Mouse-myeloma RNA polymerase B. Template specificities and the role of a transcription-stimulating factor

Primer-dependent eukaryotic RNA polymerase capable of accurate transcription from the adenovirus major late promoter in a reconstituted system

A sensitive assay for detection of eukaryotic RNA polymerase II has been developed. This assay depends on the ability of polymerase II to elongate a small RNA primer, oligo(U), hybridized to a single-stranded homopolymeric DNA template, poly(dA). The poly(dA).oligo(U)-dependent RNA polymerase II from calf thymus has been purified approximately 10,000-fold using this assay. The purified enzyme contains four polypeptides of apparent Mr 180,000, 140,000, 24,000, and 16,000 and is fully active in accurate initiation of transcription from the adenovirus major late promoter in the presence of transcription factors from HeLa cells. The poly(dA).oligo(U)-dependent RNA polymerase activity can be detected in crude cell extracts from a variety of tissue culture cells and appears to be largely due to polymerase II, since 90-95% of this activity is inhibited by alpha-amanitin at a concentration of 1 microgram/ml.

An oestrogen receptor activator protein in rat uterine cytosol

Earlier reports of oestrogen receptor binding to DNA indicated that a protein which does not bind oestrogen might be involved in the conversion of the 4S oestradiol receptor to the 5S form but no direct evidence for the existence of this protein was presented. This receptor transformation or activation step is thought to be a requirement for events in the nucleus. We considered it likely that such a protein might be similar to the cytoplasmic proteins which stimulate eukaryotic RNA polymerases. These are basic proteins which are not adsorbed to DEAE cellulose and have a sedimentation coefficient of approximately 3S. To examine this possibility, we fractionated unlabelled uterine cytosol by DEAE-cellulose chromatography. Unlabelled cytosol was used to avoid the possibility that such a factor might be retained on the column as a component of the receptor--oestradiol complex. Here we present evidence of a protein present in uterine cytosol which forms a complex with the 4S form of the oestrogen receptor to produce a 5S-activated form. This activated form binds to uterine nuclei, DNA-cellulose and native calf thymus DNA. The cytosol protein, which we call receptor activation factor, does not bind oestradiol, has a sedimentation coefficient of approximately 3S and does not bind to DEAE-cellulose.

DNA-dependent RNA polymerases from Drosophila melanogaster adults: isolation and partial characterization

In preparation for the isolation and biochemical characterization of putative RNA polymerase mutants, DNA-dependent RNA polymerases of Drosophila melanogaster adults were isolated and partially characterized. Approximately 70% of the female adult RNA polymerase is located in ovaries. Multiple forms of ovarian RNA polymerases I and II are separable by DEAE-Sephadex chromatography. The two forms of RNA polymerase II differ in ammonium sulfate optima. RNA polymerase IIA is more active with double-stranded DNA as template, whereas RNA polymerase IIB transcribes single-stranded DNA most efficiently. Rechromatography of RNA polymerase IIA on DEAE-Sephadex results in the loss of ability of this form to transcribed double-stranded DNA most efficiently. Ovariectomized carcasses have two forms of RNA polymerase I and one form of RNA polymerase II and each transcribes single-stranded DNA most efficiently. As judged by gel filtration chromatography, female adult extracts have forms of RNA polymerase II that differ in molecular weight and template preference.

The influence of brain cytosol on RNA synthesis and RNA products of isolated mouse brain nuclei

The incubation of isolated nuclei obtained from 10-day-old mouse brain in the presence of brain cell cytosol resulted in an increase in the synthesis of RNA. Under conditions of saturating concentrations of nucleoside triphosphates, the influence of cytosol could not be duplicated by the addition of cyclic nucleotides. The stimulatory activity of cytosol on brain nuclear RNA synthesis could not be attributed to either alterations in the permeability of the nuclear envelope or an increased uptake of radioactively-labeled precursors. Sucrose gradient analysis demonstrated that the RNA products synthesized by nuclei isolated from 10-day-old and adult mouse brain were of a relatively low molecular weight. However, the addition of cytosol resulted in a significant increase in the size of the RNA transcripts. In contrast to the observations with 10-day-old and adult brain nuclei, the RNA from 2-day-old mouse brain nuclei was larger in size and relatively unaffected by the presence of cytosol. Although cytosol caused an increase in the amounts of poly[A]-RNA in nuclei of 2-day-old and adult animals, no comparable effect could be measured in nuclei from 10-day-old brain tissue.

Protein which interacts with a stimulatory factor of RNA polymerase II of Ehrlich ascites tumor cells

When partially purified Ehrlich ascites tumor RNA polymerase II was further purified on a column of phosphocellulose, stimulation of its catalysis of RNA synthesis by stimulatory factor S-II was greatly decreased. This decrease in sensitivity to the stimulatory factor was reversible: the enzyme eluted from phosphocellulose became sensitive to the factor when mixed with a protein fraction eluted from the phosphocellulose at high salt concentration. Evidence was obtained that this protein, named helper protein, binds, to the enzyme eluted from phosphocellulose, causing it to recover sensitivity to stimulatory factor S-II.

Characterization of a protein factor stimulating RNA synthesis by DNA-dependent RNA polymerase II from plant cell cultures

During purification of DNA-dependent RNA polymerase II (or B) from cell cultures of parsley a protein fraction was separated by phosphocellulose chromatography which enhanced RNA synthesis in the presence of native homologous DNA. This 'stimulatory factor' was characterized in respect to some effects on the reaction catalyzed by RNA polymerase II. In the presence of the factor the metal ion requirements as well as the ionic strength for optimal RNA synthesis were markedly changed; addition of the factor to RNA polymerase II purified by cellulose chromatography restored those enzyme properties which had apparently changed upon this purification step. The chain length of the RNA product synthesized is favouring the view that the factor acts mainly by stabilizing the elongation step during transcription. The stimulatory factor was further purified by several steps of column chromatography. As derived from the results of gel electrophoresis under denaturing conditions the factor consists of several small polypeptides. Those of Mr = 26000, 25000 and 14000 apparently have counterparts among the smaller subunits of highly purified RNA polymerase II from parsley cells. Another polypeptide of the factor, with Mr = 30000, was only found in those preparations of RNA polymerase II which had not been subjected to phosphocellulose chromatography.

A protein cofactor that stimulates the activity of DNA-dependent RNA polymerase I on double-stranded DNA

Partially purified rat liver RNA polymerase I chromatographed on ribosomal RNA-Sepharose loses most (96%) of its activity assayed on native calf-thymus DNA templates, but loses little (8%) of its activity assayed on poly(deoxycytidylic acid) template. Polymerase I is not stimulated by polymerase II protein factor, or by bovine serum albumin. However, it is stimulated by histones, polylysine, and spermine. Addition of a protein fraction eluted by high ionic strength from the rRNA-Sepharose also restores activity on native calf-thymus DNA. Further purification yields a fraction containing two proteins of 11 000 and 12 000 molecular weight. Both proteins are distinct from histones by electrophoresis in sodium dodecyl sulfate and in acid urea. Both proteins are basic, insensitive to heat, bind to DNA, and stimulate polymerase I activity. The degree of stimulation of polymerase I is dependent upon both the enzyme/DNA and the factor/DNA ratio. The protein factors also stimulate polymerase II activity about half as effectively as polymerase I.

Template activity of synthetic deoxyribonucleotide polymers in the eukaryotic DNA-dependent RNA polymerase reaction

Template specificities of the eukaryotic DNA-dependent RNA polymerases A and B from rat liver, pea, and cauliflower have been investigated using synthetic polydeoxyribonucleotides. Polymerases A and B from the three species exhibit different specificities for single-stranded homopolymers: polymerase A preferentially reads poly(dT) and poly (dC). and polymerase B poly (dC). This preferential reading appears to be a property of eukaryotic DNA-dependent RNA polymerases. Polymerases A and B transcribe synthetic polyribonucleotides also, but at a reduced rate. The polyribonucleotides which can be read by DNA-dependent RNA polymerases have a base sequence similar to that of the polydeoxyribonucleotides, which are effeciently transcribed, suggesting that the base sequence of the template rather than its conformation is crucial in the template specificity for synthetic polymers. Competition experiments with polydeoxyribonucleotides indicate that the enzymes have different binding specificities, which are not the same as their template specificities.

RNA polymerases from a rat hepatoma. Partial purification and comparison of properties with corresponding liver enzymes

DNA-dependent RNA polymerases were extracted from the nuclei of poorly differentiated tumor, Morris hepatoma 3924A, and purified by an initial chromatography on a DEAE-Sephadex column followed by fractionation on phosphocellulose and finally on a second DEAE-Sephadex column. Three major forms of RNA polymerase (IA, IB and II) were resolved chromatographically. Enzymes IA, IB and II eluted from DEAE-Sephadex at 75, 150 and 210 mM (NH4)2SO4, respectively. The specific activities (nmol UMP incorporated mg protein per 15 min) of polymerases IA, IB and II were 40, 43 and 182, respectively. Concurrently, DNA-dependent RNA polymerases were extracted from normal liver and subjected to similar chromatographic procedure. Upon the final DEAE-Sephadex chromatography, enzymes IA, IB and II eluted at 110, 180 and 210 mM (NH4)2SO4, respectively. The recovery of polymerases IA, IB and II after purification was 0.21, 0,28 and 0.42 unit/mg DNA, respectively, for hepatoma enzymes and 0.07, 0.05 and 0.42 unit/mg DNA for the corresponding liver enzymes.

An ATPase depending on the presence of single-stranded DNA from mouse myeloma

An ATPase was purified from mouse myeloma MOPC 70E the activity of which depends on the presence of single-stranded DNA and divalent cations such as Mg2+, Mn2+, Ca2+, Ni2+ or Fe2+. The enzyme splits both ribonucleoside and deoxyribonucleoside triphosphates but preferentially ATP and dATP yielding nucleoside diphosphates and inorganic phosphate. The enzyme has an absolute requirement for single-stranded DNA. Alternating double-stranded polydeoxynucleotides are only slight effective, and native double-stranded DNA, single-stranded and double-stranded RNAs as well as DNA - RNA hybrids are ineffective in stimulating the ATPase. The enzyme has further characterized by sedimentation in a sucrose density gradient (s20, w = 5.5 S) and by isoelectric focussing in an ampholine pH gradient (pI = 6.5).

Transcription of DNAs of known sequence after injection into eggs and oocytes of Xenopus laevis

1. When the synthetic polynucleotide, poly[d(A-T) - d(A-T)] is injected into the eggs and oocytes of Xenopus laevis, a stimulation of RNA synthesis results. Analysis of extracted RNA by high-voltage electrophoresis, shows that this stimulation of RNA synthesis is due to the production of poly[r(A-U)] transcripts. The rate of poly[r(A-U)] synthesis is calculated to be at least ten-fold greater in eggs than in oocytes. The amount of poly[r(A-U)] detectable in injected eggs has reached a maximum by 1.5 h after injection; in oocytes, however, poly[r(A-U)] continues to accumulate between the third and 16th hour after injection. The transcripts range in length from less than 80 nucleotides up to over 2000 nucleotides long. The co-injection of poly[d(A-T)] - d(A-T)] and alpha-amanitin into oocytes, has shown that the synthesis of poly[r(A-U)] is approximately 90% inhibited at a concentration of alpha-amanitin which has no effect on the capacity of the oocyte to synthesize ribosomal and 4-S RNA; thus the nucleoplasmic RNA polymerases IIa and/or IIb, are implicated as playing a major role in poly[r(A-U)] synthesis in oocytes. 2. When poly(dG) - poly(d-C), poly(dA), poly(dA) - poly(dT) and poly[d(I-C) - d(I-C)] are individually injected into eggs only poly[d(I-C) - d(I-C)] is transcribed as efficiently as poly[d(A-T) - d(A-T)]. 3. When calf thymus native or denatured DNA, polyoma, T2, T4 and phiX DNAs are individually injected into eggs only the injection of calf thymus native DNA causes a detectable stimulation of RNA synthesis. 4. The activities of crude preparations of egg and oocyte RNA polymerases are tested in vitro with different DNA templates. In contrast to the situation in vivo, it is found that poly[d(A-T1 - d(A-T)] is as efficiently transcribed in vitro by oocyte polymerase as by egg polymerase. Additionally poly[d(A-T) - d(A-T)] is transcribed ten-fold more efficiently in vitro than calf thymus native DNA. When poly(dA) - poly(dT), poly(dA), phiX, T2, and calf thymus denatured DNA are tested in vitro, only calf thymus denatured DNA is transcribed to a significant extent. The above results are discussed in relation to the known synthetic activities of Xenopus eggs and oocytes.

DNA-dependent RNA polymerases I and II from kidney. Effect of polyamines on the in vitro transcription of DNA and chromatin

DNA-dependent RNA polymerases I and II were purified from pig kidney nuclei by chromatography on DEAE-Sephadex and phosphocellulose. When nonlimiting amounts of double-stranded DNA were used as the template, the in vitro transcription was markedly stimulated by spermidine and spermine. Maximal stimulation of RNA polymerase I occurred at 2-5 mM spermidine and 0.5-2 mM spermine, whereas optimal polyamine concentrations for RNA polymerase II were 5-10 and 1-5 mM for spermidine and spermine, respectively. DNA transcription by polymerase II was stimulated to a greater extent than that of polymerase I. Higher spermine (5-10 mM) concentrations were strong inhibitors of both polymerases under these conditions. The apparent Km of RNA polymerases I and II for UTP was unchanged at optimal polyamine concentration; under the same conditions the maximal reaction velocity was increased two- to three-fold and was essentially due to an increase in the rate of chain elongation. Thus, in a typical experiment the average chain length as determined by the UMP/uridine ratio increased from 570 to 1330 and the chain elongation rate increased from 0.64 to 1.44 nucleotides times sec-1 in the presence of spermine. When limiting quantities of native DNA were employed as the template, both RNA polymerases I and II were inhibited by 1-2 mM spermine. Kidney chromatin could be transcribed by homologous RNA polymerases with an efficiency ranging from 2 to 10% of that with native DNA. When chromatin was used in nonlimiting amounts instead of DNA, RNA polymerase II activity was again stimulated about two-fold at 2 mM spermine. Under these conditions, RNA polymerase I activity was inhibited by spermine. The inhibition of RNA synthesis in vitro at limiting quantities of templates (DNA or chromatin) could be overcome by preincubation of the enzyme with templates before polyamines were added. This inhibition thus appears to be due to a block in the initiation of RNA chains. Similar inhibition of transcription by RNA polymerase II was also observed with limiting quantities of chromatin as the template.

Increased frequency of initiation of RNA synthesis due to a protein factor from chicken myeloblastosis nuclei

The mechanism of the effect of an RNA polymerase II (RNA nucleotidyltransferase II) stimulation factor isolated from the nuclei of chicken myeloblastosis cells was studied. The stimulation requires the presence of all four nucleoside triphosphates and depends upon an exogenous DNA template. In the absence of the factor, RNA synthesis ceases after 20-30 min, but in the presence of the factor, synthesis continues up to 60-80 min. Addition of the factor at 35 min after incubation causes resumption of RNA synthesis. The factor greatly stimulates the activity of RNA polymerase II at low enzyme concentrations. The RNA polymerase activity is more sensitive to alpha-amanitin inhibition when the factor is present. Experiments of [gamma-32P]ATP incorporation reveal that the factor provides for an increased frequency of initiation of RNA chains, both of the primary initiation events and re-initiation after previous ones were completed. A slightly higher rate of RNA chain growth was also observed with this factor but the ultimate size of RNA synthesized was not affected, as determined by formaldehyde/sucrose gradient centrifugation. These data suggest that the factor functions at the initiation stages of the RNA polymerase reaction.

Deoxyribonucleic acid-dependent ribonucleic acid polymerases from murine spleen cells. Increased amounts of the nucleolar species in leukaemic tissue

1. In the spleens of infected mice, the Friend leukaemia virus induces a sharp increase in the ability of subsequently isolated nuclei to incorporate exogenous UTP into an acid-insoluble product. Inhibitor studies indicate that the incremental RNA synthesis proceeds from a DNA template and that both nucleolar and nucleoplasmic activities are involved. 2. The partially purified DNA-dependent RNA polymerases from control and virus-infected tissue are indistinguishable with respect to chromatographic mobility, dependence on bivalent cations, ionic strength, pH and their susceptibility to alpha-amanitin. The RNA polymerases of the murine spleen resemble the enzymes of other mammalian tissue in these properties. 3. A comparison of the amount of polymerase solubilized from normal and infected tissue correlates with the activity observed in assays of the respective nuclei. These experiments indicated that the increase in nucleolar RNA synthesis after infection is mediated by increased extractable polymerase I activity whereas the change in nucleoplasmic RNA synthesis results from an alteration of chromatin or a chromatin-associated factor.