Proteins associated with heterogeneous nuclear RNA in eukaryotic cells

When HeLa cell nuclei axe mechanically disrupted in either hypotonic or isotonic buffers, heterogeneous nuclear RNA is recovered from the post-nucleolar fraction in the form of EDTA-resistant ribonucleoprotein particles, which sediment between 40 S and 250 S in sucrose gradients containing 0.01 m or 0.15 m-NaCl. That the RNA in these particles is HnRNA² is indicated by its heterodisperse sedimentation (20 to 80 S) and its continued synthesis in concentrations of actinomycin D that selectively inhibit the synthesis of ribosomal RNA. The specificity of the HnRNA-protein complexes is evidenced by the failure of deliberate attempts to generate artificial RNP by the addition of deproteinized HnRNA to intact or disrupted nuclei at low ionic strength.The proteins bound to HnRNA are complex. In HeLa cells, HnRNP particles contain proteins with molecular weights from 39,000 to approximately 180,000 (sodium dodecyl sulfate-polyacrylamide gel electrophoresis) and isoelectric points between 4.9 and 8.3 (analytical isoelectric focusing). They are readily distinguishable from proteins in other cell fractions, including those in chromatin.Exposure of HeLa HnRNP particles to 0.5 m-NaCl reduces their average sedimentation velocity by approximately 30%. CsCl density-gradient analysis reveals that this is accompanied by the loss of a major portion of the proteins. However, a significant fraction of the HnRNP (25 to 30%) is resistant to high salt concentrations and continues to band at the same density as native HnRNP (1.43 g/cm³). This is true even after prolonged exposure (24 h) to high salt. The salt-resistant HnRNP is enriched for proteins above 60,000 molecular weight. In at least these two respects, this sub-class of HnRNP resembles “messenger RNP” prepared from cytoplasmic polyribosomes, which is also salt-stable and contains relatively high molecular weight proteins.HnRNP particles can also be recovered from HeLa cell nuclei lysed in high salt but these contain many extra proteins, notably histones, and sediment much faster in sucrose gradients than particles prepared as above. HnRNP is not liberated by extracting HeLa nuclei in 0.14 m-NaCl, pH 8.0 (Samarina et al., 1967) unless the temperature is 20 °C or higher. In this case the particles are converted to 45 S structures, which contain partially degraded HnRNA. 45 S particles can also be produced by subjecting 40 to 250 S HnRNP to a very limited digestion with pancreatic ribonuclease (1 to 2 hits/molecule).HnRNP particles have similar sedimentation velocities (40 to 300 S) when isolated under physiological ionic conditions from a variety of mammalian cells, including WI38 human diploid fibroblasts, mouse L-cells, monkey kidney cells and rat liver. However, electrophoresis reveals a distinct pattern of HnRNP proteins for each cell type. It is proposed that this cell-specificity reflects a situation in which HnRNA molecules that differ in nucleotide sequence are complexed with different sets of proteins, so that the resulting HnRNP particles are biochemically distinct at each genetic locus. This hypothesis is discussed in relation to the cytology of lampbrush and polytene chromosomes.     

Comparative studies of the effects of galactosamine and actinomycin D on nuclear ribonucleoprotein particles from rat liver

Nuclear ribonucleoprotein particles of 75S were obtained from rat liver nuclei after mild sonication and isotonic salt extraction only when the preparation was carried out in the presence of a cytosolic ribonuclease inhibitor. Particles of 38S were isolated in the absence of inhibitor. The 38S nuclear ribonucleoprotein (nRNP) particles showed a protein/RNA ratio of 8, and a buoyant density of 1.39 g/ml in cesium chloride solution. They were further characterized by the pattern of their proteins on sodium dodecylsulfate (SDS)-acrylamide gel electrophoresis. Incorporation of [³H]cytidine into nuclear RNA was reduced to approx. 20% of controls 3 and 6 h after administration of galactosamine or actinomycin D. However, when [³H]cytidine was administered 30 min prior to the drugs a decrease of radioactivity in 38S nRNP particles to 43 and 81% of controls was found after 3 h. The yield of 38S particles 3 h after galactosamine or actinomycin D dropped to 41% and 78% of controls, and after 6 h to 43 and 70%, respectively. Six hours after galactosamine or actinomycin D treatment, the protein to RNA ratio increased to 13.3 and 9.1. No significant changes in protein patterns 3 h after treatment with galactosamine or actinomycin D were observed. Possible mechanisms, such as impaired transport of 38S nRNP particles after actinomycin D treatment or increased loss of particles due to a defective nuclear membrane after galactosamine administration are discussed.     

Synthesis of messenger and ribosomal RNA precursors in isolated nuclei of the cellular slime mold Dictyostelium discoideum

When incubated with all four ribonucleoside triphosphates, isolated nuclei of the cellular slime mold, Dictyostelium discoideum, will synthesize RNA linearly for 10 to 50 minutes, depending on the salt concentration of the reaction. A fraction (10 to 30%) of the RNA labeled in isolated nuclei binds to immobilized polyuridylic acid. By the following criteria this RNA species is identical to the messenger RNA precursor characterized in whole cells: (a) both contain polyadenylic acid sequences of identical size; (b) they have the same base composition; (c) they have the same mean size as determined by dimethylsulfoxide—sucrose centrifugation; (d) they renature to excess nuclear DNA with similar kinetics; and (e) synthesis of both RNAs is resistant to 2 to 3 μg of actinomycin D/ml. Two independent RNA polymerase activities appear to synthesize poly(A)-containing RNA in isolated nuclei. One is equally active at 0.01 m-KCl and 0.25 m-KCl and is resistant to α-amanitin; the other is considerably more active at the higher salt concentration and is sensitive to α-amanitin. By the criteria of sedimentation coefficients, base composition and sensitivity of synthesis to actinomycin D, the remainder (70 to 90%) of the RNA synthesized by isolated nuclei was identical to cellular ribosomal RNA or its precursors.     

REPOPULATION OF THE POSTMITOTIC NUCLEOLUS BY PREFORMED RNA

This study is concerned with the fate of the nucleolar contents, particularly nucleolar RNA, during mitosis Mitotic cells harvested from monolayer cultures of Chinese hamster embryonal cells, KB6 (human) cells, or L929 (mouse) cells were allowed to proceed into interphase in the presence or absence (control) of 0.04–0 08 µg/ml of actinomycin D, a concentration which preferentially inhibits nucleolar (ribosomal) RNA synthesis 3 hr after mitosis, control cells had large, irregularly shaped nucleoli which stained intensely for RNA with azure B and for protein with fast green. In cells which had returned to interphase in the presence of actinomycin D, nucleoli were segregated into two components easily resolvable in the light microscope, and one of these components stained intensely for RNA with azure B. Both nucleolar components stained for protein with fast green In parallel experiments, cultures were incubated with 0.04–0 08 µg/ml actinomycin D for 3 hr before harvesting of mitotic cells, then mitotic cells were washed and allowed to return to interphase in the absence of actinomycin D. 3 hr after mitosis, nuclei of such cells were devoid of large RNA-containing structures, though small, refractile nucleolus-like bodies were observed by phase-contrast microscopy or in material stained for total protein. These experiments indicate that nucleolar RNA made several hours before mitosis persists in the mitotic cell and repopulates nucleoli when they reform after mitosis     

A COMPARISON BETWEEN HETEROGENEOUS NUCLEAR RNA AND POLYSOMAL MESSENGER RNA IN HELA CELLS BY RNA-DNA HYBRIDIZATION

Heterogeneous nuclear RNA (HnRNA) and mRNA from cytoplasmic polyribosomes of HeLa cells have been compared by RNA-DNA hybridization tests. 1 µg of HeLa cell DNA binds 0.05–0.10 µg of either HnRNA or mRNA. In addition, HeLa DNA that is preexposed to unlabeled HnRNA was found to have a reduced capacity to bind either HnRNA or mRNA. The results are compatible with considerable sequence similarity in the two types of RNA but, as is discussed, firm conclusions are precluded by imperfections of the hybridization reaction as presently employed.     

LIGHT AND ELECTRON MICROSCOPIC RADIOAUTOGRAPHY OF HEPATIC CELL NUCLEOLI IN MICE TREATED WITH ACTINOMYCIN D

Nucleolar partition induced by actinomycin D was used to demonstrate some aspects of nucleolar RNA synthesis and release in mouse hepatic cells, with light and electron microscopic radioautography. The effect of the drug on RNA synthesis and nucleolar morphology was studied when actinomycin D treatment preceded labeling with tritiated orotic acid. Nucleolar partition, consisting of a segegration into granular and fibrillar parts was visible if a dosage of 25 µg of actinomycin D was used, but nucleolar RNA was still synthesized. After a dosage of 400 µg of actinomycin D, nucleolar RNA synthesis was completely stopped If labeling with tritiated orotic acid preceded treatment with 400 µg of actinomycin D, labeled nucleolar RNA was present 15 min after actinomycin D treatment while high resolution radioautography showed an association of silver grains with the granular component. At 30 min after actinomicyn D treatment all labeling was lost. Since labeling was associated with the granular component the progressive loss of label as a result of actinomycin D treatment indicated a release of nucleolar granules. The correlation between this release and the loss of 28S RNA from actinomycin D treated nucleoli as described in the literature is discussed.     

The behaviour of heterogeneous nuclear ribonucleic acid in partially and completely denaturing conditions

It is shown that the heterogeneous nuclear RNA (HnRNA) synthesized in the presence of actinomycin and at low and high temperatures sediments in low-ionic-strength sucrose gradients between the rRNA components, similar to the unmethylated RNA synthesized under ;step-down' conditions. If the ionic strength is increased then the HnRNA sediments more rapidly than 28S rRNA, with a large proportion about the 45S precursor rRNA position. Initially this was thought to be due to aggregation of the HnRNA; however, centrifugation and electrophoresis in completely denaturing conditions suggest that the molecular weight of this species of RNA is very large The experiments reveal that HnRNA is conformationally unstable relative to the nucleolar RNA and that the slower sedimentation rate of HnRNA in 5mm-EDTA-Tris base-sucrose gradients reflects the greater expansion of the HnRNA relative to the nucleolar RNA. The implications of this finding are discussed.     

Stability of ribosomes of Staphylococcus aureus S6 sublethally heated in different buffers.

Cells of Staphylococcus aureus heated at 52 degrees C in magnesium-chelating buffers [pH 7.2, 50 mM potassium phosphate or 50 mM tris(hydroxymethyl)-aminomethane containing 1 mM ethylenediaminetetraacetic acid] leaked 260-nm absorbing material, shown to be RNA, and suffered destruction of their ribosomes. These cells did not regain their salt tolerance when repair was carried out in the presence of actinomycin D (5 microgram/ml). Cells similarly heated in magnesium-conserving buffers [pH 7.2, 50 mM tris(hydroxymethyl)aminomethane containing 10 mM MgCl2 or piperazine buffer] did not leak RNA, suffered no ribosomal damage when heated for 15 min, and recovered, at least partially, in the presence of actinomycin D. Ribosomal damage, is therefore, a consequence of Mg2+ loss and is not an effect of heat per se. Cells suspended in either Mg2+-chelating or Mg2+-conserving buffers lost salt tolerance to about the same extent during heating at 52 degrees C. Therefore, sublethal heat injury can not be attributed to ribosomal damage.     

The effect of inhibition of RNA synthesis by actinomycin D on the population of basic polypeptides of the 30S unclear ribonucleoprotein particles

In rats injected intraperitoneally with actinomycin D (2 mg/kg body weight) 12 h earlier, the yield of the 30S ribonucleoprotein particles isolated from liver nuclei by extraction with 0.1 M NaCl at pH 8.0 decreased by 60 per cent. The protein-to-RNA ratio of these particles increased to 32:1 from the ratio 4.4:1 found in the same particles isolated from the nuclei of liver of control rats. The particles isolated from the liver nuclei of rats injected with actinomycin D were depleted of all charge isomers of the two most prominent polypeptides (33,000 and 39,000 daltons) present in the particles of liver of control animals. The most abundant protein in these particles was a 43,000 dalton polypeptide. This polypeptide is the least prominent of the 3 major polypeptides present in the control particles. The same charge isomers of the 43,000 dalton polypeptide were present in the nuclear ribonucleoprotein particles isolated from the liver of control animals and from the liver of animals treated with actinomycin D 12 h earlier. In control animals the nuclear ribonucleoprotein monoparticles isolated from kidney contained 3 major polypeptides of the same molecular weight with the same distribution of their charge isomers as were present in the particles isolated from liver nuclei. The injection of actinomycin D 12 h earlier was without any effect on the protein composition of the 30S nuclear ribonucleoprotein particles of rat kidney.     

In organello transcription in maize mitochondria and its sensitivity to inhibitors of RNA synthesis

Purified mitochondrial preparations from etiolated maize shoots support the incorporation of radioactivity from labeled UTP into RNA. The incorporation is linear with time for up to 2 hours, shows Michaelis-Menton kinetics with respect to the concentration of the labeled substrate, UTP, and has salt and pH optima which are different than those previously reported for RNA synthesis by isolated chloroplasts. When a crude mitochondrial preparation is subjected to isopycnic sucrose gradient centrifugation, the bulk of the RNA synthetic activity co-sediments with mitochondrial marker enzymes and with the mitochondrial 26S and 18S rRNAs. Maize mitochondrial RNA synthesis is prevented by actinomycin D and ethidium bromide but unaffected by α-amanitin. It is strongly inhibited by rifampicin at concentrations which have no effect on nuclear and chloroplast RNA synthesis, but only moderately inhibited by rifampicin at concentrations which completely inhibit bacterial RNA synthesis. The optimization, cell fractionation, and inhibitor data all suggest that contaminating organelles and bacteria do not contribute appreciably to the RNA synthesis in purified mitochondrial preparations.     

Detection of 8-hydroxydeoxyguanosine in K562 human hematopoietic cells by high-performance capillary electrophoresis

A method for the detection of 8-hydroxydeoxyguanosine by high-performance capillary electrophoresis (HPCE) was developed. Separations were performed in an uncoated silica capillary (44 cm × 75 μm I.D.) with a P/ACE system with diode-array detector. The separation of purine deoxynucleosides and 8-hydroxydeoxyguanosine was optimized with regard to pH, temperature, applied potential and hydrodynamic injection time. Optimum conditions were 20 mM borate buffer (pH 9.5), 25°C, 25 kV, 20 s load and detection at 254 nm. This method allowed the detection of 8-hydroxydeoxyguanosine in the presence of a 10⁵-fold higher amount of deoxyguanosine. Isolated nuclei from K562 human hematopoietic cells were treated with 15 mM hydrogen peroxide for 2 h. The nuclei were extensively dialyzed and DNA was isolated, enzymatically hydrolyzed to the deoxynucleosides and analyzed by HPCE. DNA from hydrogen peroxide treated nuclei had a 4-fold higher content of 8-hydroxydeoxyguanosine than untreated controls. HPCE analysis of 8-hydroxydeoxyguanosine is fast and simple. Furthermore, it requires a very small sample volume, which makes it useful for biomedical and clinical applications.     

Translocation of nucleolar phosphoprotein B23 ( ) induced by selective inhibitors of ribosome synthesis

To elucidate the possible role of nucleolar phosphoprotein B23 in ribosome synthesis, drugs which inhibit the processing of ribosomal RNA were employed. After treatment with actinomycin D, toyocamycin or high doses of α-amanitin, a uniform nucleoplasmic fluorescence was observed. Low doses of α-amanitin and the protein synthesis inhibitor puromycin and cycloheximide had no effect on protein B23 translocation. By ELISA immunoassay, there was a 60% decrease in the amount of protein B23 in the nucleoli of the actinomycin D-treated cells as compared with the control nucleoli. Conversely, the amount of protein B23 in the nucleoplasm (excluding nucleoli) was 3-fold higher in the actinomycin D-treated cells. Preribosomal ribunucleoprotein particles (pre-rRNPs) were extracted from isolated nucleoli of Novikoff hepatoma ascites cells and fractionated on sucrose density gradients. Protein B23 was found co-localized with the pre-rRNPs as determined by ELISA assays which agrees with previous studies. The proteins in these 80 S and 55 S pre-ribosomal ribonucleoprotein particles were fractionated by 10% gel electrophoresis. Immunoblots showed protein B23 was present in both pre-rRNPs.     

Nucleolar and nucleoplasmic RNA polymerase activity in different regions of rat brain during postnatal development.

RNA polymerase activities of whole nuclei, of isolated and purified nucleoli and of the nucleoplasmic fractions obtained from cerebral hemispheres, cerebellum and brain stem of rat at different days of postnatal development have been determined. In the whole nuclei the fraction of RNA polymerase which is sensitive to alpha-amanitin, is strongly affected by salt concentration; at low ionic strength most of the activity is resistant to the drug while at high ionic strength the enzymatic activity shows a greater sensitivity to the drug. In isolated nucleoli RNA synthesis is not inhibited at all by alpha-amanitin. The biosynthesis of RNA, at low ionic strength, is inhibited by low doses of actinomycin D, whereas at high ionic strength it is remarkably inhibited only by higher doses of the drug. The sensitivity of the reaction to alpha-amanitin and actinomycin D provide good evidence that UTP or GTP incorporation into RNA in purified nuclei and nucleoli, is dependent on RNA polymerases acting on DNA template and is not dependent on homopolymer formation. These results show that in the whole brain nuclei at low ionic strength there is a preferential synthesis of rRNA, whereas at high ionic strength the synthesis of heterogenous RNA predominates. In isolated nucleoli the synthesis of RNA is restricted to rRNA.     

THE ACTION OF α-AMANITIN ON RNA SYNTHESIS IN CHINESE HAMSTER OVARY CELLS : Ultrastructural and Biochemical Studies

α-Amanitin acts in vitro as a selective inhibitor of the nucleoplasmic form B RNA polymerases. Treatment of Chinese hamster ovary (CHO) cells with this drug leads principally to a severe fragmentation of the nucleoli. While the ultrastructural lesions induced by α-amanitin in CHO cells and in rat or mouse liver are quite similar, the results diverge concerning the effect on RNA synthesis. It has been shown that in rat or mouse liver α-amanitin blocks both extranucleolar and nucleolar RNA synthesis. Our autoradiographic and biochemical evidence indicates that in CHO cells high molecular weight extranucleolar RNA synthesis (HnRNA) is blocked by the α-amanitin treatment, whereas nucleolar RNA (preribosomal RNA) synthesis remains unaffected even several hours after the inhibition of extranucleolar RNA synthesis. Furthermore, the processing of this RNA as well as its transport to the cytoplasm seem only slightly affected by the treatment. Finally, under these conditions, the synthesis of the low molecular RNA species (4–5S) still occurs, though less actively. The results are interpreted as evidence for a selective impairment of HnRNA synthesis by α-amanitin in CHO cells.     

Concentration of particular high molecular mass phosphoproteins in rat liver nuclei and nuclear matrix decreases following inhibition of RNA synthesis by α-amanitin

Purified liver nuclei were isolated from rats treated with non-lethal doses of α-amanitin, actinomycin D, galactosamine or cycloheximide. The nuclei were incubated in the presence of adenosine 5′-[γ-³²P]triphosphate, and digested with DNAase or DNAase plus high salt concentrations to prepare nuclear residual structures. Using SDS-polyacrylamide gel electrophoresis followed by autoradiography, samples from untreated rats were shown to contain major phosphoproteins in the range 76–260 kDa, with a prominent triplet of bands with 110, 117 and 128 kDa. Treatment of animals with α-amanitin or high doses of actinomycin D and galactosamine caused a significant decrease in the concentration of a few phosphorylated species, including the 110 kDa protein in whole nuclei, and their disappearance from the nuclear matrix or residual ribonucleoprotein structures after 1–3 h. The changes were reversible, complete recovery being observed after 5 h in the case of α-amanitin. No similar results were obtained with nuclei from rats treated with the translation inhibitor cycloheximide. The data are discussed in view of a possible effect of certain high molecular mass phosphoproteins on reactions of the heterogeneous nuclear RNA/mRNA pathway in the cell.     

RNA Synthesis in isolated living and fixed nuclei ofAcetabularia

Summary Isolated, gently fixed nuclei ofAcetabularia mediterranea are capable of incorporating nucleotides into RNA. This has been demonstrated by (a) sensitivity of the synthesized products to RNase, (b) inhibition of RNA synthesis by actinomycin D and (c) incubation of nuclei without CTP and GTP. Experiments with -amanitin show that at least two RNA polymerases are active in isolated fixed nuclei. Also isolated, living nuclei incorporate nucleotides into RNA. RNA synthesis was located autoradiographically and quantified by a TV-analysator.     

A tentative initiation inhibitor of chromosomal heterogeneous RNA synthesis

The nucleoside analogue 5,6-dichloro-1-β-d-ribofuranosylbenzimidazole inhibits labelling of chromosomal, high molecular weight RNA in the salivary gland cells of Chironomus tentans but does not interfere with the synthesis of ribosomal RNA and chromosomal low molecular weight RNA. When DRB2 was added after an initial labelling period (pulse-chase experiment) the radioactivity diminished preferentially in the lower molecular weight region of the HnRNA spectrum. After short chase periods the activity decreased moderately, or even increased, in the higher molecular weight region of the spectrum (75–100 S). After prolonged chases there was an overall and similar reduction in the activity in the whole HnRNA distribution. If the glands were preincubated in DRB for a short period before exposure to radioactive precursors, the label was again diminished more in HnRNA of low molecular weight than in that of higher molecular weight. When α-amanitin or actinomycin D, both known to be inhibitors of RNA chain elongation, replaced DRB in pulse-chase experiments, labelling of HnRNA was depressed in all size classes to the same extent. The accumulated data suggest that DRB acts, in explanted salivary gland cells, at the polymerase level by interfering with the initiation of chromosomal HnRNA synthesis.     

Four fluorochromes for the demonstration and microfluorometric estimation of RNA

Summary Microfluorometric estimates of total RNA were made in selected test material stained with berberine sulfate, acridine orange, and Hoechst 33258. These measurements were compared with those obtained with propidium iodide, which is known to interact only with double-stranded nucleic acids. It was observed that all of the fluorochromes, including propidium iodide, yielded very similar patterns of fluorescence in the various types of material tested. In isolated thymocyte and hepatocyte nuclei stained with either propidium iodide or Hoechst 33258 at pH 2, it was evident that RNA could be estimated only indirectly by measuring the amount of fluorescence before and after extraction with RNase. It was apparent that the total fluorescence of small thymocyte nuclei was affected much less by RNase extraction than that of 2c hepatocyte nuclei. Attempts to obtain direct estimates of RNA by exposing the preparations to DNase were not successful: the fluorescence of thymocyte nuclei dropped almost to zero, and hepatocyte nuclei could no longer be assigned to distinct ploidy classes. In addition, since the highly condensed chromatin of thymocyte nuclei was stained much more prominently than the looser chromatin of hepatocyte nuclei with Hoechst 33258, it was apparent that this fluorochrome — when used at pH 2 — has potential usefulness as a probe of organizational differences in chromatin.