DNA recombination in vitro initiated by Ca/Mg-dependent endonuclease from cell nuclei of human splenocytes

The system of DNA recombination in vitro was constructed. It comprises two plasmids, the derivatives of pBR322 deleted in the genes for tetracycline resistance, and the recombinogenic extract of the thymus lymphocytes nuclei of mice. The system permits to study the effect of proteins and factors on the efficiency of recombination resulting in reconstruction of the tetracycline resistance gene. Double-strand cuts in one of the deleted plasmids were necessary for recombination. Double-strand cuts by Ca/Mg-dependent endonuclease of the human spleen lymphocytes nuclei were more efficient as compared with the ones of DNAase I, restriction endonucleases PaeI and SalI in the initiation of recombination. The possible role of Ca/Mg-dependent endonuclease in recombination in vivo is discussed.     

Isolation of Ca/Mg-dependent endonuclease of cell nuclei as the basic component in the chromatin nuclease complex of human lymphocytes

Highly purified preparations of Ca/Mg-dependent cell nuclear endonuclease have been obtained from human spleen lymphocytes. The purification was 2000-fold, and the enzyme was a polypeptide with a molecular weight of 57-54 kD. The study of its binding with monoclonal antibody enzyme, produced by various hybridoma strains obtained upon the immunization of mice with non-fractionated nuclear extract has shown that Ca/Mg-dependent endonuclease was the best expressed endonuclease of lymphocyte cellular nuclei. Possible production of some other cell nuclear endonucleases during processing of CH/Mg-dependent endonuclease is suggested.     

Characteristics of the effect of Ca/Mg-dependent endonuclease from cell nuclei of human lymphocytes on J kappa-cluster of immunoglobulin genes

The cleavage of the murine J kappa-segments by purified Ca/Mg-dependent endonuclease was studied. The enzyme was shown to cleave specifically the J kappa-segments introducing the double strand breaks in 5'-regions of the J kappa-genes. The number of thus generated discreet fragments does not change during incubation. Specificity of the enzyme is not changed by substitution of Ca/Mg for Mn. The enzyme activity is inhibited by 0.1 M NaCl as well as its specificity. Comparison of the enzyme with the known nuclease activities that cleave specifically the J kappa-segments demonstrated that the activities of the latter are determined by Ca/Mg-dependent endonuclease. The results suggest the possible participation of Ca/Mg-dependent endonuclease in Ig-genes recombination.     

Specificity of fragmentation of DNA from pBR322 plasmid by Ca,Mg-dependent endonuclease from cell nuclei of human lymphocytes

Fragmentation of the plasmid pBR322 DNA by a purified preparation of Ca/Mg-dependent endonuclease has been studied. It was shown that on the first steps of reaction the double-stranded cuts are introduced into the superhelical DNA independent of singlestranded ones. The doublestranded cuts are introduced into superhelical and linear DNA in 12 sites enriched with GC-pairs, 9 of them include pentanucleotide CGCGG(CCGCC) that is functionally significant. Relaxation of the plasmid DNA by topoisomerase I blocks the sitespecific action of the enzyme. Ca/Mg-dependent endonuclease is concluded to be topologically dependent enzyme, possibly, participating in the recombination processes.     

Use of monoclonal antibodies in comparative studies of Ca, Mg-dependent endonuclease in cell nuclei

Eight hybridoma cell lines derived from fusion between myeloma X-63 and mouse splenocytes were found to secrete monoclonal antibodies against Ca/Mg-dependent endonuclease of human spleen cell nuclei. Two of them, termed N and S, were used in comparative research of enzymes from different organs and species of animals. The data obtained show that N and S antibodies recognize different antigenic determinants of the enzyme molecule. Cross-reactions of antibodies with different antigens having similar antigenic determinants, exist in Ca/Mg-endonuclease of such species as man, mouse, rat and cattle. The evolutionary conservatism of this enzyme is suggested. The data show that the existence of tissue-specific (thymus-specific and spleen-specific) isoforms of Ca/Mg-endonuclease of cell nuclei is possible.     

Changes in Ca, Mg-dependent endonuclease of DNA in isolated nuclei of human lymphocytes in lymphoproliferative diseases

Ca, Mg-dependent endonuclease is one of the main DNAses of lymphocyte chromatin. It's activity is known to increase in the immune response and to decrease in spontaneous and experimental CLL. These observations became a basis for analysis of possible clinical meaning of it's enzymatic activity assay. Donors' peripheral blood lymphocytes being tested, normal level of endonucleolysis for men and children was defined. Except that patients with different clinical forms of lymphoproliferative diseases such as chronic lympholeukemia, non-Hodgkin lymphomas, Hodgkin's disease were observed. The results showed that Ca, Mg-dependent endonucleolysis activity was decreased in comparison to donors' one. Ca, Mg-dependent endonucleolysis activity was the same in the group of patients with non-malignant pathology and in donors' one. Successful treatment and remission state of our patients was associated with alteration of the Ca, Mg-dependent endonucleolysis activity to normal level as well as immunological parameters. That is why the activity of Ca, Mg-dependent endonucleolysis is suggested to be a new criterion of immune state and lymphocyte malignant transformation.     

Ca/Mg-dependent endonuclease from porcine liver. Purification, properties, and sequence specificity

A rapid and reproducible method for the purification of the Ca/Mg-endonuclease from porcine and rat liver and for the stabilization of the enzyme activity is presented. The optimum conditions for enzyme activity were determined. The enzyme degrades double-stranded DNA endonucleolytically. In the course of digestion of form I closed circular SV 40 DNA, the form II nicked circular DNA is the prominent intermediate product. Digestion of hen erythrocyte nuclei with added endonuclease produces a ladder of mono- and oligonucleosomal fragments similar to that generated by micrococcal nuclease digestion. Determination of the 5'-terminal nucleotides indicates the absence of a significant base specificity. Analyzing the cleavage pattern of end-labeled pBR322 restriction fragments on sequencing gels shows that the enzyme exhibits a weak preference for dinucleotides with A in the 5'-position; dinucleotides with 5%-C are less readily cleaved. Digestion of end-labeled pBR322 DNA, followed by electrophoresis in agarose gels produces a "smear"-like fragmentation pattern with weak superimposed bands, while micrococcal nuclease generates a different and much more distinct pattern. These data show that the sequence specificity of the enzyme is less pronounced than that of micrococcal nuclease and that the sites preferentially cleaved are not the same.     

Ca, Mg-dependent endonuclease activity in different subpopulations of spleen cells from normal and erythroleukemic mice

We have detected Ca²⁺,Mg²⁺-dependent endonuclease activity in spleen cells of normal, Friend erythroleukemic, and phenylhydrazine-treated mice. When nuclei were isolated and incubated in the presence of Ca²⁺ and Mg²⁺ ions, the activity resulted in the production of 3′-OH termini in the cellular DNA and the release of chromatin due to internucleosomal DNA fragmentation. This enzyme activity was chromatin-bound and could be extracted from chromatin in an active form in 0.35 M KC1. The majority of endonuclease activity from erythroleukemic spleens was present in nuclei of precursor erythroid cells of low buoyant density (1.025–1.05 g/ml). Uninfected normal splenic tissue contained an endonuclease activity which was almost entirely confined to a B-lymphocyte population of high buoyant density (>1.07 g/ml). Erythroid cell-enriched spleens from phenylhydrazine-treated mice exhibited a distribution of endonuclease activity in cells at low and high densities reflecting a mixture of erythroid and lymphoid cells. Cloned erythroleukemic cell lines propagated in vitro lacked cells of low density and showed no detectable endonuclease activity. However, nuclei from these cell lines were susceptible to exogenously added endonuclease extracted from erythroleukemic spleen cells. These same cell lines propagated as subcutaneous tumors contained endonuclease activity and a morphologically-similar low-density cell population which accounted for the endonuclease activity in these tumors. Nuclei from cloned lymphoid cell lines, representing different B-lymphocyte phenotypes, showed differences in the presence of endonuclease activity. Among the cell lines tested, only those expressing late B-cell markers showed detectable endonuclease activity.     

Role of a disorder in poly(ADP-ribosylation) in the activation of Ca/Mg-dependent endonuclease

The nuclei from the control and irradiated (3 h after irradiation at a dose of 10 Gy) thymocytes were preincubated with NAD in conditions optimal for poly (ADP) ribosylation. This was shown to decrease by 6-7- and 2-3 times, respectively, the rate of autolytic cleavage of DNA by Ca/Mg-dependent endonuclease. The inhibitors of poly (ADP-riboso)-polymerase, nicotine amide and thymidine, removed the effect of NAD. The data obtained prompt an assumption that the post-irradiation activation of Ca/Mg-nuclease in thymocytes is associated with the disturbance of its post-translation modification, poly(ADP)ribosylation.     

Ca/Mg-dependent endonuclease as a probe for detecting chromatin changes in lymphocytes in chronic lymphoid leukemia

Chromatin fragmentation of bovine peripheral blood lymphocytes from normal animals and the ones suffering from chronic lympholeucosis (CLL) by DNase I, micrococcal nuclease and purified Ca/Mg-dependent endonuclease from nuclei of human splenocytes was studied. The lymphocytes chromatin from CLL animals was shown to be more resistant to nucleases, than the one from normal animals. It was found that difference between fragmentation of chromatin samples from normal and CLL bovines was more dramatic when Ca/Mg- dependent endonuclease was used versus traditionally exploited DNase I and micrococcal nuclease. The data suggest that purified Ca/Mg-dependent endonuclease can be a useful enzymatic probe for detection of lymphocytes chromatin changes during CLL.     

Isolation and purification of calcium and magnesium dependent endonuclease from rat liver nuclei

An endonuclease associated with rat liver chromatin was extracted with 0.6 M NaCl and purified by ammonium sulfate fractionation and Sephadex G-100 gel filtration. The enzyme produces single strand scissions on native DNA at neutral pH in the presence of 1 mM CaCl₂ and 5 mM MgCl₂. Alkali-denatured DNA was not nicked by the enzyme. Omission of Ca²⁺ reduced the enzyme activity to about one seventh. Without Ca²⁺, however, Mn²⁺ was more effective than Mg²⁺. The molecular weight of the enzyme is about 27,000.     

Isolation of the protein B23/nucleophosmin from HeLa cell nuclei

Endogenous forms of the protein B23 were for the first time isolated from HeLa cell nuclei and their structural states were analyzed. It was demonstrated that incubation of HeLa cell nuclei in 10 mM Tris-HCl buffer (pH 7.4) led, not only to their swelling, but also to the release of several nuclear proteins, including the protein B23. PAGE of the supernatant fraction allowed nine major stained protein bands to be detected; the bands were identified by MALDI mass spectrometry (matrix-assisted laser desorption and ionization). The proteins in the range of 35–40 kDa were identified as nucleophosmin, glyceraldehyde 3-phosphate dehydrogenase (GAPDH), and heterogeneous nuclear ribonucleoprotein (hnRNP) A2/B1. Analysis of the N- and C-terminal amino acid sequences showed the presence of the isoforms B23.1 and B23.2, GAPDH, and the isoform hnRNP B1 and made it possible to describe the C-and N-terminal processing patterns and demonstrate the presence of isoform B23.2 at a protein level.     

Isolation of the protein B23/nucleophosmin from HeLa cell nuclei

Endogenous forms of the protein B23 were for the first time isolated from HeLa cell nuclei and their structural states were analyzed. It was demonstrated that incubation of HeLa cell nuclei in 10 mM Tris-HCl buffer (pH 7.4) led, not only to their swelling, but also to the release of several nuclear proteins, including the protein B23. PAGE of the supernatant fraction allowed nine major stained protein bands to be detected; the bands were identified by MALDI mass spectrometry (matrix-assisted laser desorption and ionization). The proteins in the range of 35-40 kDa were identified as nucleophosmin, glyceraldehyde 3-phosphate dehydrogenase (GAPDH), and heterogeneous nuclear ribonucleoprotein (hnRNP) A2/B1. Analysis of the N- and C-terminal amino acid sequences showed the presence of the isoforms B23.1 and B23.2, GAPDH, and the isoform hnRNP B1 and made it possible to describe the C- and N- terminal processing patterns and demonstrate the presence of isoform B23.2 at a protein level.     

Isolation and restriction endonuclease analysis of mycobacterial DNA

A method for the isolation of DNA from mycobacteria propagated in vitro is described that utilizes organic solvents to extract lipoidal components from the outer membrane, and digestion with a protease (nagarse) and lysozyme to penetrate the cell wall. The mycobacterial cells were lysed by the addition of detergent and the DNA was purified by digestion with pronase, sequential phenol and chloroform extractions, and digestion with RNAase A. The isolated DNA, which was obtained in good yields, was of a relatively high Mr and could be readily digested by restriction endonucleases. By this method, the genomes of Mycobacterium avium, M. intracellulare, M. lepraemurium, 'M. lufu', M. marinum, M. phlei, M. scrofulaceum, M. smegmatis and M. tuberculosis were isolated and the restriction endonuclease digestion patterns analysed. Each species could be distinguished by the digestion patterns, indicating that this approach can be used for identifying mycobacterial species. This approach is also sufficiently sensitive to differentiate strains since we were able to distinguish two independently isolated strains of M. tuberculosis, H37 and H4. In addition, no evidence was obtained for the presence of methylcytosine residues in the sequences 5'.CCGG.3',5'.CCCGGG.3',5'.CC(A/T) GG.3' or for methyladenine at 5'.GATC.3' in the DNA of the nine mycobacterial species examined using pairs of restriction enzymes that recognize and cleave at the same nucleotide sequence but differ in their sensitivity to 5-methylcytosine or 6N-methyladenine.     

Single-turnover analysis of mutant human apurinic/apyrimidinic endonuclease

Apurinic/apyrimidinic endonuclease (AP endo) is a key enzyme in the repair of oxidatively damaged DNA. Using single-turnover conditions, we recently described substrate binding parameters for wild type human AP endo. In this study, we utilized four enzyme mutants, D283A, D308A, D283A/D308A, and H309N, and assayed them under steady state and single-turnover conditions. The turnover number of the single aspartate mutants was decreased 10-30-fold in comparison to that of the wild type. The decrease in the turnover number was accompanied by a 17- and 50-fold decrease in the forward rate constant (kon) for substrate binding by D308A and D283A, respectively. The dissociation rate constant for substrate (koff) was unchanged for the D308A mutant but was 10 times faster for the D283A mutant than for the wild type. The apparent Km values for both of the single aspartate mutants were about equal to their respective KD values. To account for the kinetic behavior of the D308A mutant, it was necessary to insert a conformational change into the kinetic scheme. In contrast to the single aspartate mutants, the turnover number for the double mutant was 500-fold lower than that of the wild type, its apparent Km was 2.5-fold higher, and binding to substrate was weak. Mutation of His309 caused the greatest decrease in activity, resulting in a turnover number that was more than 30000-fold lower than that of the wild type and an apparent Km that was 13-fold higher, supporting the notion that His309 is intimately involved in catalysis. Molecular dynamics simulation techniques suggested that conversion of either aspartate to alanine resulted in major shifts in the spatial localization of key amino acids. Despite the fact that the two aspartates flank His309, the movement they engendered was distinct, consistent with the differences in catalytic behavior. We suggest that the conformation of the active site is largely maintained by the two aspartates, which enable efficient binding and cleavage of abasic site-containing DNA.     

Isolation of intact nuclei from Euglena gracilis

A method for the isolation of nuclei from the lower eukaryote, Euglena gracilis, utilizing MES buffer at pH 5.5 and sodium meta bisulfite is presented. The method takes advantage of the finding that sodium meta bisulfite reversibly alters the density of the nuclei allowing them to be separated from cytoplasmic fragments and unbroken whole cells. Nuclei are obtained in a yield of 25–37 %, appear intact ultrastructurally, and contain acid-soluble proteins in an amount relatively the same as found in higher cell nuclei.     

Isolation and restriction endonuclease analysis of a mycoplasma plasmid

A 1.7-kb plasmid was isolated from a large colony type strain of Mycoplasma mycoides subsp. mycoides. It was cloned into the Escherichia coli vector M13mp19, and DNA from the resultant recombinant was used to construct a restriction map of the plasmid. Because mycoplasmas show deviation from normal coding patterns, the availability of a mycoplasma plasmid could be useful in the development of a cloning vector for them.