Studies on nuclear proteins. The binding of extra acidic proteins to deoxyribonucleoprotein during the preparation of nuclear proteins

γ-Irradiated DNA Activates Histone Hl-specific Proteinase of Rat Liver Nuclei

We investigated the effect of various forms of DNA (double- and single-stranded calf thymus DNA, circular plasmid DNA, gamma- and UV-irradiated DNA and DNAase I-treated double-stranded DNA) aggregated with histones, on the proteolysis of these histones by proteinase associated with the rat liver nuclear scaffold. It was shown that the nuclear scaffold-associated proteinase is able to degrade selectively the histone H1 only in the presence of the DNA containing single-strand breaks induced by gamma-radiation or DNAase I treatment as well as in the presence of heat-denatured DNA. This proteinase is not activated by the double-stranded circular plasmid DNA or by UV-treated double-stranded DNA. Histone H1-specific proteinase (HSP) activated by gamma-irradiated DNA is inhibited by inhibitors of serine proteinases such as antipain, leupeptin, phenylmethylsulphonyl fluoride, as well as by dithiothreitol. The results lead us to suggest that DNA-activated HSP from rat liver nuclei is involved in the regulation of the access of repair enzymes to the damage portions of DNA within chromatin.

Analysis of protein incorporation of radioactive isotopes in the Chinese hamster ovary cell cycle by electronic sorting and gel microelectrophoresis

The patterns of [3H]-leucine and [32P]-phosphate incorporation of proteins extracted with varying molarities of sodium chloride were analyzed from nuclei physically sorted from six fluorescence windows after propidium iodine staining of the G0 + G1 and G2 + M phases of the Chinese hamster ovary (CHO) cell cycle. Eight hundred nanograms of protein were used in each electrophoretic analysis obtained from 200,000 nuclei, a portion of the sample, from each window. Autoradiography was performed in a two-dimensional polyacrylamide gel ultra-microelectrophoresis apparatus (UMEA) designed and fabricated in this laboratory. There was a net reduction and/or loss of [3H]-leucine- and [32P]-phosphate-labeled protein regions from the autoradiographs occurring primarily in the G2 + M phase. Two phosphorylated proteins that were stage specific were observed in partitions of the G2 + M phase. The use of isolated proteins and the coelectrophoresis of these markers demonstrated the similarity in mobility of a number of proteins seen in the autoradiographs of proteins extracted with high and low salt molarities and implied they are synonymous. Coelectrophoresis indicated that a substantial number of high molecular weight proteins that decreased or disappeared at late stages of G2 + M and early mitosis were composed, in part, of nucleolar proteins.

Intranuclear compartmentalization of DNA-dependent RNA polymerases: association of RNA polymerase I with nucleolar organizing chromosomes

The compartmentalization of chromatin-bound RNA polymerases was examined with HeLa chromosomes fractionated according to their size in sucrose/glycerol gradients. There was a good correlation between the enrichment of nucleolus-organizing chromosomes, i.e., D and G group chromosomes, and the level of chromosome-associated RNA polymerase form I activity. A profile of DEAE-Sephadex chromatography of enzymes solubilized from chromosome fractions also supported the view that form I was associated with D and G group chromosomes. The amount of form I associated with unfractionated chromosomes was nearly identical to that of nuclei, indicating that this enzyme is probably quantitatively conserved even when chromatin undergoes extensive condensation. Since the chromatin-bound form I enzyme can be reactivated with heparin, it seems that this enzyme is in the initiated state, probably being bound to rDNA throughout the mitotic cycle. Thus, the absence of rRNA synthesis in mitosis is due to neither unavailability of enzyme to rDNA nor to the release of some factors necessary for transcriptional processes. Form II enzyme was associated uniformly with all chromosome fractions. Taken together, the present findings suggest that the intranuclear compartmentalization of RNA polymerases persists not only in interphase stages, but also in mitosis, during which most other nuclear proteins are released into the cytoplasm.

Histone-dependent reconstitution and nucleosomal localization of a nonhistone chromosomal protein: the H2A-specific protease

We have described earlier a chromatin-bound protease with unique specificity for histone H2A [Eickbush, T. H., Watson, D. K., & Moudrianakis, E. N. (1976) Cell (Cambridge, Mass.) 9, 785--792]. In the present study, we explore the nature of interactions that form and stabilize the enzyme-chromatin system by using the activity of the protease to monitor its binding to DNA and DNA-histone complexes. During salt extraction of chromatin, the protease is released at an ionic strength between that required for the extraction of the slightly lysine-rich histones (H2A and H2B) and the arginine-rich histones (H3 and H4). The reassociation of this nonhistone protein to DNA has an absolute requirement for the H3--H4 tetramer and is only enhanced by the H2A--H2B dimer in the presence of the tetramer. We believe that the binding of the enzyme onto DNA requires some histone-elicited compaction of the helix. We have also examined the distribution of this enzyme within the chromatin fiber by isolating pools of monomer nucleosomes from micrococcal nuclease digests of 0.6 M NaCl extracted chromatin and from reconstituted DNA-protein complexes. The H2A-protease is found with these monomer nucleosome pools, and no activity can be detected in the low molecular weight products released during the digestion. Thus, by virtue of its extraction characteristics from chromatin and its association with isolated nucleosomes, this nonhistone protein exhibits properties hitherto assigned only to the inner histones.

Studies on histones and non-histone proteins from rats treated with dimethylnitrosamine

A study has been made of the histone and non-histone chromosomal proteins of rat liver after treatment in vivo with dimethylnitrosamine (DMN) (2 mg/kg). DMN was found not to affect histone turnover, as measured by 3H-labelled amino-acids incorporation. A decrease was observed in specific activity of the histones with time after injection of [14C]DMN or [14C]-formate and this was attributable to demethylation of both abnormal and normal methylation sites in these proteins. In the case of the non-histone proteins, DMN was found to increase greatly the turnover of those non-histone proteins loosely associated with chromatin DNA and RNA; turnover of those non-histone proteins tightly bound to chromatin DNA and RNA was unaffected. Demethylation of both normal and abnormal methylation sites was found to take place from both non-histone protein fractions. In the case of the loosely bound non-histone proteins a lower rate of demethylation was observed after DMN treatment.

Two modes of aggregation of artificial H1-DNA complexes depending on the rate of decrease of ionic strength

The properties of H1-DNA artificial complexes, formed at different rates of decrease of NaCl concentration from 0.9 to 0.15 M, were investigated. It was found that two distinct processes, both depending on the rate of the concentration decrease, lead to the formation of aggregates differing in: the ability to form sediments, the distribution of sedimentation constants, the initial turbidity and its changes during trypsin and DNAase I digestion, and the H1/DNA ratio in the sediments. The accessibility of DNA in the complexes to DNAase I and the properties of nonaccessible DNA fragments led us to the conclusion that, at the H1/DNA ratio equal 0.2, the H1 molecules are clustered along the DNA chain independently of the rate of complex formation.

Chromosomal proteins in hepatocarcinogenesis

The chromosomal proteins of rat liver were studied by SDS-gel electrophoresis during the process of nitrosomorpholine-induced hepatocarcinogenesis, in the primary hepatomas thus obtained, and in their metastases. It was found that an increased proteolytic activity was present in liver homogenates from carcinogen-fed animals which caused differences between the nonhistone chromosomal proteins of control and carcinogen-treated livers. These differences disappeared in the presence of the protease inhibitor PMSF. In the primary hepatomas slight quantative changes were observed: an increased amount of two proteins of 43000 and 63000 daltons molecular weight, respectively, and a decrease in the histone subfraction H 1 degrees. In the metastases both quantative and qualitative differences were detected: a strong decrease in the protein bands corresponding to the contractile proteins alpha-tubulin, beta-tubulin, and actin; an increased content of the 63000 dalton protein; the appearance of new proteins of approximately 60000, 90000, and 120000 daltons molecular weight, and the complete disappearance of histone H 1 degrees.

Solubilisation of Epstein-Barr virus (EBV)-associated nuclear antigen from Raji cells and chromatin by treatment with various molarities of NaCl

The solubilisation of Epstein-Barr virus (EBV)-associated nuclear antigen (EBNA) by treatment with various molarities of NaCl was investigated using the 125I--IgG absorption assay. Ninety percent of the antigenic activity detected using the 125I--IgG absorption assay was insoluble at 0.15 M NaCl. It could be rendered soluble by treatment with 2.0 M NaCl, but reprecipitated upon return to 0.15 M NaCl. EBNA was partially extracted from Raji chromatin by treatment with 0.35 M NaCl. The efficiency of extraction was increased by homogenisation in 2.0 M NaCl followed by dialysis to 0.35 M NaCl. The data demonstrate the close association of EBNA with Raji chromatin and suggest that it may be a chromatin-associated non-histone protein.

Multiplication of parvovirus LuIII in a synchronized culture system. IV. Association of viral structural polypeptides with the host cell chromatin

Newly synthesized structural polypeptides of parvovirus LuIII, VP1 (62,000 daltons) and VP2 (74,000 daltons), were detected in nuclei of synchronized, infected HeLa cells at 11 to 12 h postinfection, i.e., after cells had passed through the S phase of the cell cycle. At this time, most of intranuclear viral polypeptides were associated with the chromatin acidic proteins. However, 13 to 14 h postinfection, about one-third of intranuclear VP1 and VP2 also could be extracted in the fraction containing nuclear sap proteins. According to pulse-chase experiments, VP1 and VP2 accumulated in the chromatin with a time lag of 20 to 30 min. About 90% of these chromatin-associated viral polypeptides represented empty viral capsids. In addition, chromatin prepared at 14 h postinfection contained 90 to 95% of the total intranuclear viral 16S replicative-form DNA. Since viral replicative-form DNA and empty viral capsids seem to be associated specifically with cellular chromatin, we assume that this subnuclear structure is the site of the synthesis of progeny viral DNA and the formation of complete virions.

Comparison of some properties of chromatin non-histone proteins and nuclear sap proteins

The properties of rat liver and thymus non-histone and nuclear sap proteins were compared. The distribution of total, labile-bound and 0.35 M NaCl extractable non-histone proteins from one organ on polyacrylamide-gel electrophoresis in the presence of sodium dodecylsulphate is quite similar. On electrophoresis non-labelled and 32P-labelled non-histone and nuclear sap proteins from one organ differ from one another both qualitatively and quantitatively. We did not find an appreciable difference between non-labelled non-histone proteins isolated from liver and thymus. The distribution of 32P-labelled non-histone proteins from various organs differs quantitatively rather than qualitatively. Non-labelled and 32P-labelled nuclear sap proteins from liver and thymus differ significantly. 'Free' nuclear sap proteins and the proteins of ribonucleoprotein particles from thymus nuclei contain a great quantity of identical polypeptides, whereas other polypeptides are specific to each of these protein fractions. Upon incubation of nuclei with [gamma-32P]ATP the label is incorporated into all the fractions of nuclear protein. The nuclear proteins are phosphorylated at decreasing rates in the order: labile-bound non-histone proteins greater than firmly bound non-histone proteins greater than 'free' nuclear sap proteins = proteins of ribonucleoprotein particles greater than histones. Nuclear sap and non-histone proteins contain protein kinases capable of phosphorylating both these proteins and histones. Histone phosphorylation is sharply inhibited after addition of DNA, the protein kinases of nuclear sap phosphorylating less effectively the histones complexed with DNA than the non-histone proteins. Both non-histone and nuclear sap proteins contain fractions interacting in vitro with DNA. Denatured DNA binds twice as much 32P-labelled nuclear sap proteins and a little more 32P-labelled non-histone proteins than native DNA. Denatured DNA binds non-histone and nuclear sap proteins much more effectively than native DNA. It was shown by the membrane filter technique that the major part of the nuclear sap and non-histone proteins interacting with native DNA binds to it non-specifically. A certain portion of non-histone and nuclear sap proteins interacts specifically with homologous denatured DNA. The possible role of non-histone and nuclear sap proteins in the regulation of transcription is discussed.

Histone content in relation to amount of heterochromatin and developmental stage in three species of Drosophila

Relative amounts of various histone fractions in Drosophila chromatin were estimated densitometrically on electrophoretic gel separations. Several consistent and highly significant differences were obtained between larval and adult chromatin. The arginine-rich histones showed the most conspicuous changes: higher amounts of H4 in larvae, higher H3 in adults. The level of modification of these histones was clearly higher in larval than in adult chromatin. The modification of the two slower subfractions of H4 involved, in all probability, phosphorylation as well as acetylation. In all types of Drosophila chromatin studied 50% or more of the H2a molecules were phosphorylated--a remarkably high proportion. The species differences observed in relative amounts of histone were consistent in both stages of development. D. melanogaster differed from D. hydei and D. virilis in all histones except H2b, while the latter two species were generally similar. The interspecific variation in histone pattern was generally not correlated to differences in content of heterochromatin. The level of modification of H2 was, however, presumably an exception, as it was significantly lower for both larvae and adults in D. virilis than in the other two species. These differ from D. virilis in containing appreciably lower proportions of heterochromatic chromosome segments.

In vitro transcription of partially deproteinised and reconstituted chromatins from pigeon erythroid cells

The role of protein fractions extracted from chromatin preparations with NaCl concentrations up to 0.7 M in the additional repression of pigeon erythrocyte genome was investigated. The chromatins from erythroblasts and erythrocytes were dissociated with 0.7 M NaCl and reconstituted from dissociated components to obtain the "original" and "hybrid" chromatins. The protein fraction extracted from erythrocyte chromatin at 0.7 M NaCl was more efficient in the restriction of transcription with partially deproteinised chromatin from both erythroblasts and erythrocytes. The partially deproteinised chromatin from both erythorblasts and erythrocytes. The partially deproteinised chromatins were also complexed in various conditions with purified F1 or F2c histones. In such complexes, F2c histone was a stronger inhibitor of template activity than histone F1.

Heterogeneous distribution of DNA alkylation products in rat liver chromatin after in vivo administration of N,N-di[14C]methylnitrosamine

Poly-l-lysine (PL) binds to about 50% of chromatin DNA, rendering it resistant to degradation by DNAase I. Separation of the unbound DNA as acid-soluble nucleotides allows the fractionation of chromatin DNA into two zones. After in vivo administration of N,N-di[14C]methylnitrosamine, the amount of alkylation in DNA was found to be lower in the polylysine-binding regions. Some possible reasons for this heterogeneous distribution are discussed.

Studies on liver chromatin from rats treated with dimethylnitrosamine

Shortly after injecting a single low dose of N,N-dimethylnitrosamine into rats, the DNA, RNA and histones are methylated, the level in the DNA greatly exceeding that in the histones. The composition of the chromatin and the electrophoretic profiles of the histone and non-histone proteins are not detectably different from those obtained from control animals. Electric birefringence studies suggest that methylation may result in both interparticle cross-linking and some localised loosening of the DNA-protein complex complex.

Non-histone chromosomal proteins. Their isolation and role in determining specificity of transcription in vitro

We describe a method for fractionation of chromatin components by selective dissociation with salt in buffers containing 5 M urea in combination with cromatography on hydroxyapatite at 4 degrees C. This results in two histone and four non-histone fractions which are recovered in high yield and with minimal proteolytic contamination. Template capacity measurements of the isolated chromatins and pre-saturation competition hybridization experiments support the idea that a group of non-histone proteins activate the transcription of specific DNA sequences which were not transcribed from purified DNA to the same extent. In reconstitution experiments a non-histone protein fraction, NH4, prepared from lymphocyte chromatin by hydroxyapatite chromatography is shown to cause transcription in vitro of lymphocyte-specific RNA sequences. A subfraction with a molecular weight of 30 000 comprising 40% of the NH4 fraction protein is characteristic for this tissue and not found in liver chromatin.

Histone-like protein in the prokaryote Thermoplasma acidophilum

The DNA of the prokaryote Thermoplasma acidophilum is associated with a histone-like protein that has the following properties: it has a high content (23%) of basic amino acids, is positively charged at neutral pH, is soluble in acid, and can stabilize DNA against thermal denaturation. In polyacrylamide gel electrophoresis, in the presence of either sodium dodecylsulfate or urea, it migrates at the same rate as histone IV (F2a1) of calf thymus. The amino acid composition, however, it unusually rich in the amides of acidic amino acids (16-20%), and it does not appear to be closely homologous to any of the classes of eukaryotic histones. Escherichia coli DNA, on the other hand, was associated with no detectable acid-soluble proteins, and the nucleoprotein thermally denatured at a lower temperature than pure DNA.

Preparation and some properties of strongly acidic proteins from calf-thymus nucleohistone

The isolation of acidic proteins from calf-thymus nucleohistone (starting from purified nuclei) is reported. The method involved dissociation in 1 M KCl solution. Denaturating agents were not used at all. After electrophoresis on polyacrylamide gel, fractions containing a small number of components were obtained. The fractions display high ratios of acidic to basic amino acids, the ratios ranging from 4.0 to 1.5. In all fractions, the major components were of molecular weights in the ranges 12000-15000 and 24000-28000 as determined by gel-disc electrophoresis in dodecylsulphate and by equilibrium ultracentrifugation. Minor components of high molecular weights were also present. Amino-acid analyses are also reported. The tryptophan content was determined by a fluorometric method. Circular dichroism spectra depict a very low content of alpha-helicity that did not increase at higher ionic strength. A marked RNA-polymerase activity was found in one fraction.