Evidence for the nuclear origin of RNA polymerases identified in the cytosol: release of enzymes from the nuclei isolated in isotonic sucrose

Phosphorylation of acid-soluble chromatin proteins from tissues of different species by purified cyclic GMP-dependent protein kinase

1. Phosphorylation of acid-soluble chromatin proteins from thymus or liver of calf, rabbit, pig, rat, rooster and trout by purified cyclic GMP-dependent protein kinase was studied in vitro using acetic acid-urea slab gel electrophoresis and autoradiography. 2. HMG 14, histone H1 and an unknown band representing probably a proteolytic fragment of histone H1 were phosphorylated in all mammals studied. 3. In avian liver, HMG 14 showed no phosphorylation and histone H1 was replaced by a H1(0)/H5-like heavily phosphorylated protein. 4. The only 32P-acceptor in trout liver apparently belongs to the C/D-family of acid-soluble chromatin proteins. H6-protein was not phosphorylated.

Nucleocytoplasmic RNA transport

A number of closely related post-transcriptional facets of RNA metabolism show nuclear compartmentation, including capping, methylation, splicing reactions, and packaging in ribonucleoprotein particles (RNP). These nuclear 'processing' events are followed by the translocation of the finished product across the nuclear envelope. Due to the inherent complexity of these interrelated events, in vitro systems have been designed to examine the processes separately, particularly so with regard to translocation. A few studies have utilized nuclear transplantation/microinjection techniques and specialized systems to show that RNA transport occurs as a regulated phenomenon. While isolated nuclei swell in aqueous media and dramatic loss of nuclear protein is associated with this swelling, loss of RNA is not substantial, and most studies on RNA translocation have employed isolated nuclei. The quantity of RNA transported from isolated nuclei is related to hydrolysis of high-energy phosphate bonds in nucleotide additives. The RNA is released predominantly in RNP: messenger-like RNA is released in RNP which have buoyant density and polypeptide composition similar to cytoplasmic messenger RNP, but which have distinctly different composition from those in heterogeneous nuclear RNP. Mature 18 and 28S ribosomal RNA is released in 40 and 60S RNP which represent mature ribosomal subunits. RNA transport proceeds with characteristics of an energy-requiring process, and proceeds independently of the presence or state of fluidity of nuclear membranes. The energy for transport appears to be utilized by a nucleoside triphosphatase (NTPase) which is distributed mainly within heterochromatin at the peripheral lamina. Photoaffinity labeling has identified the pertinent NTPase as a 46 kD polypeptide which is associated with nuclear envelope and matrix preparations. The NTPase does not appear to be modulated via direct phosphorylation or to reflect kinase-phosphatase activities. A large number of additives (including RNA and insulin) produce parallel effects upon RNA transport and nuclear envelope NTPase, strengthening the correlative relationship between these activities. Of particular interest has been the finding that carcinogens induce specific, long-lasting increases in nuclear envelope (and matrix) NTPase; this derangement may underlie the alterations in RNA transport associated with cancer and carcinogenesis.(ABSTRACT TRUNCATED AT 400 WORDS)

Accurate initiation of rat ribosomal RNA gene transcription using a fractionated nuclear extract from normal liver and a hepatoma

Nuclear extracts obtained from normal rat liver and from Morris hepatoma 3924A were fractionated by DEAE-Sephadex chromatography. The fraction eluted with 175 mM (NH4)2SO4 (DE-B), which contains greater than 90% of RNA polymerase I activity, supported accurate transcription of cloned rat rDNA. A similar fraction obtained from the cytosol had all of the factors required for rDNA transcription. However, its transcriptional activity was at most one-sixth that of the corresponding nuclear fraction, as determined by the amount of protein needed to produce a similar quantity of the transcript. Unfractionated nuclear or cytosol preparations did not yield an accurate transcript. Optimal KCl and magnesium concentrations for rDNA transcription were 60 mM and 5-7.5 mM, respectively. The extent of transcriptional activity was in the following order: hepatoma nuclear fraction DE-B greater than whole cell extract derived from rat mammary adenocarcinoma cells much greater than normal liver fraction DE-B. The hepatoma preparation produced at least 10 times the amount of transcript produced by the corresponding liver nuclear preparation. Transcriptional activity was proportional to the levels of RNA polymerase I and to the rate of rRNA synthesis in these tissues.

Eukaryotic RNA polymerases

This review will attempt to cover the present information on the multiple forms of eukaryotic DNA-dependent RNA polymerases, both at the structural and functional level. Nuclear RNA polymerases constitute a group of three large multimeric enzymes, each with a different and complex subunit structure and distinct specificity. The review will include a detailed description of their molecular structure. The current approaches to elucidate subunit function via chemical modification, phosphorylation, enzyme reconstitution, immunological studies, and mutant analysis will be described. In vitro reconstituted systems are available for the accurate transcription of cloned genes coding for rRNA, tRNA, 5 SRNA, and mRNA. These systems will be described with special attention to the cellular factors required for specific transcription. A section on future prospects will address questions concerning the significance of the complex subunit structure of the nuclear enzymes; the organization and regulation of the gene coding for RNA polymerase subunits; the obtention of mutants affected at the level of factors, or RNA polymerases; the mechanism of template recognition by factors and RNA polymerase.

Modulation of RNA transport by polyvinylpyrrolidone

A number of studies have documented substantial loss of nuclear protein during aqueous nuclear isolation procedures. This loss can, to some extent, be counteracted by addition of impermeable macromolecules like polyvinylpyrrolidone, which prevent nuclear swelling. While nucleic acids appear to be much less susceptible to leakage during isolation, the effects of these additives on RNA release during in vitro incubation have not been examined. Here we show that addition of polyvinylpyrrolidone results in significant decreases in RNA transport; inhibition becomes maximal at 50-75 microM addition.

A study on the RNA polymerase activities in bovine thyroid nuclei isolated in isotonic sucrose, hypertonic sucrose or in anhydrous glycerol media. Influence of the isolation procedure on the electrophoretic pattern of acid soluble nuclear proteins

After differential pelleting of bovine thyroid bound RNA polymerase II was the more enriched enzyme activity in the nuclear fraction, and coincided best with the DNA profile. The RNA polymerase I + III activity was compared in nuclear fractions isolated either in 0.25 M sucrose (wet tissue) or in anhydrous glycerol (lyophilized tissue) or in 2.4 M sucrose (lyophilized tissue). Although the nuclei were more resistant to the isolation procedure in glycerol, more proteins were extracted by that procedure than during the isolation in 2.4 M sucrose. With the 2.4 M sucrose method a twofold enrichment of RNA polymerase I + III activity in respect to DNA occurred in the nuclei pointing to an exclusive localization of these activities within the nucleus. Using the same isolation procedure the different classes of histones were better resolved upon polyacrylamide gel electrophoresis.

Nuclear localization of aspartate transcabamoylase in Saccharomyces cerevisiae

The cytochemical technique using the in situ precipitation of orthophosphate ions liberated specifically by the aspartate carbamoyltransferase (ATCase) (EC 2.1.3.2) reaction indicated that in Saccharomyces cerevisiae this enzyme is confined to the nucleus. This observation is in accordance with the result reported by Bernhardt and Davis (1972), Proc. Natl. Acad. Sci. U. S. A. 69:1868-1872) on Neurospora crassa. The nuclear compartmentation was also observed in a mutant strain lacking proteinase B activity. This finding indicates that this proteinase is not involved in the nuclear accumulation of ATCase, and that the activity observed in the nucleus corresponds to the multifunctional form associated with the uracil path-specific carbamoylphosphate synthetase and sensitive to feedback inhibition by UTP. In a ura2 strain transformed by nonintegrated pFL1 plasmids bearing the URA2-ATCase activity encoding gene, the lead phosphate precipitate was observed predominantly in the cytoplasm. This finding enhances the reliability of the technique used by eliminating the possibility of an artifactual displacement of an originally cytoplasmic reaction product during the preparation of the material for electron microscopy. On the other hand, nuclei isolated under hypoosmotic conditions do not exhibit the ATCase activity that is recovered in the cytosolic fractions after differential centrifugation of the lysate in Percoll gradient. A release of the protein from the nuclei during the lysis step, consistent with its nucleoplasmic localization, is postulated.

Phosphorylation of high mobility group protein HMG 14 by a cyclic GMP-dependent protein kinase from avian liver nucleoli

A cyclic GMP-dependent protein kinase was previously found in the 0.3 M NaCl extract of avian liver nucleoli [1]. The kinase phosphorylates preferentially a protein of a molecular weight of approximately 11,000 present in calf thymus histone mixture (type IIA, Sigma) and in isolated liver nucleoli. Further studies with purified protein substrates have now indicated that the chromatin-associated protein, which is preferentially phosphorylated by the cyclic GMP-dependent kinase, is high mobility group protein HMG 14. Histone H1 was also a relatively good phosphate acceptor but in this case the phosphorylation was not cyclic GMP-dependent and therefore due to a different protein kinase present in the partially purified nucleolar extract. Acid hydrolysis of the phosphorylated HMG 14 and subsequent analysis by chromatography and high-voltage electrophoresis indicated that the phosphorylated amino acid residue in HMG 14 is phosphoserine.

Transcriptionally active RNA polymerases from Morris hepatomas and rat liver. Elucidation of the mechanism for the preferential increase in the tumour RNA polymerase I

The amount and/or activity of DNA-dependent RNA polymerase I, Ii and III from resting liver, regenerating liver and a series of Morris hepatomas (5123D, 7800, 7777, 3924A) were determined after extraction of the enzymes from whole tissue homogenates and subsequent fractionation by DEAE-Sephadex column chromatography. When compared with resting liver, the tumours exhibited a characteristic enzyme pattern in which polymerase I, but not II, was increased. The increase in RNA polymerase I was proportional to the tumour growth rates. Alterations in polymerase III were confined to the most rapidly proliferating hepatomas. By contrast, all classes of RNA polymerase were found to be increased during liver regeneration. Relative to resting liver, the fastest growing tumour, 3924A, exhibited the highest activities and/or amounts of RNA polymerase I (8-fold) and III (5-fold) per g of tissue. These alterations in the tumour RNA polymerases were reflected in corresponding increases in the transcriptionally active (bound or chromatin-associated) enzyme population. The mechanisms underlying the augmented synthesis of RNA in vitro by bound polymerase I from hepatoma 3924A were elucidated by product analysis. The results indicated that, relative to liver RNA polymerase I, the tumour enzyme produced more nascent RNA chains and elongated these chains at a faster rate. The number of 3'-termini, as measured by incorporation into uridine, was higher in the hepatoma even under conditions which prevented re-initiation. suggesting increased amount of transcriptionally active RNA polymerase I in the tumour.

A facile procedure for purifying maize chloroplast RNA polymerase from whole cell homogenates

Two DNA-dependent RNA polymerases have been purified from homogenates of maize leaves by a relatively rapid procedure involving Sepharose 4B and DEAE-cellulose chromatography followed by resolution of two RNA polymerasies on phosphocellulose. The RNA polymerase eluting from phosphocellulose at 0.11 M (NH4)2SO4 is inhibited strongly by low levels of alpha-amanitin and possesses catalytic properties and polypeptide subunits like those of maize nuclear RNA polymerase II. The RNA polymerase eluting from phosphocellulose at 0.15 M (NH4)2SO4 resembles the RNA polymerase solubilized from isolated maize chloroplasts in many ways. This enzyme and that isolated from chloroplasts are resistant to alpha-amanitin and rifamycin-SV at high concentrations. Both RNA polymerases have virtually the same Mn2+ and Mg2+ optima, Mg2+/Mn2+ activity ratios, (NH4)2SO4 sensitivity, kinetics of UMP incorporation, and temperature optima. Electrophoresis of this phosphocellulose-purified RNA polymerase on denaturing polyacrylamide slab gels reveals 14 heavily stainable polypeptides that are identical in number and molecular mass to those from chloroplast RNA polymerase. Moreover, two-dimensional tryptic maps of the 14 polypeptides from the phosphocellulose-purified RNA polymerase are very similar to the maps of corresponding polypeptides from chloroplast RNA polymerase. Using this method, relatively large quantities (0.5 mg/kg leaves) of a form of chloroplast RNA polymerase can be prepared in a few days.

Synthesis and processing of RNA by isolated human placental nuclei

Conditions for isolating intact and active nuclei from human term pacenta and for studying their transcription products are described. The isolated nuclei can synthesize cell-free RNA for a prolonged period at 29 degree C in a medium containing 100 mM KCl and 5 mM MgCl2. Actinomycin D inhibited 92 per cent of RNA synthesis, whereas approximately 60 per cent of RNA synthesis was sensitive to alpha-amanitin. When nuclei were incubated at 29 degrees C for 1 h, about 27 per cent of the newly synthesized RNA was released into the medium outside the nucleus. Analysis of this released material by affinity chromatography on an oligo(dT)-cellulose column revealed that 2.4 per cent of the total released RNA was adsorbed at high salt concentration. Most of this fraction was eluted with a low-salt buffer at 45 degrees C and the remainder by 50 per cent formamide, conditions that are necessary for elution of poly(A)-containing mRNP particles from oligo(dT)-cellulose. These results show that placental nuclei incubated in vitro synthesize poly(A)-containing RNA, which is released as a protein-bound complex. This procedure allows exploration of changes in mRNA release during placental development.

The subcellular biochemistry of thyroid

In this review the subcellular localization of enzymes and constituents in thyroid is discussed. Conditions and results of differential pelleting and gradient centrifugation studies are described with special attention to the validity of the markets used (Table VI). Special approaches to the isolation and characterization of thyroid organelles and membranes are extensively reviewed (Table VII). Subcellular fractionation of thyroid tissue has been shown to be an arduous task. Classic approaches for differential pelleting and gradient centrifugation, which have been proved successful for rat liver, are not always equally satisfactory for thyroid. The major problem is the toughness of the tissue requiring rather traumatizing homogenizing procedures. Nevertheless, the fractionation procedures did allow the subcellular localization of some enzymes and constituents to be established with a high degree of certainty. Furthermore, enriched subcellular fractions have been isolated which have been useful for biochemical studies concerning the specific function of this tissue.

A cyclic GMP-dependent histone kinase bound to liver nucleoli

A method of steady-state electrophoresis in polyacrylamide gels was used to analyze the presence of cyclic nucleotide binding components in cell extracts. Multiple cyclic AMP and cyclic GMP binding components were detected in soluble cytoplasmic and nuclear extracts derived from avian liver, but only a single cyclic GMP binding protein was found in the 0.3 M NaCl extract of liver nucleoli. In the presence of cyclic GMP, this protein phosphorylated efficiently a calf thymus histone mixture and an endogenous nucleolar protein, which migrated identically with histone H4 in sodium dodecyl sulfate polyacrylamide gel electrophoresis. The isoelectric point of the cyclic GMP-binding protein was 4.8. Addition of cyclic GMP did not influence the activity of the endogenous nucleolar RNA polymerase.

Inhibition of endogenous RNA polymerase activity from thymus chromatin by transcortin-hydrocortisone complex

A transortin-hydrocortisone complex has been isolated from human serum by affinity chromatography on oxidized corticosterone coupled to AH-Sepharose 4B. The influence of this complex and of hydrocortisone alone on endogenous RNA polymerase activity from thymus chromatin have been tested. Results show that hydrocortisone alone has no effect on RNA polymerase activity from thymus chromatin. Under the same experimental conditions, The transcortin-hydrocortisone complex induces an important decrease in the incorporation of UMP into RNA. The dose response of thymic RNA polymerase to transcortin-hydrocortisone complex and the effects of alpha-amanitin on this response are also reported.

RNA synthesis and control of cell division in the yeast S. cerevisiae

Cells of the yeast Saccharomyces cerevisiae rapidly accumulated in the G1 phase of the cell cycle when exposed to the chelating agents o-phenanthroline (OP) or 8-hydroxyquinoline (HQ). Zinc salts fully reversed the growth-inhibitory effect of both OP and HQ. Cells treated with these chelating agents showed limited RNA accumulation and little RNA degradation. Rates of RNA synthesis were drastically reduced by low concentrations of these compounds. Whereas rates of protein synthesis were essentially unaffected. Rates of synthesis of mRNA and tRNA were less affected than were rates of synthesis of high molecular weight RNA. Processing of ribosomal precursor RNA was altered. these results suggest that the primary effect of OP and HQ is on rRNA synthesis. RNA metabolism must therefore have a key role in the regulation of the cell cycle.

In vitro RNA synthesis and expression of vitellogenin gene in isolated chicken liver nuclei

Optimal conditions for prolonged in vitro synthesis of RNA in isolated chicken liver nuclei have been described. It is shown by incorporation of gamma32P-GTP into RNA, analysis of the product on sucrose density gradient, and digestion with alkaline phosphatase and ribonuclease A that there is reinitiation of RNA synthesis. Polynucleotide kinase activity has been ruled out as explanation for the incorporation of gamma32P-GTP. alpha-Amanitin inhibits RNA synthesis by about 50%. Nuclei prepared from estradiol-treated chicks have twice the RNA synthesis activity as the controls. RNA is synthesized in the presence of Hg-UTP and the mercurated product separated by affinity chromatography on sulfhydryl-Sepharose column under stringent conditions. Vitellogenin mRNA sequences are measured by hybridization with DNA complementary to vitellogenin mRNA. Estradiol treatment leads to a 10-fold increase in vitellogenin mRNA sequences.