Action Of Micrococcal Nuclease Research Articles

Molecular and toxicological mechanisms behind the effects of chromium (VI) on the male reproductive system of Mytilus galloprovincialis: First evidence for poly-ADP-ribosylation of protamine-like II

Studies on the molecular mechanisms of heavy metal toxicity in invertebrate reproduction are limited. Given that PARP-catalysed ADP-ribosylation is also involved in counteracting heavy metal toxicity and maintaining genomic integrity, and that PARylation is implicated in chromatin remodelling but its role in sperm chromatin remains to be elucidated, we investigated the effects of chromium(VI) at 1, 10 and 100 nM on the reproductive health of Mytilus galloprovincialis. The damage to the gonads was assessed by morphological analyses and the damage indices PARP and ɣH2A.X were measured. Changes in the binding of protamine-like (PL) to DNA and the possibility of poly(ADP-ribosyl)ation of PL proteins were also investigated. Gonadal chromium accumulation and morphological damage were found, especially when the mussels were exposed to the highest dose of chromium(VI). In addition, the maximum expression of gonadal ɣH2A.X and PARP were obtained at 100 and 10 nM Cr(VI), respectively. Interestingly, for the first time in all exposed conditions, poly(ADP)-ribosylation was detected on PL-II, which, together with PL-III and PL-IV, are the major nuclear basic proteins of Mytilus galloprovincialis sperm chromatin. Since PL-II is involved in the final high level of sperm chromatin compaction, this post-translational modification altered the binding of the PL protein to DNA, favouring the action of micrococcal nuclease on sperm chromatin. This study provides new insights into the effects of chromium(VI) on Mytilus galloprovincialis reproductive system and proposes a molecular mechanism hypothesis describing the toxic effects of this metal on PL-DNA binding, sperm chromatin and gonads.

Rearrangements of chromatin structure during spermatogenesis of squid.

A stepwise replacement of somatic histones on sperm-specific proteins (we have termed them illexines I1 and I2) is found to occur during spermatogenesis of squid Illex argentinus [Kadura, S.N. and Khrapunov, S.N. (1988) Eur. J. Biochem. 175, 603-607]. The chromatin from nuclei of squid immature testes has a nucleosomal DNA repeat which corresponds to the nucleosomal repeat of calf thymus chromatin (195 +/- 5 bp). As spermatozoa become mature and illexine I2 accumulates in the chromatin, the nucleosomal structure of the latter disappears and chromatin compacting takes place. The chromatin DNA from squid spermatozoa is highly resistant to micrococcal nuclease action. Spectrophotometry and spectrofluorimetry were to establish that neither illexine I1 nor illexine I2 forms a globular structure in solution under any conditions studied. Illexine I2 (approx. 7 kDa) shows a high affinity to DNA and remains bound to it under conditions when complexes of illexine I1 (approx. 9 kDa) and salmine (approx. 4.5 kDa) with DNA completely dissociate. This fact, allowing for a similar content (about 75%) of arginine in illexine I2 and salmine, suggests high clustering of arginine residues in the composition of illexine I2. It is suggested that the initial stage of histone substitution with illexine I1, which has a more moderate affinity to DNA than illexine I2, prepares chromatin for the formation of a highly packed structure by illexine I2 during squid spermatogenesis.

Structure of human sperm chromatin: a study on the accessibility of DNA to macromolecules.

The structure of human sperm chromatin compared with somatic chromatin (liver) was studied by titration of the exposed DNA-phosphate groups with poly-1-lysine (3000 and 28,100 MW) and by their susceptibility to the hydrolytic action of micrococcal nuclease and DNase I. With both sizes of polylysine used, the binding values were significantly lower for sperm chromatin (0.31 +/- 0.05) than for liver chromatin (0.52 +/- 0.05), indicating the presence of about 30% and 52% of free phosphate groups, respectively. Interaction with liver chromatin left no polylysine molecules partially unbound ("wastage") even when 28,100 MW polylysine was used; on the contrary, sperm chromatin showed 26% of "wasted" polylysine even when the smaller polymer was used, indicating that in sperm chromatin the accessible DNA zones are usually no longer than 42 A, that is, 12 base pair. Sperm chromatin was notably more susceptible to both micrococcal nuclease and DNase I action than liver chromatin. However, in the presence of saturating concentrations of polylysine they were similarly protected. Micrococcal nuclease and DNase I hydrolysis products of sperm fractions when submitted to electrophoresis produced a polydisperse smearing pattern along the gel that was difficult to correlate with the presence of nucleosomal structure.

DNA- and RNA-binding proteins of chromatin from Escherichia coli

The different proteins present in chromatin of Escherichia coli have been analyzed by a variety of techniques. The chromatin was isolated using a previously published procedure (Sjåstad, K., Fadnes, P., Krüger, P.G. Lossius, I. and Kleppe, K. (1982) J. Gen. Microbiol. 128, 3037) and solubilized by the action of micrococcal nuclease or DNAase I. The DNA-protein and RNA-protein complexes thus obtained were purified by sucrose gradient centrifugation and isopycnic gradient centrifugation in metrizamide in low ionic strength. The protein: DNA ratio of the DNA-protein complexes was estimated from the latter method and found to be approx. 1.75. The protein components were analyzed further by one- and two-dimensional gel electrophoresis. Approx. 15 major polypeptides were detected in the DNA-protein complex, whereas 10 were present in the RNA-protein complex. The majority of the polypeptides in both complexes had acidic isoelectric pH. The polypeptides in the two complexes differed markedly and only two polypeptides, having molecular weights of 57 000 and 37 000, respectively, were found to be common in both complexes. In agreement with earlier studies, the basic protein HU was not present in the DNA-protein complex. Affinity studies of the proteins from chromatin using DNA- and RNA-Sepharose columns in general confirmed the above conclusions. The two-dimensional gel electrophoretic patterns of the proteins in the different complexes were compared with those of proteins in the inner and outer membranes. Only one of the major polypeptides present in the inner membrane, having a molecular weight of 57 000, was enriched in the DNA-protein complex.

Helix-destabilization of deoxyribonucleic acid and poly[d(A-T)·d(A-T)] by bovine seminal ribonuclease

A ribonuclease isolated earlier from bovine seminal plasma by DNA-affinity chromatography (Ramakrishnamurti, T. and Pandit, M.W. (1983) J. Chromatogr. 260, 216–222) has now been shown by thermal denaturation studies to destabilize the double-helical structure of DNA and poly[d(A-T)·d(A-T)]. Thermal denaturation profiles of DNA in the presence of the protein are much more complicated due to the denaturation of protein itself in the temperature range over which DNA predominantly melts. The protein shows relatively stronger affinity towards denatured DNA as compared to native DNA. The action of micrococcal nuclease on DNA and its complexes with ribonuclease A and bovine seminal ribonuclease indicates that both of these proteins destabilize the double-helical structure of native DNA and thereby render the DNA more sensitive to the micrococcal nuclease.

O-phenantroline-CuSO4-induced redistribution of nuclear proteins.

Incubation of rat liver nuclei with the o-phenantroline-CuSO4 (OP-Cu) complex under conditions not causing any DNA cleavage, enhanced the susceptibility of chromatin to the action of micrococcal nuclease. The released nucleosomal fraction had less coextracted nonhistone proteins, while the nuclear matrix was enriched in nonhistone proteins when compared with the controls. These changes were interpreted as the consequence of a displacement of nonhistone proteins from their closer association with the chromatin complex and a concomitant exposure of chromatin regions in a state less protected by nonhistone proteins.

Chromatin structure during male gametogenesis of grass carp

1. 1. The nucleosome organization of chromatin was observed on all stages of grass carp ( Ctenopharyngodon idella) sperm maturation. The average nucleosome repeat of 200 base pairs does not change throughout the spermatogenesis process. 2. 2. The resistance of sperm chromatin DNA to micrococcal nuclease action is increased in contrast with immature testis chromatin. 3. 3. The histone complement is not replaced during sperm maturation but there is an accumulation of one histone HI subfraction. 4. 4. The non-histone chromatin proteins with mol. wt in range of 43,000–67,000 change throughout the gametogenesis process and sperm chromatin contains a specific pattern of these nonhistone proteins. 5. 5. A possible role of higher-order levels of chromatin organization in determination of compact sperm chromatin structure is discussed.

Isolation, properties and nucleolytic degradation of chromatin from Escherichia coli.

A new procedure has been developed for the isolation of the chromosome complex, termed chromatin, from Escherichia coli. The bacteria were subjected to low ionic strength and T4 lysozyme, followed by detergent treatment analogous to that employed for the isolation of eukaryotic chromosomes. The chromatin was an insoluble viscous material which contained approximately equal amounts of DNA and RNA. The protein content of the chromatin was almost three times greater than the nucleic acid content. Electron microscopy revealed that the chromatin was highly condensed, having multiple loops and beaded structures with various diameters. The chromatin could be completely solubilized by both micrococcal nuclease and DNAase I, whereas RNAase had no effect. The initial degradation by micrococcal nuclease resulted in the production of a DNA-protein particle, sedimentation coefficient 10S, and an RNA-protein complex of 24S. Further degradation led to a decrease in sedimentation coefficient of the DNA-protein complex, but not of the RNA-protein particle. The peak size of the DNA of the initial DNA-protein particle was approximately 2400 bp. The action of micrococcal nuclease also resulted in the production of several discrete RNA species of various sizes. Several low molecular weight proteins (12000-27000) were found in the DNA-protein complex. The DNA-binding protein HU was present in the undigested chromatin; varying amounts of HU were, however, detected in the DNA-protein and RNA-protein particles.

Nucleosomal structure of SV40 minichromosome as revealed by micrococcal nuclease action

FEBS LettersVolume 125, Issue 1 p. 35-38 Full-length articleFree Access Nucleosomal structure of SV40 minichromosome as revealed by micrococcal nuclease action Sergei Nedospasov, Sergei Nedospasov Institute of Molecular Biology, USSR Academy of Sciences, Vavilov str. 32, B-334, Moscow, USSRSearch for more papers by this authorAlexander Shakhov, Alexander Shakhov Institute of Molecular Biology, USSR Academy of Sciences, Vavilov str. 32, B-334, Moscow, USSRSearch for more papers by this authorGeorgii Georgiev, Georgii Georgiev Institute of Molecular Biology, USSR Academy of Sciences, Vavilov str. 32, B-334, Moscow, USSRSearch for more papers by this author Sergei Nedospasov, Sergei Nedospasov Institute of Molecular Biology, USSR Academy of Sciences, Vavilov str. 32, B-334, Moscow, USSRSearch for more papers by this authorAlexander Shakhov, Alexander Shakhov Institute of Molecular Biology, USSR Academy of Sciences, Vavilov str. 32, B-334, Moscow, USSRSearch for more papers by this authorGeorgii Georgiev, Georgii Georgiev Institute of Molecular Biology, USSR Academy of Sciences, Vavilov str. 32, B-334, Moscow, USSRSearch for more papers by this author First published: March 09, 1981 https://doi.org/10.1016/0014-5793(81)80990-8Citations: 4AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat Citing Literature Volume125, Issue1March 09, 1981Pages 35-38 ReferencesRelatedInformation

Structure of the filamentous bacteriophage fl. Location of the A, C, and D minor coat proteins.

The location within the virion of the A, C, and D minor coat proteins of the filamentous bacteriophage fl has been analyzed. The A protein is present in approximately 5 copies/particle and is located at the tip of normal length phage, miniphage, and fl/pBR322 chimeric phage, a longer than normal length phage. The mole ratios of the A, C, and D proteins are the same for each type of particle, consistent with a model of phage organization in which the minor coat proteins are clustered near or at the ends of the phage. Normal length phage were fragmented by passing them through a French press, and those fragments that contained the A protein were separated from those that did not by treating the mixture with anti-A protein antibody. Analysis of the protein compositions of the two populations of fragments showed that the A and D proteins were found together in one population of fragments and that most, it not all, of the C protein was found in the other. These results show that the D protein is located near or at the A protein end of the phage and that the C protein is located in a region near or at the opposite end. Treatment of the virion with proteases which lowered the infectivity of the phage resulted in particles in which only the A protein was cleaved to any detectable extent. These particles remained resistant to the action of micrococcal nuclease.

Segregation of rapidly acetylated histones into a chromatin fraction released from intact nuclei by the action of micrococcal nuclease.

It has been previously shown that micrococcal nuclease digestion and subsequent fractionation of hen oviduct nuclei generates fractions enriched (first supernatant fraction - 1SF) and depleted (second supernatant fraction - 2SF) in ovalbumin genes, while a third fraction, the pellet fraction, contains about the same level of this gene as whole chromatin (Bloom and Anderson (1978) Cell 15, 141-150). We have utilized this fractionation method in an attempt to assess the extent and kinetics of histone acetylation associated with chromatin from the 1SF, 2SF, and pellet fraction. Hepatoma Tissue Culture (HTC) cells were labelled for 30 minutes in vivo with 3H-acetate, nuclei isolated and the chromatin fractionated. The specific activity of the histones in the 1SF was slightly greater than that of the 2SF (1.2 to 1.6 fold difference) independent of the length of nuclease digestion. If the labelling period is followed by short (10 to 60 minute) treatment of the cells with sodium butyrate, the more rapidly as well as more extensively acetylated histones are also preferentially found in the 1SF. This is in part the result of segregation of chromatin particles into the 1SF as the histones associated with these particles become hyperacetylated. That is, the extent of histone acetylation regulates the distribution of chromatin in the 1SF, 2SF and pellet fraction.

Analysis of DNA double- and single-strand breaks by two dimensional electrophorresis: action of micrococcal nuclease on chromatin and DNA, and degradation in vivo of lens fiber chromatin

We describe a novel system for two dimensional electrophoresis at neutral and alkaline pH for determining the double-stranded and single-stranded lengths of DNA. With this system we analysed the mode of micrococcal nuclease digestion of DNA in cellular and SV40 viral chromatin and of supercoiled SV40 DNA. The enzyme reaction occurred in two steps : the enzyme first introduced single-strand breaks, then converted these to double-strand breaks by an adjacent cleavage on the opposite strand. Digestion of cellular chromatin DNA occurred by a similar mechanism. Chromatin fragments produced by limited micrococcal nuclease action contained many single-strand breaks, which may be important when this method is used to prepare chromatin fragments for biochemical and biophysical studies. Nucleosome monomer to tetramer produced at later stages of digestion contained few if any single-strand breaks.

Transcriptionally active mononucleosomes from trout testis are heterogeneous in composition.

Limited micrococcal nuclease action on trout testis nuclei yields two mononucleosome subsets, MN1 and MN2, enriched in transcribed DNA sequences. MN1 is soluble and MN2 insoluble in 0.1 M NaCl. Electrophoresis of intact MN1 and MN2 mononucleosomes in 4% polyacrylamide gels shows that each fraction is heterogeneous and four major and several minor subcomponents can be resolved. Dissociation of the protein components of these nucleosomal particles by two-dimensional electrophoresis shows that the major component of MN1 possesses stoichiometric amounts of the four inner histones and of the high mobility group protein H6, associated with DNA fragments of 140 base pairs in length. The major component of MN2 possesses equimolar amounts of the four inner histones plus 1 molecule of H1 and H6, complexed with DNA fragments of 220 base pairs in size.

Limited action of micrococcal nuclease on trout testis nuclei generates two mononucleosome subsets enriched in transcribed DNA sequences.

Hybridization experiments show that DNA extracted from two distinct subsets of mononucleosomes (MNI and MN2) generated by a limited action of micrococcal nuclease on trout testis nuclei is enriched approximately 7-fold in sequences that are transcribed into cytoplasmic polyadenylated RNA in trout testis cells. Both subsets of mononucleosomes contain eight core histones, but MNI also possesses one or two molecules of a small, basic, high-mobility-group (HMG) protein H6 [Levy W., B., Connor, W. & Dixon, G. H. (1979) J. Biol. Chem. 254, 609-620], bound to a DNA fragment of 140 base pairs. In contrast, MN2 contains 1 molecule of H1 but no H6, and its DNA length is somewhat longer at 140-190 base pairs. The preferential release of these two subsets of mononucleosomes is correlated with the presence of a second larger HMG protein, HMG-T, in the linker regions flanking both types of mononucleosomes. The HMG-T-containing linker regions appear to be considerably more susceptible to attack by micrococcal nuclease than H1-containing linkers. Cross-reassociation reactions between the DNA from MN1 and MN2 subsets indicate that they share a significant extent of sequence overlap but also that each subset contains specific sequences that are absent in the other subset.

Effects of nuclear disruption on the macromolecular composition of nucleosome subfractions

The macromolecular composition of nucleosomal subfractions obtained by limited action of micrococcal nuclease upon trout testis chromatin has been analyzed with the purpose of comparison with the properties of transcriptionally active nucleosomal fractions derived by similar treatment of intact nuclei. The results indicate that when the native chromatin structure of intact nuclei is disrupted prior to the nuclease action, the nucleosomal subfractions that are subsequently generated have an altered composition.

A study of an endogenous nucleolytic reaction and of the action of micrococcal nuclease and DNAase I on a salt-soluble, compact form of chromatin

The endogenous nucleolytic reaction occurring in rabbit thymus nuclear lysates has been studied at extended incubation times (up to 4 h). Production of nucleosomal polymers containing multiples of 205 base pairs of DNA was observed. The stability of the bands and the low release (1%) of acid-soluble nucleotides indicated there was only a small fraction of sensitive DNA between the subunits. The salt-soluble chromatin formed in the endogenous reaction at short incubation times (14–24 min) and purified over Sephadex G-200 has been treated with micrococcal nuclease and DNAase I. With micrococcal nuclease, nucleosomal polymers containing multiples of 201 base pairs of DNA were formed. Extensive digestion revealed a core subunit containing 145 base pairs of DNA. With DNAase I only random degradation was observed and nucleosomal complexes were not produced.

Periodicity and fragment size of DNA from mouse TLT hepatoma chromatin and chromatin fractions using endogenous and exogenous nucleases

The action of micrococcal nuclease, DNase I and DNase II on mouse TLT hepatoma chromatin revealing the periodicity of its structure as visualized by denaturing and non-denaturing gel electrophoresis, was consistent with the action of these enzymes on other chromatins. Micrococcal nuclease showed a complex subnucleosome fragment pattern based on multiples of 10 base pairs with a prominant couplet at 140/160 base pairs and the absence of the 80 base pair fragment. This couplet of the core and minimal nucleosome fragments was conspicuously present in the mononucleosomes found in the 11S fractions of a glycerol gradient centrifugation. DNase I and II produced a fairly even distribution of a 10 base pair increasing series of fragments to about 180 base pairs, a pattern also repeated in the DNA of nucleosome glycerol-gradient fractions. In limited digestions by these nucleases multinucleosomic DNA fragments are pronounced. These fragment lengths are multiples of an estimated average repeat length of nucleosome DNA of 180 base pairs. The action of the endogenous Mg/Ca-stimulated endonuclease produced only limited cuts in the hepatoma chromatin resulting primarily in multi-nucleosomic DNA fragment lengths and only upon lengthy digestion limited subnucleosomic, 10-base-pair multiple fragments are produced. The putative euchromatin-enriched fractions (50-75S) of the glycerol gradient centrifugation of autodigested chromatin, similarly, contained primarily the multinucleosomic DNA fragment lengths. These results are consistent with our previous electron microscopic demonstration that autodigested chromatin as well as the putative euchromatin-enriched fractions were composed of multi-nucleosomic chromatin segments containing a full complement of histones.

Selective association of the trout-specific H6 protein with chromatin regions susceptible to DNase I and DNase II: possible location of HMG-T in the spacer region between core nucleosomes.

Nuclei and chromatin from trout testis cells were digested with three different nucleases (DNase I, DNase II, and micrococcal nuclease), and the acid-soluble proteins that were solubilized and those remaining bound to the nuclease-resistant DNA were compared electrophoretically. With the conditions described by H. Weintraub and M Groudine [(1976) science, 193, 848-856], which we previously found to be selective in digesting actively transcribed regions in trout testis chromatin, a single chromosomal protein, H6, was solubilized. The nucleosomal histones and H1 remained insoluble, bound to the resistant DNA. In contrast, digestion with micrococcal nuclease led to a preferential solubilization of a second protein, HMG-T, together with the release of some nucleosomal histones and H1 into the soluble fraction. DNase II also discriminated between "active" and "inactive" chromatins; when a DNase II-solubilized "active" chromatin fraction was prepared, it too was enriched in H6 and HMG-T. Thus, both H6 and HMG-T, the two major low-salt extractable chromosomal nonhistone the two major low-salt extractable chromosomal nonhistone proteins from trout testis, are associated with chromatin regions selectively sensitive to nucleases. The preferential solubilization of HMG-T by micrococcal nuclease action suggests that it might be located at the internucleosomal "spacer" region.

Action of micrococcal nuclease on chromatin and the location of histone H1

Digestion of rat liver chromatin with micrococcal nuclease at 2°C yields fragments containing multiples of 198±6 base-pairs, which represents the DNA content of a unit of the structure. Digestion at 37°C results in degradation of these fragments from the ends and also in the release of a histone, H1. This suggests an association of H1 with the region of DNA that links adjacent units of the structure. Two further lines of evidence lead to the same idea. If H1 is removed before digestion, then cleavage between units is eightfold more rapid. And while the removal of H1 has little effect on the sedimentation coefficient of the smallest, or monomer, fragment, it causes a marked reduction in the sedimentation coefficients of dimers and higher multimers.

Differential nuclease action on nuclei and chromatin from developing germ cells of the echinoderm [formula omitted

Intact nuclei of Holothuria tubulosa subjected to micrococcal nuclease action were found almost entirely resistant to in situ digestion and only partially digested after disrupting the nuclear envelope with a cell disruption bomb. Solubilization of isolated chromatin was also affected by the method of preparation. Sucrose gradient patterns from early stages of gonad maturation revealed a distribution of discrete particles containing a major monomeric species. A slower sedimenting component was also present but became absent from digests upon completion of gonad growth, when chromatin is fully condensed. At this stage the rate of solubilization was drastically reduced. These data suggest that substantial changes in the structural organization of chromatin occur with development, even though the histone complement in this organism remains unaltered during spermiogenesis.