It has been found that many animal tissues contain "acid" desoxyribonucleases with pH optima near 5.2. A chemical method for the determination of this activity is described. The pancreatic desoxyribonuclease crystallized by Kunitz and shown to have a neutral pH optimum occurs in the pancreas together with the "acid" enzyme, but only the "neutral" enzyme occurs in the pancreatic juice. The ratio of "neutral" to "acid" DNAase activities in the pancreas is greater than 200, but in all other tissues examined there is no appreciable concentration of the neutral enzyme. It is concluded that neutral DNAase, like trypsin or lipase, has a digestive function. Some problems in the activation of the secretory enzyme in neutral pancreatic extracts are described. This activation can be interpreted in terms of a specific inhibitor or an inactive form of the enzyme. A comparison of the "acid" DNAase activities of different organs of the calf, horse, chicken, mouse, and rat indicates a possible connection between the DNAase concentration of a tissue and its capacity for proliferation or regeneration. However, the comparative DNAase activities of fetal and adult tissues do not support the view that DNAase function is limited to some simple role in the mechanics of cell division. Studies on the incorporation of glycine-N¹⁵ into the desoxypentose nucleic acids of avian red cells, and mouse liver, pancreas, and kidney show that the N¹⁵ uptake into the DNA of the chromosome is most rapid in tissues with high DNAase concentrations. No N¹⁵ incorporation is observed in the DNA of avian red cells, which have negligible concentrations of the enzyme. The analyses of tissues and nuclei isolated in non-aqueous media show that the bulk of the enzyme occurs in the cytoplasm of the cell, and that nuclear concentrations vary from tissue to tissue. A theory relating the DNAase activity of the cell to its over-all desoxypentose nucleotide metabolism is discussed. No evidence has been found for the presence of inhibitors of the "acid" DNAase in animal tissues.     

Repair of depurinated DNA with enzymes from rat liver chromatin.

DNA from T7 phage containing AP (apurinic/apyrimidinic) sites was repaired by the successive actions of three chromatin enzymes [AP endodeoxyribonuclease, DNAase IV (5'----3'-exodeoxyribonuclease) and DNA polymerase-beta] prepared from rat liver and T4-phage DNA ligase. Since DNA ligase is also found in rat liver chromatin, all the activities used for the successful repair in vitro are thus present in the chromatin of a eukaryotic cell. Our results show, in particular, that the chromatin DNAase IV is capable of excising the AP site from the DNA strand nicked by the chromatin AP endodeoxyribonuclease. We did not try to combine all the enzymes, since competition between some of them might have prevented the repair; we have, for instance, shown that DNA ligase can seal the incision 5' to the AP site made by the AP endodeoxyribonuclease. Changes in chromatin structure during repair might perhaps prevent this competition when nuclear DNA is repaired in the living cell.     

Effect of exogenous DNAses on various stages of DNA replication in microorganisms

Effect of DNAase 1 on DNA synthesis and cell division was studied in microorganisms deficient in some stages of DNA replication initiation. The DNA synthesis induced by exogenous DNAase was found to be a replicative origin since it was registered from the "origin" of chromosomal replication under the conditions of initiation of proteins functioning. Stimulation of DNA synthesis in bacterial cells having mutations in DNA B and DNA G genes by DNAase 1 indicates that exogenous DNAases participate in replicative fork during the DNA synthesis.     

Nucleosome structure in Aspergillus nidulans

The structure of chromatin from Aspergillus nidulans was studied using micrococcal nuclease and DNAase I. Limited digestion with micrococcal nuclease revealed a nucleosomal repeat of 154 base pairs for Aspergillus and 198 base pairs for rat liver. With more extensive digestion, both types of chromatin gave a similar quasi-limit product with a prominent fragment at 140 base pairs. The similarity of the two limit digests suggests that the structure of the 140 base pair nucleosome core is conserved. This implies that the difference in nucleosome repeat lengths between Aspergillus and rat liver is caused by a difference in the length of the DNA between two nucleosome cores. Digestion of Aspergillus chromatin with DNAase I produced a pattern of single-stranded fragments at intervals of 10 bases which was similar to that produced from rat liver chromatin.     

Characterization of alkaline nuclease from rat liver mitochondria.

The alkaline nuclease (pH optimum 9.0) has been purified about 500-fold in 25% yield from the extract of rat liver mitochondria. The enzyme cleaves yeast RNA, poly(U), poly(U), poly(C) and denatured DNA to yield oligonucleotides with 5'-phosphoryl and 3'-hydroxyl ends. The enzyme has a molecular weight of about 60 000, a sedimentation coefficient of 4 S and an isoelectric point of 9.0. The behaviors of RNAase activity of the nuclease are identical with those of DNAase activity in column chromatography as well as in catalytic nature. The affinities of RNAase activity for substrate, Mg2+, spermidine and polyvinyl sulfate are lower than those of DNAase activity. The alkaline nuclease activity measured in the homogenate of regenerating rat liver is not significantly changed.     

ACTION OF MITOCHONDRIAL DNAASE I IN DESTROYING THE CAPACITY OF ISOLATED CELL NUCLEI TO FORM GELS

1. DNA prepared from non-gelable rat liver nuclei isolated in the presence of disrupted mitochondria at pH 6.0, has been compared with DNA obtained from gelable nuclei isolated at pH 4.0. The DNA of the non-gelable nuclei is partially depolymerized relative to the DNA of the gelable nuclei. 2. It has been found that sufficiently small quantities of crystallized DNAase I can cleave a very large part of the DNA of gelable nuclei isolated at pH 4 from the residual protein of these nuclei without causing extensive depolymerization of the DNA. At the same time the gelable nuclei are rendered non-gelable. 3. Partially purified DNAase II can also render gelable nuclei isolated at pH 4 non-gelable, and in so doing presumably also cleaves the DNA from the residual protein of the nuclei. 4. Mitochondrial DNAase I appears to be the enzyme responsible to a large extent for the cleavage of DNA from the residual protein of gelable rat liver cell nuclei with concomitant destruction of the gel-forming capability of these nuclei, when the nuclei are subjected to the action of disrupted mitochondria at pH 6.0 during the isolation procedure. 5. Mitochondrial DNAase II does not appear to exert appreciable action on nuclei during the course of isolation of the nuclei at pH 6.0 in the presence of disrupted mitochondria. 6. It is probable that DNAase I is not the sole enzyme responsible for destroying the gelability of nuclei isolated at pH 6.0 in the presence of disrupted mitochondria. Protease may be involved. 7. Sodium dodecyl sulfate at pH 6.0–6.3 cleaves the DNA of isolated gelable nuclei from the residual protein of these nuclei over a period of 2 to 3 hours. At pH 7.0–7.5, however, there is negligible cleavage over a period of 96 hours. 8. If non-gelable nuclei are isolated at pH 6.0 in the presence of disrupted mitochondria, DNA subsequently can be removed from them by the use of detergent at pH values ranging from 6.0–7.5 without the necessity of incubation in the detergent solution, since the DNA had already been detached from the residual protein by the action of the mitochondrial enzyme system during isolation of the nuclei.     

Nuclear DNAase of the yeast Candida tropicalis

Using stepwise extraction of chromatin from Candida tropicalis by NaCl (0.1-1.0 M) the protein dissociated by 0.3 and 0.6 M NaCl (fractions 0.3 and 0.6) possessing the DNAase activity were obtained. These DNAases are activated by Mg2+ and cause preferential hydrolysis of heat-denaturated DNA. Fraction 0.3 DNAase has a maximum at neutral values of pH (around 7.0) and causes endonucleolytic hydrolysis of DNA. Fraction 0.6 DNAase causes exonucleolytic hydrolysis of DNA but a maximum at alkaline pH (8.0). The properties of isolated chromatin DNAases of Candida tropicalis differ from those of the known DNAases of the yeast Saccharomyces cerevisiae.     

Effect of Ca2+, Mg2+-dependent deoxyribonuclease on DNA synthesis in cell nuclei from embryos of the sea urchin Strongylocentrotus intermedius

The sea urchin embryo nuclei which retained their ability to maintain the DNA synthesis in an in vitro system were isolated. The DNA synthesis isolated nuclei was shown to be an ATP-dependent process which is inhibited by low concentrations of actinomycin D, a polymerase alpha araCTP inhibitor. The newly synthesized DNA is represented by short fragments of about 4S. After addition of Ca2+, Mg2+-dependent DNAase to sea urchin embryo nuclei, the synthesis of short DNA fragments is enhanced. This stimulating effect of Ca2+, Mg2+-dependent DNAase is ATP-dependent and is observed only within a narrow range of enzyme concentrations (of the order of 1-5 units of DNAase activity per ml of incubation sample). The increase in the enzyme concentration to 10 or more units of activity results in the depression of DNA synthesis. It is concluded that DNA replication in sea urchin embryo nuclei depends on the presence of active DNAases as well as on the number of accessible initiation sites of DNA replication.     

Neutral sphingomyelinase: Localization in rat liver nuclei and involvement in regeneration/proliferation

We have studied the localization of neutral sphingomyelinase (N-SMase) in rat liver nuclei. The levels of neutral sphingomyelinase in regenerating liver nuclei were also assessed.We found that rat liver nuclei contain a sphingomyelinase having a pH optima of 7.2 and a kDa of 92. In intact nuclei, neutral sphingomyelinase was associated predominantly with the nuclear envelope. In regenerating/proliferating rat liver (during DNA synthesis), neutral sphingomyelinase was translocated from the nuclear envelope to the nuclear matrix. The levels of sphingomyelin in whole nuclei decreased in reverse proportion to an increase in the levels of neutral sphingomyelinase. By contrast, there was a corresponding increase in the levels of ceramide and sphingosine during cell regeneration/proliferation. Thus, endogenous nuclear neutral sphingomyelinase may play a role in the regulation of sphingomyelin levels and in relevant signal transduction reactions involving cell regeneration/proliferation. The potential significance of ceramide generation may be aimed at programmed cell death to allow the regeneration of liver mediated via target proteins such as, ceramide activated protein kinases/phospholipases or other unknown mechanisms.Abbreviations N-SMase neutral sphingomyelinase - A-SMase acid sphingomyelinase     

Different repeat lengths in rat satellite I DNA containing chromatin and bulk chromatin.

The nucleosome repeat structure of a rat liver chromatin component containing the satellite I DNA (repeat length 370 bp) was investigated. Digestion experiments with micrococcal nuclease, DNAase II, and the Ca2+/Mg2+-dependent endogenous nuclease of rat liver nuclei revealed a repeat unit of 185 nucleotide pairs which is shorter by approximately 10 bp than the repeat unit of the bulk chromatin of this cell type. The difference seems not to be related to the histone composition which was found to be similar in the two types of chromatin.     

Deoxyribonuclease II as a probe for chromatin structure. I. Location of cleavage sites

DNAase II has been shown to cleave condensed mouse liver chromatin at 100-bp² intervals while chromatin in the extended form is cleaved at 200-bp intervals (Altenburger et al., 1976). Evidence is presented here that DNA digestion patterns of a half-nucleosomal periodicity are also obtained upon DNAase II digestion of chicken erythrocyte nuclei and yeast nuclei, both of which differ in their repeat lengths (210 and 165 bp) from mouse liver chromatin. In the digestion of mouse liver nuclei a shift from the 100-bp to the 200-bp cleavage mode takes place when the concentration of monovalent cations present during digestion is decreased below 1 mM. When soluble chromatin prepared by micrococcal nuclease is digested with DNAase II the same type of shift occurs, albeit at higher ionic strength.In order to map the positions of the DNAase II cleavage sites on the DNA relative to the positions of the nucleosome cores, the susceptibility of DNAase II-derived DNA termini to exonuclease III was investigated. In addition, oligonucleosome fractions from HaeIII and micrococcal nuclease digests were end-labelled with polynucleotide kinase and digested with DNAase II under conditions leading to 100 and 200-bp digestion patterns. Analysis of the chain lengths of the resulting radioactively labelled fragments together with the results of the exonuclease assay allow the following conclusions. In the 200-bp digestion mode, DNAase II cleaves exclusively in the internucleosomal linker region. Also in the 100-bp mode cleavage occurs initially in the linker region. Subsequently, DNAase II cleaves at intranucleosomal locations, which are not, however, in the centre of the nucleosome but instead around positions 20 and 125 of the DNA associated with the nucleosome core. At late stages of digestion intranucleosomal cuts predominate and linkers that are still intact are largely resistant to DNAase II due to interactions between adjacent nucleosomes. These findings offer an explanation for the sensitivity of DNAase II to the higher-order structure of chromatin.     

DNAase I sensitivity of genes expressed during myogenesis.

Cultures of a rat myogenic cell line were used to examine the question of whether in proliferating precursor cells genes which are programmed to be expressed later in development, in the same cell lineage, differ in DNAase I sensitivity from genes which are never expressed in these cells. Nuclei isolated from proliferating mononucleated myoblasts, differentiated cultures containing multinucleaged fibers, and rat brain, were treated with DNAase I. The sensitivity of the genes coding for the muscle-specific alpha-actin, myosin light chain 2 and the nonmuscle beta-actin was measured by blot hybridization of nuclear DNA with the corresponding cloned cDNA and genomic DNA probes. The sensitivity of these genes was compared to that of a gene not expressed in the muscle tissue. The results showed that in the muscle precursor cells, the potentiality of tissue-specific genes to be expressed is not reflected in DNAase I sensitivity. The changes which render these genes preferentially sensitive to DNAase I take place during the transition to terminal differentiation. The results showed also that the region of DNAase I sensitivity of the alpha-actin gene in the differentiated cells ends between 40 to 700 bp 5' to the structural gene. No DNAase I hypersensitive site was detected 5' to the alpha-actin gene.     

Nutritional regulation of differentiation and synthesis of an exocytoplasmic deoxyriboendonuclease in Streptomyces antibioticus

Streptomyces antibioticus produces a cell-wall-located deoxyriboendonuclease (DNAase) the synthesis of which in submerged and surface cultures is related to the growth rate. DNAase synthesis always preceded aerial mycelium formation in surface cultures. Production of aerial mycelium began at the end of exponential growth or in the early stationary phase; it was absent in cultures grown on nutrient agar/glucose or in media with a high concentration of casein hydrolysate. These nutritional conditions also impaired production of the DNAase. External DNA substrates were not degraded by mycelium producing the DNAase. These observations lead us to suggest a role for the enzyme in the developmental cycle of S. antibioticus.     

Nuclear endogenous Ca2+-dependent endodeoxyribonuclease in differentiating chick embryonic lens fibers

During terminal differentiation of lens epithelial cells into fiber cells, nuclei become pycnotic and DNA degradation occurs. We investigated the putative role in this process of an endogenous DNAase. After incubation of isolated nuclei of both cell types at 37 degrees C, DNAase activity was revealed by DNA size analysis on 0.3-1% neutral and alkaline agarose, one- and two-dimensional gels. This DNAase activity is more prominent in lens fiber nuclei than in epithelial nuclei at all the embryonic stages probably because of a preexisting higher concentration of divalent cations in the former. This activity is calcium or magnesium dependent in both types of nuclei.     

Interaction of lysine-rich histone and DNA in chromatin structure.

The heat denaturation and renaturation curves of rat liver and ascites hepatoma (AH 108A) chromatins were measured. In these renaturation curves, there are small sigmoidal regions. These sigmoidal regions remained in redenaturation curves and were largely stable to DNAase I digestion. When the chromatins were treated stepwise with NaClO4 and lysine-rich histones were removed, the sigmoidal regions in the renaturation curves disappeared. These results suggested that the sigmoidal regions reflected the interaction of DNA and lysine-rich histones.