Gene/Protein Disease Symptom Drug Enzyme Compound
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Query: UNIPROT:P06889 (Mol)
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Oligomers of chromatin subunits (oligonucleosomes) were prepared by a mild digestion of chromatin with staphylococcal nuclease followed by a purification of a high molecular weight material (hexanucleosomes and larger DNP particles) by gel chromatography. The main finding is that a mild removal of histone H1 from the oligonucleosome preparation by treatment with tRNA in the absence of any significant hydrodynamic shearing leads to the formation of free DNA molecules which constitute 5-6% of the total oligonucleosomal DNA. The size of nucleosome-free DNA stretches in H1-depleted hydrodynamically sheared chromatin is about 6000 base pairs and their content is apparently 10-12% of the total DNA. These and related findings are discussed in terms of the previously proposed "asymmetric hairpin" model of DNA packing in chromatin [1-4]. Different kinds of the asymmetric hairpin are considered and ambiguities in interpretations of experimental data are pointed out.
Mol Biol Rep 1976 Sep
PMID:Free DNA stretches in histone H1-depleted chromatin and their possible relation to chromomere structure. 100 4

The biphasic nature of the time course of the action of staphylococcal nuclease on thymus nucleohistone was confirmed by studying the hydrolysis of this nucleoprotein at various enzyme concentrations. The transition from the rapid first to the sluggish second phase of the time course was particularly distinct at the highest enzyme concentrations. The rapid initial phase of the hydrolysis curve leveled off sharply when between 60 and 65 per cent of the total TNH phosphorus had been converted to acid-soluble phosphorus compounds. The insoluble complexes of TNH with protamines were found to be very resistant against the action of staphylococcal nuclease. The time course of the action of staphylococcal nuclease on a commercial nucleoprotamine of salmon testicles was found to become very sluggish when between 35 and 40 per cent of its total phosphorus had been converted to acid-soluble phosphorus compounds. When nucleoprotamines prepared in the laboratory from the secreted sperm cell suspension of Brown Brook Trout were digested with staphylococcal nuclease, only between 15 and 20 per cent of the total phosphorus were cleaved to acid-soluble phosphorus compounds during the rapid phase of the nuclease action. The respective values for the phosphorus fractions available for magnesium-binding and those susceptible to the rapid cleavage by staphylococcal nuclease were found to be very similar.
Mol Cell Biochem 1975 Mar 27
PMID:The action of staphylococcal nuclease (EC-number 3. 1. 4. 7.) on thymus nucleohistone (TNH) and on some nucleoprotamines. 112 11

The carbocyclic analog of 2'-deoxyguanosine (CdG) is active against herpes simplex virus (HSV), human cytomegalovirus, and human hepatitis-B virus. In order to understand the mechanism of action of this compound against HSV, we have evaluated (a) the incorporation of [3H]CdG into viral and host DNA in HEp-2 cells infected with HSV and (b) the interaction of the 5'-triphosphate of CdG (CdG-TP) with the HSV DNA polymerase and human DNA polymerases alpha, beta, and gamma (EC 2.7.7.7). Incubation of HSV-1-infected HEp-2 cells with [3H]CdG resulted in the incorporation of CdG into both the HSV and the host cell DNA. These results indicated that CdG-TP was used as a substrate for HSV DNA polymerase and for at least one of the cellular DNA polymerases. Degradation of both viral and host DNA with micrococcal nuclease and spleen phosphodiesterase indicated that CdG was incorporated primarily into internal positions in both DNAs. The viral DNA containing CdG sedimented in neutral and alkaline sucrose gradients in the same way as did viral DNA labeled with [3H]thymidine, indicating that the HSV DNA containing CdG was similar in size to untreated HSV DNA. CdG-TP was a competitive inhibitor of the incorporation of dGTP into DNA by the HSV DNA polymerase (Ki of 0.35 microM) and the human DNA polymerase alpha (Ki of 1 microM). CdG-TP was not a potent inhibitor of either DNA polymerase beta or gamma. Using DNA-sequencing technology, CdG-TP was found to be an efficient substrate for HSV DNA polymerase. Incorporation of CdG monophosphate (CdG-MP) into the DNA by HSV DNA polymerase did not interfere with subsequent chain extension. These results suggested that the antiviral activity of CdG was due to its incorporation into the DNA and subsequent disruption of viral functions. In contrast, CdG-TP was not as good as dGTP as a substrate for DNA synthesis by DNA polymerase alpha, and incorporation of CdG-MP by DNA polymerase alpha inhibited further DNA chain elongation.
Mol Pharmacol 1992 Feb
PMID:Incorporation of the carbocyclic analog of 2'-deoxyguanosine into the DNA of herpes simplex virus and of HEp-2 cells infected with herpes simplex virus. 131 7

Nuclear magnetic resonance spectroscopy has been used to investigate a synthetic peptide (YVYKPNNTHE) corresponding to residues 113 to 122 of staphylococcal nuclease. In the major folded state of the protein this region forms a type VIa beta-turn containing a cis Lys116-Pro117 peptide bond. There is, however, no evidence for any significant population of such a turn in the peptide in aqueous solution and the X-Pro bond is predominantly in the trans configuration. The peptide exhibits several well-resolved minor resonances due to the presence of a small fraction (4 +/- 2%) of the cis-proline isomer. The ratio of cis to trans isomer populations was found to be independent of temperature between 5 degrees C and 70 degrees C, indicating that delta H for the isomerism is close to zero. Using magnetization transfer techniques the rate of trans to cis interconversion was found to be 0.025(+/- 0.013) s-1 at 50 degrees C. The thermodynamics and kinetics of isomerism in the peptide are very similar to those estimated for the Lys116-Pro117 peptide bond in unfolded nuclease, suggesting that the cis-trans equilibrium in the unfolded protein is largely determined by the residues adjacent to Pro117 in the sequence. These results are consistent with previous suggestions that the cis-proline bond is stabilized late in the folding process and that the predominance of the cis form in folded nuclease is due to stabilizing interactions within the protein that give rise to a favorable enthalpy term.
J Mol Biol 1992 Nov 20
PMID:A peptide model for proline isomerism in the unfolded state of staphylococcal nuclease. 145 44

The globular domain of the linker histone H5 has been expressed in Escherichia coli. The purified peptide is functional as it permits chromatosome protection during micrococcal nuclease digestion of chromatin reconstituted with the peptide, indicating that it binds correctly at the dyad axis of the nucleosomal core particle. The globular domain residue lysine 64 is highly conserved within the linker histone family, and site-directed mutagenesis has been used to assess the importance of this residue in the binding of the globular domain of linker histone H5 to the nucleosome. Recombinant peptides mutated at lysine 64 are unable to elicit chromatosome protection to the same degree as the wild-type peptide, and since they appear to be fully folded, these observations confirm a major role for this residue in determining the effective interaction between the globular domain of histone H5 and the nucleosome.
J Mol Biol 1992 Feb 05
PMID:Site-directed mutagenesis studies on the binding of the globular domain of linker histone H5 to the nucleosome. 154 12

U1 small nuclear RNA is synthesized as a precursor with several extra nucleotides at its 3' end. We show that in Xenopus laevis oocytes, removal of the terminal two nucleotides occurs after the RNA has transited through the cytoplasm and returned to the nucleus. The activity is controlled by an inhibitor of processing, which we call TPI, for 3'-terminal processing inhibitor. This inhibitor is sensitive to both micrococcal nuclease and trypsin treatment, indicating that it is a nucleoprotein. TPI inhibits the 3' processing of pre-U1 RNAs that have 5' ends containing m7G caps but not mature m2,2,7G caps; this finding suggests that TPI interacts directly or indirectly with the 5' end of pre-U1 RNA. The inhibition of processing by TPI, almost complete at 19 degrees C, is reversibly inactivated at slightly higher temperatures. TPI activity is solely in the soluble fraction of oocyte nuclear extracts, in contrast to the 3'-terminal processing activity, which is present in both the particulate and soluble fractions. We propose that the differential processing of the 3'-terminal nucleotides of pre-U1 RNA after its return from the cytoplasm, but not before its exit from the nucleus, may be due to the association of TPI with the m7G cap on the newly synthesized pre-U1 RNA.
Mol Cell Biol 1992 Apr
PMID:Nuclear processing of the 3'-terminal nucleotides of pre-U1 RNA in Xenopus laevis oocytes. 154 11

We have cloned and sequenced a gene (nuc) from the IncW plasmid pSa which shows amino acid sequence similarity to staphylococcal nuclease (EC 3.1.4.7) and to the parB locus of plasmid RP4. The 525 bp open reading frame encodes a 174-amino-acid potential polypeptide of 19.7 kDa. Expression of the gene was confirmed using an in vitro transcription-translation assay which produced a protein of identical size. Nuclease activity was demonstrated using DNA as the substrate in toluidine blue-DNA agar plates. The deduced amino acid sequence revealed a signal sequence, and TnphoA insertion within the open reading frame indicated that a portion of the protein is transported across the bacterial cell membrane.
Mol Microbiol 1992 Feb
PMID:A gene near the plasmid pSa origin of replication encodes a nuclease. 156 Jul 81

The importance of polynucleotide size for immunogenicity was tested with size-fractionated Z-DNA. High molecular weight Z-DNA, larger than 1000 bp, was fragmented by digestion with micrococcal nuclease. Fractions corresponding to less than 60, 60-120, 100-200, 200-400 and 400-900 bp were isolated by gel filtration on Sepharose 4B. These fractions and the greater than 1000 bp Z-DNA were mixed with methylated BSA and the complexes were injected into C57BL/6 mice with RIBI adjuvant. Only one of four mice responded to the less than 60 bp immunogen. All the fractions larger than 60 bp induced specific anti-Z-DNA antibodies, mostly of IgG isotype, in all animals injected. Fractions larger than 200 bp induced antisera of higher titer than did 60-120 or 100-200 bp fractions. All positive sera reacted with Z-DNA but not with B-DNA and only very weakly with denatured DNA. In competitive assays, similar concentrations of fragments larger than 60 bp inhibited binding to immobilized Z-DNA. A higher concentration of less than 60 bp fragments was required for competitive binding. Even for a highly immunogenic nucleic acid that differs from the B-DNA conformation, a polynucleotide larger than 100 bp is much more immunogenic than smaller fragments.
Mol Immunol 1992 May
PMID:Immunogenicity of Z-DNA depends on the size of polynucleotide presented in complexes with methylated BSA. 158 29

Atlantic salmon (Salmo salar) were treated with 17-beta estradiol to induce vitellogenin synthesis in liver. This led to an increase in liver wet weight and total DNA. After incubation with micrococcal nuclease (EC 3.1.31.1) less soluble chromatin was obtained from nuclei of the estradiol treated than the control fish, but active gene regions were solubilized by the nuclease. Thus, in the estradiol treated fish soluble mononucleosomes contained hybridizable vitellogenin gene sequences. As a result of estradiol treatment the content in total liver of putrescine rose 3-fold, that of spermidine 2-fold, while spermine was unchanged. In muscle no significant changes were observed. The regulatory functions of polyamines during gene expression were investigated by binding (14C)spermine to isolated liver nuclei depleted of endogenous polyamines. The number of binding sites was higher in nuclei of estradiol treated than control fish. (14C)spermine associated preferentially with micrococcal nuclease insensitive chromatin. Thus, the high content of putrescine and spermidine in liver supported the view of polyamine accumulation in proliferating tissues. The preferential binding to condensed chromatin indicated a stabilizing effect of polyamines on the organization of inactive chromatin structures.
Mol Cell Biochem 1992 Jan 15
PMID:Polyamines in liver and their influence on chromatin condensation after 17-beta estradiol treatment of Atlantic salmon. 161 18

The Saccharomyces cerevisiae transcription factors (TF) IIIB and IIIC assemble onto their respective DNA-binding sites on the SUP4 tRNA(Tyr) gene at 0 degrees C. RNA polymerase III specifically associates at 0 degrees C with this TFIIIC-TFIIIB-DNA complex to form a stable "closed" promoter complex in which the DNA surrounding the transcriptional start retains its duplex form. Promoter "opening" is a temperature-dependent and readily reversible process that involves up to 22 unwound base-pairs of DNA, and can be followed by analyzing the hyperreactivity of thymine to KMnO4 oxidation. This promoter opening increases progressively from 10 degrees C to 40 degrees C, with at least two regions within the transcription bubble appearing to melt independently. In contrast, the temperature dependence of forming an initiated transcription complex containing a 17 nucleotide nascent RNA chain displays a sharp transition between 10 degrees C and 15 degrees C. When RNA polymerase initiates transcription under conditions that limit the nascent RNA chain to less than six nucleotides, there is no displacement of the transcription bubble. These transcription complexes are distinguishable from "open" promoter complexes in their maintenance of the transcription bubble at 0 degrees C, and from transcription complexes with more extended (17 nucleotide) RNA chains in their sensitivity to disruption by heparin. In light of recent results by others that demonstrate a requirement for an RNA transcription factor in a Bombyx mori-based in vitro RNA polymerase III transcription system, we have searched for a comparable component in the S. cerevisiae-derived system. We show that if an RNA component is required in the yeast-derived system, it is not susceptible to inactivation by massive amounts of micrococcal nuclease, RNase A, or RNase T1.
J Mol Biol 1992 Jul 05
PMID:Formation of open and elongating transcription complexes by RNA polymerase III. 161 62


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