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Histochemical correlation between glycogen, nucleic acids and nucleases in pre-neoplastic and neoplastic lesions of rat liver after short-term administration of N-nitrosomorpholine.

After 7 weeks of oral administration of the carcinogen N-nitrosomorpholine (12 mg NNM ad 100 ml of drinking water) to male rats, marked hepatocellular changes were found predominantly in the centers of the lobules. These were loss of glycogen, disorganisation of the basophilic bodies and, sometimes, loss of cytoplasmic basophilia or pyroninophilia, necrotic cells and increase in the activity of acid DNAse and RNAse. These centrilobular alterations were reversible after withdrawal of the carcinogen. They are, therefore, attributed to the nonspecific-toxic effect of the carcinogen. In peripheral and midzonal regions of the lobules basically different cellular changes appeared which were unimportant during the phase of intoxication, but became prominent after cessation of the carcinogenic treatment. These lesions were: excessive storage of glycogen, displacement of basophilic bodies and an increase in cytoplasmic acidophilia. The hepatocytes showing these cytoplasmic changes initially formed foci. Neoplastic nodules and frank hepatocellular carcinomas developed later. During these later stages of the experiment both the foci and the nodules consisted of 4 main types of altered hepatocytes: 1) "clear" glycogen storage cells, 2) acidophilic cells, 3) vacuolated (fat storing) cells, 4) basophilic (pyroninophilic) cells poor in, or free from, glycogen. The larger nodules and carcinomas contained predominantly basophilic cells. The activity of nucleases, especially that of acid DNAse, decreased in small foci which as a rule developed later than the foci of glycogen storage. In most cells of neoplastic nodules and carcinomas the activity of these enzymes disappeared, but it reappeared in necrotic cells. The progressive alterations in the activity of the nucleases seemed to be related to the phenotypic expression of malignancy and could be a sign of a fundamental metabolic change taking place during a relatively late step in the malignant transformation.

Animals↗

Excision of chromosomal DNA loops by treatment of permeabilised cells with Bal 31 nuclease.

The specificity of long-range fragmentation of human nucleolar genes by Bal 31 nuclease was studied using fractionation of cleavage products by pulsed field gel electrophoresis, followed by Southern hybridization. It was found that limited treatment of permeabilised cells with this nuclease results in accumulation of DNA scissions in matrix attachment areas. Consequently, chromosomal DNA loops and their oligomers are released from the genome.

Cell Line↗

Characterization of restriction nuclease prepared chromatin by electron microscopy.

Chromatin was solubilized from rat liver nuclei by digestion with the restriction nuclease EcoRI or HaeIII in the presence or absence of EDTA and sodium chloride. The samples were investigated by electron microscopy after positive and negative staining with uranyl acetate under a number of conditions. Depending on the salt concentration during solubilization the chromatin appeared as beads on the string or in more compact form. Solenoid- and superbead-like structures were seen as had been reported for chromatin solubilized with micrococcal nuclease.

Animals↗

Nuclease activity in human metaphase chromosomes substituted with 5'-bromodeoxyuridine.

Human metaphase chromosomes, substituted with 5'-bromodeoxyuridine (BrdUrd) for one, two or three rounds of replication, were briefly pretreated with ultraviolet light (UV), in the presence of 33258 Hoechst, and subsequently digested with either exonuclease III or S1 nuclease. Pretreatment alone was not sufficient to induce sister chromatid differential staining (SCD), but allowed subsequent digestion with exonuclease III or S1. Such enzymes were found to induce SCD with ethidium bromide, as unifilarly BrdUrd-substituted chromatids (TB) were more resistant than bifilarly substituted chromatids (BB). Other experiments with DNase I or the AluI and HaeIII restriction endonucleases showed that only HaeIII was capable of inducing SCD by attacking BB more than TB chromatids preincubated with UV in the presence of Hoechst. SCD with exonuclease III/S1 nuclease seems to be due to (1) UV-induced DNA debromination occurring twice in BB as opposed to TB chromatids, and (2) alteration of chromatin protein structure occurring to a different extent in differently BrdUrd-substituted chromatids. Our findings with endonucleases, on the contrary, may depend on the capacity of enzymatic cleavage to cancel the different protein alterations induced differentially by UV in TB as opposed to BB chromatids.

Bromodeoxyuridine↗

Chromatin regions, released by endogenous nucleases, are enriched in immunogenic tissue-specific proteins.

Localization of immunogenic tissue-specific proteins in chromatin regions, hypersensitive to endogenous nucleases, has been studied using rabbit antibodies against rat thymus chromatin. It is shown that the first 1-2,5% of the chromatin (calculating on DNA), released by Mg2+-, Mn2+- and Ca2+/Mg2+-dependent nuclear endonucleases are drastically enriched in tissue-specific antigenic determinants. The released chromatin fractions are found to contain a heterogeneous set of nonhistone proteins and are deficient in histones. The cleavage of nuclear DNA by endogenous acidic nuclease, independent on bivalent ions, resulted in a significantly less enrichment of the released fractions with immunogenic proteins.

Animals↗

Partial purification and characterization of a double-stranded RNA-specific nuclease from human placenta.

A double-stranded RNA-specific nuclease (ds RNase) has been isolated and partially purified from human placenta by DEAE-cellulose and DNA-cellulose column chromatography. Denatured DNA-cellulose retained most of the single-stranded RNA-specific nuclease (ss RNase) activity, whereas the ds RNase came out in the void volume. N-ethylmaleimide at a concentration of 5 mM, selectively inhibited ds RNase activity by 60% under the conditions in which the ss RNase activity was inhibited to an extent of 7%. The ds RNase was specifically inhibited by Penicillium chrysogenum viral ds RNA and by ethidium bromide. The partially purified ds RNase showed requirements for Mg+ whereas Mn2+ and NH4+ ions were inhibitory. The DEAE-enzyme cleaved 32P-labelled 45S ribosomal precursor RNAs from Yoshida ascites sarcoma cells into species that had similar electrophoretic mobilities as the mature rRNAs.

Ammonia↗

Characterization of plant satellite DNA using restriction nucleases.

The structural organization of satellite DNAs of mustard Brassica nigra and lemon Citrus limon has been studied by digestion with restriction nucleases. Analysis of DNA products produced by EcoRI and Bam I shows that two satellite DNAs contain long range periodicities belonging to several repeated sequences. The periodicities in two satellite DNAs differ characteristically, however, they have been found to contain common homologous sequences. Using the restriction nuclease Bsp I, a highly periodical fractions has been found in Citrus satellite DNA, composed of Bsp I fragments ranging from 80 to 1240 basepain. The major repeat units comprise five Bsp I fragments ranging from 80 to 200 bp. These fractions characterized by a high content of 5-methyl-cytosine.

DNA Restriction Enzymes↗

Relationship between expression of a major apurinic/apyrimidinic endonuclease (APEX nuclease) and susceptibility to genotoxic agents in human glioma cell lines.

The multifunctional DNA repair enzyme (APEX nuclease) having apurinic/apyrimidinic (AP) endonuclease, 3'-5' exonuclease, DNA 3' repair diesterase and DNA 3'-phosphatase activities is thought to be involved in repair of AP sites and single-strand breaks with 3'-blocked termini. To investigate the biological role of the enzyme, we studied the correlation between APEX AP endonuclease activity in several human glioma cell lines having various degree of its expression and cellular susceptibility to cytotoxic agents such as methyl methanesulfonate (MMS), 1-(4-amino-2-methyl-5-pyrimidinyl)methyl-3- (2-chloroethyl)-3-nitrosourea hydrochloride (ACNU), cis-diamminedichloroplatinum(II) (CDDP), etoposide (VP-16), hydrogen peroxide (H2O2), hyperthermia and X-ray. The cell lines having lower APEX expression showed higher sensitivity to MMS and H2O2 which are known to induce AP sites and single strand breaks on DNA, respectively. The cellular susceptibility to the other agents tested was not significantly correlated to the APEX expression. The present results are thought to support the notion that APEX nuclease plays an important role on repair of AP sites and single-strand DNA breaks with 3'-blocked termini in mammalian cells.

Antineoplastic Agents↗

Activity of nucleases in the rat brain during training with emotionally varying reinforcement.

Training of rats with emotionally positive and negative reinforcements leads to increase in activity of acid (pH of 5.0) and alkaline (pH of 8.0) nucleases in the neocortex, hippocampus, areas of the midbrain (including the hypothalamus, subthalamus, and thalamus), and caudal section of the brain stem. However, the dynamics of nuclease activation differ depending on the emotional type of reinforcement and level of trainability of the animals. When intensities of enzyme activity are compared in the structures investigated, maximal activation is found in the caudal section of the brain stem.

Animals↗

The US3 protein kinase of herpes simplex virus type 2 is associated with phosphorylation of the UL12 alkaline nuclease in vitro.

Herpes simplex virus type 2 (HSV-2) gene US3 encodes a serine-threonine protein kinase. We previously described the isolation of a US3-inactivated mutant which is able to replicate in Vero cells but not in murine macrophages. To learn more about the biological role of the US3 protein kinase, we have sought to identify the target proteins of the enzyme. Studies of in vitro phosphorylation with extracts of infected cells demonstrate that the US3 protein kinase is involved in phosphorylation of the UL12 alkaline nuclease in vitro, suggesting that the nuclease is a possible target of the protein kinase.

Animals↗

Overproduction of the ATP-dependent nuclease AddAB improves the structural stability of a model plasmid system in Bacillus subtilis.

The effect of the ATP-dependent exonuclease AddAB complex on the structural stability of plasmid pGP1 in Bacillus subtilis was studied. Using deletion mutagenesis and gene amplification techniques, B. subtilis strains were constructed either lacking or overproducing the AddAB complex, a key enzyme in homologous recombination. The deletion mutant possessed no residual ATP-dependent nuclease activity; in contrast, the nuclease activity was up to 30 times higher in lysates of strains carrying multiple copies of the addAB genes in the chromosome. Southern blot analyses of these strains indicated that a linear relationship exists between the number of chromosomal gene copies and the level of AddAB activity. The structural stability of pGP1 was analyzed in the AddAB-deficient and over-producing backgrounds. Frequencies of deletion formation in the plasmid, as monitored by the expression of the pGP1-encoded penP-lacZ fusion on media containing X-gal, were shown to be increased at least 25-fold in the addAB knock-out mutant, whereas the stability of pGP1 was improved up to 15-fold in strains overproducing the AddAB enzyme. A possible explanation for these findings is that interactions between AddAB and plasmid molecules prevent the formation of secondary structures that constitute potential deletion target sites, and thereby enhance the structural stability of plasmids.

Bacillus subtilis↗

Role of flhDC in the expression of the nuclease gene nucA, cell division and flagellar synthesis in Serratia marcescens.

We investigated in Serratia marcescens the functions of the flhDC operon, which controls motility and cell division in enteric bacteria. Included in our evaluations were investigation of cell division, flagellar synthesis and regulation of the expression of nuclease (encoded by the nucA(Sm) gene, one of the virulence factors). Interruption of the chromosomal flhDC operon in S. marcescens CH-1 resulted in aberrant cell division and loss of nuclease and flagella. Expression of nucA(Sm) and other mutated phenotypes was restored in the flhDC mutant by the induction of overexpression of flhDC in a multicopy plasmid. Multicopied flhDC also induced the formation of differentiated cells (polyploid aseptate cells with oversynthesis of peritrichous flagella) in broth culture using minimal growth medium. Expression of the flhDC operon showed positive autoregulation, and was growth phase dependent (upregulated in early log phase). In addition, flhDC expression was inhibited when the temperature increased from 30 to 37 degrees C, and when osmolarity was increased, but was not influenced by glucose catabolite repression. These results show that FlhD/FlhC is a multifunctional transcriptional activator involved in the process of cell differentiation, swarming and virulence factor expression.

Amino Acid Sequence↗

The quantitative analysis of multiple mRNA species using oligonucleotide probes in an S1 nuclease protection assay.

The quantitative measurement of steady-state mRNA levels is fundamental to the analysis of gene expression. A variety of techniques are widely used to achieve this including Northern blotting, RNase protection, and S1 nuclease protection. We describe here in detail a relatively recent extension of the S1 nuclease protection technique (1) in which radiolabeled oligonucleotides are used as probes in a solution hybridization assay (2). The principle advantage of this technique is that it allows, in a single RNA sample, the simultaneous measurement of the relative levels of at least six mRNA species, including that of a control mRNA. Further, a large number of RNA samples can be analyzed at one time.

Nucleic Acid Hybridization↗

Purification and characterization of a Serratia marcescens nuclease produced by Escherichia coli.

The primary structure and physical chemical properties were determined of a nuclease expressed and secreted by Escherichia coli. The plasmid p403-SD2 carried a DNA sequence isolated from Serratia marcescens encoding the enzyme. During cultivation of the E. coli cells, 85% of the enzyme was released to the growth medium. The enzyme was purified and exhibited a single band with a molecular weight about 30,600 daltons on SDS-PAGE similar to nuclease isolated from S. marcescens. The amino acid composition and the amino acid sequence determined directly confirmed the primary structure of 245 amino acids predicted from the DNA sequence, and, in addition, the two disulfide bridges were assigned. Several physical chemical properties were examined. The ability of the enzyme to cross the outer membrane is proposed to depend upon the formation of the proper structures during the folding process.

Amino Acid Sequence↗

DNA repair nucleases.

Stability of DNA largely depends on accuracy of repair mechanisms, which remove structural anomalies induced by exogenous and endogenous agents or introduced by DNA metabolism, such as replication. Most repair mechanisms include nucleolytic processing of DNA, where nucleases cleave a phosphodiester bond between a deoxyribose and a phosphate residue, thereby producing 5'-terminal phosphate and 3'-terminal hydroxyl groups. Exonucleases hydrolyse nucleotides from either the 5' or 3' end of DNA, while endonucleases incise internal sites of DNA. Flap endonucleases cleave DNA flap structures at or near the junction between single-stranded and double-stranded regions. DNA nucleases play a crucial role in mismatch repair, nucleotide excision repair, base excision repair and double-strand break repair. In addition, nucleolytic repair functions are required during replication to remove misincorporated nucleotides, Okazaki fragments and 3' tails that may be formed after repair of stalled replication forks.

Bacterial Proteins↗

A fluorogenic 5' nuclease (TaqMan) assay to assess dosage of a marker tightly linked to red skin color in autotetraploid potato.

We have recently identified an allele of dihydroflavonol 4-reductase ( dfr) that cosegregates with the ability of potato ( Solanum tuberosum L) to produce red pelargonidin-based anthocyanin pigments. A rapid assay to assess dosage of this allele in cultivated potato, an autotetraploid, would be useful for breeding programs that develop red-skinned cultivars. To identify regions of dfr that are conserved between alleles, as well as regions that are variable, a portion of the gene was sequenced from several cultivated and wild potato clones. In one region the sequence of the 'red' dfr allele differed at two nucleotide positions from the three other sequence classes observed. A fluorogenic oligonucleotide probe labeled with 6-FAM was designed to anneal specifically to the red allele in this region, while a second probe labeled with VIC was designed to anneal to the 'not-red' dfr alleles. PCR primers that annealed to conserved sequences flanking the variable region were also developed. When subjected to a fluorogenic 5' nuclease (TaqMan) allelic discrimination assay all diploid clones tested clustered into three distinct groups based on the relative amounts of FAM and VIC released. These three groups represented clones homozygous for the red allele, heterozygous for the red allele, and homozygous for the not-red allele(s). When tetraploid clones were tested they separated into five distinct clusters, three of which were shared with diploid clones. The five clusters were interpreted to represent clones quadruplex, triplex, duplex, simplex and nulliplex for the red dfr allele. This interpretation was supported by monitoring the segregation of red allele dosage in several tetraploid crosses. To the best of our knowledge this is the first report of a fluorogenic 5' nuclease assay being used for allelic discrimination in an autopolyploid.

Alcohol Oxidoreductases↗

Differential expression of human COMT alleles in brain and lymphoblasts detected by RT-coupled 5' nuclease assay.

RATIONALE: A common polymorphism, Val158Met, alters catechol- O-methyltransferase (COMT) enzyme activity and has been linked to psychiatric phenotypes. Bray et al. (2003) reported that COMT is subject to differential allele expression in brain, finding modest (13-22%) underexpression of a haplotype containing Val158. However, disparate findings by another group who used the same method, but in lymphoblasts, raise the issues of tissue specificity, magnitude of differential expression, and identity of loci altering expression. OBJECTIVES: We measured COMT allele expression ratios in heterozygous human lymphoblast cell lines and brains. METHODS: Using transcribed single nucleotide polymorphisms as endogenous reporters, we developed an RT-coupled 5' nuclease assay for allele expression ratios and applied it to 63 COMT rs4818(C>G) heterozygotes and 68 Val158Met [rs4680(G>A)] heterozygotes. RESULTS: For rs4818(C>G), the C allele was overexpressed relative to the G allele in 18 of 27 lymphoblast lines and 23 of 36 brains. For Val158Met, Met158 was overexpressed relative to Val158 in all (29 of 29) lymphoblast lines and all (39 of 39) brains. Each of the 22 rs4818 heterozygotes without differential allele expression was a Val158/Val158 homozygote. The Met158 allele was overexpressed by 65-77% when compared with Val158 in lymphoblasts and brain. Haplotype augmented ability to predict expression in brain only. However, the expression of the Val158 allele on the high-expressing haplotype was only 19% higher than Val158 alleles on the other haplotype background. CONCLUSIONS: COMT alleles are differentially expressed. The Met158 allele predicts higher mRNA expression in both brain and lymphoblasts. As exemplified here, the RT-coupled 5' nuclease assay is a reliable method for the quantitative evaluation of cis-acting regulatory effects.

Alleles↗

Yeast silencers create domains of nuclease-resistant chromatin in an SIR4-dependent manner.

Previous analysis of the repression of the silent mating type loci in Saccharomyces cerevisiae has linked the mechanism of silencing to the formation of a chromatin domain at the silenced loci. In this study, a TRP1 reporter gene was used to examine changes in chromatin structure in a neutral environment. This enabled the chromatin structure organized by yeast silencers to be compared directly with changes effected by the yeast alpha2 repressor. It was found that silencers mediate the formation of lengthy nuclease-resistant domains on the DNA, rather than specifically positioning nucleosomes over promoter regions as the alpha2 repressor does. Silencing at the TRP1 reporter gene closely resembled silencing at the HMR and HML loci. Repression of the test gene was optimal when two silencers flanking the reporter gene were used, mimicking the situation at the silent loci. In addition, both repression of the reporter gene and the formation of nuclease-resistant chromatin domains was SIR4 dependent.

Aldose-Ketose Isomerases↗