Animal DNA-dependent RNA polymerases. Partial purification and properties of three classes of RNA polymerases from uninfected and adenovirus-infected HeLa cells

Transfer RNAs: diversity in form and function

As the adaptor that decodes mRNA sequence into protein, the basic aspects of tRNA structure and function are central to all studies of biology. Yet the complexities of their properties and cellular roles go beyond the view of tRNAs as static participants in protein synthesis. Detailed analyses through more than 60 years of study have revealed tRNAs to be a fascinatingly diverse group of molecules in form and function, impacting cell biology, physiology, disease and synthetic biology. This review analyzes tRNA structure, biosynthesis and function, and includes topics that demonstrate their diversity and growing importance.

Ribonucleic acid (RNA) biosynthesis in human cancer

In many respects, the most remarkable chemical substances within the genome of eukaryotic cells are remarkable proteins which are the critical structural and functional units of living cells. The specifications for everything that goes in the cell are natural digital-to-digital decoding process in an archive sequence by deoxyribonucleic acid (DNA) and an articulate construction by ribonucleic acid (RNA). The products of DNA transcription are long polymers of ribonucleotides rather than deoxyribonucleotides and are termed ribonucleic acids. Certain deoxyribonucleotide sequences, or genes, give rise to transfer RNA (tRNA) and other ribosomal RNA (rRNA) when transcribed. The ribonucleotide sequences fold extensively and rRNA is associated with specific proteins to yield the essential cell components, ribosomes. Transcription of other special sequences yields messenger RNAs (mRNAs) that contain ribonucleotide sequences that will be ultimately translated into new types of amino acid sequences of functional cellular protein molecules. This switch to a different variety of cellular molecular sequences is complex, but each sequence of the three ribonucleotides specifies the insertion of one particular amino acid into the polypeptide chain under production. Whilst mRNA is considered the vehicle by which genetic information is transmitted from the genome and allocated in the appropriate cytoplasmic sites for translation into protein via cap-dependent mechanism, the actual translation depends also on the presence of other so-called household and luxury protein molecules. Recent evidence suggests RNA species are required at initiation, because treatment of cells with antibiotics or drugs that inhibit RNA synthesis cause a decrease in protein synthesis. The rRNA is necessary as a structural constituent of the ribosomes upon which translation takes place, whereas tRNA is necessary as an adaptor in amino acid activation and elongation protein chains to ribosomes. In this article, we review malignant tumor, with stem like properties, and recent technical advances into the phenomenon of micro-particles and micro-vesicles containing cell-free nucleic acids that circulate plasma. New areas of research have been opened into screening tumor telomerase progression, prognosis of aptamers targeting cell surface, monitoring the efficacy of anticancer therapies, oncogenic transformation of host cell, and RNA polymerases role in the cell cycle progression and differentiation.

Preference of human mitochondrial RNA polymerase for superhelical templates with mitochondrial promoters

The RNA polymerase of HeLa cell mitochondria has been purified free of endonuclease and DNA topoisomerase activities, permitting evaluation of the effect of template topology on transcription in vitro. On single-stranded DNA templates, transcription is nonspecific and does not require mitochondrial DNA sequences. In contrast, duplex DNA templates are efficiently transcribed only when they (1) carry the mitochondrial D-loop region and (2) are negatively supercoiled. These findings suggest a role for template superhelicity in modulating mitochondrial transcription in vivo.

The enhanced rate of transcription of methyl mercury-exposed DNA by RNA polymerase is not sufficient to explain the stimulatory effect of methyl mercury on RNA synthesis in isolated nuclei

Previous work demonstrated two stimulatory effects of methyl mercury on nucleic acid synthesis: (1) in isolated nuclei, methyl mercury stimulates RNA synthesis which is catalyzed by RNA polymerase II [Frenkel and Randles, J. Biol. Chem. 257, 6275-6279 (1982)]. (2) Brief exposure of purified DNA to methyl mercury increases the rate of its transcription by purified RNA polymerase II [Frenkel, Cain, and Chao, Biochem. Biophys. Res. Commun. 127, 849-856 (1985)]. The latter effect was considered as a possible mechanism of the former. Two lines of evidence are presented here which demonstrate that the latter effect is not a sufficient explanation for the former. (1) Mercuric perchlorate has been found to increase the rate of DNA transcription by purified polymerase and the template properties of the mercuric perchlorate-exposed DNA have been found to resemble those of methyl mercury-exposed DNA. Nevertheless, mercuric perchlorate has been shown not to stimulate RNA synthesis in isolated HeLa nuclei. (2) In isolated nuclei of the B50 rat neuroblastoma cell line, RNA synthesis has been found to be stimulated only minimally by methyl mercury. Nevertheless, RNA polymerase II purified from the B50 cells has been found to transcribe methyl mercury-exposed DNA at a higher rate than unexposed control DNA.

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.

Organization and expression of non-Alu family interspersed repetitive DNA sequences in the mouse genome

The mouse genome is complex with regard to DNA sequence organization and transcriptional activity. To more fully understand the role of interspersed repetitive DNA sequences we have isolated and characterized five different mouse non-Alu DNA sequence families. We have found that: (1) the distribution of repetitive sequences is non-random in the genome; (2) two of the five families (Bam5 and R) were previously described by Fanning (1982) and Gebhard et al. (1982), respectively. We found that these two families are linked to each other and are found adjacent to seven of seven studied structural genes but in randomly selected DNA fragments showed much less significant linkage. (3) The position of the Bam5 and R family repeat units relative to beta-globin and relative to a housekeeping gene has been evolutionarily conserved in mice and humans. (4) Three previously undescribed families representing from 200 to 40,000 copies per genome have been characterized and shown to have equivalent human sequences. (5) All five families studied are represented in RNA polymerase II transcripts. Little RNA polymerase III transcription homologous to these three families could be detected. The structural and functional features of these five families defined in this paper provide a basis for studies on the functional role of interspersed repetitive DNA in the mouse.

Vaccinia virus RNA polymerase associated with nuclei of infected HeLa cells

Though vaccinia virus DNA and RNA replication take place predominantly in the cytoplasm of an infected cell, virus formation requires the presence of a functional nucleus in a yet undefined manner. When the nuclei from cells infected for 3 h are isolated and purified, they are found to synthesize five times more RNA in vitro than do corresponding nuclei from noninfected cells. Fifty percent of the RNA synthesized in vitro by nuclei from infected cells is vaccinia specific, and this vaccinia RNA synthesis is resistant to alpha-amanitin concentrations up to 100 micrograms/ml. Furthermore, when the RNA polymerase activities of these nuclei are separated on DEAE-Sephadex columns, 56% of the total nuclear enzyme activity is found to be the vaccinia-specific RNA polymerase known to be alpha-amanitin resistant. The nucleus associated vaccinia RNA polymerase represents 18% of the total cellular vaccinia RNA polymerase. This synthesis of vaccinia RNA in the nucleus may explain the nuclear requirement for vaccinia virus maturation.

Small RNA molecules related to the Alu family of repetitive DNA sequences

A rodent 4.5S RNA molecule with extensive homology to the Alu family of interspersed repetitive DNA sequences has been found physically associated with polyadenylated nuclear and cytoplasmic RNAs (W. Jelinek and L. Leinwand, Cell 15:205-214, 1978; S. Haynes et al., Mol. Cell. Biol. 1:573-583, 1981). In this report, we describe a 4.5S RNA molecule in rat cells whose RNase fingerprints are identical to those of the equivalent mouse molecule. We show that the rat 4.5S RNA is part of a small family of RNA molecules, all sharing sequence homology to the Alu family of DNA sequences. These RNAs are synthesized by RNA polymerase III and are developmentally regulated and short-lived in the cytoplasm. Of this family of small RNAs, only the 4.5S RNA is found associated with polyadenylated RNA.

Small RNA molecules related to the Alu family of repetitive DNA sequences

A rodent 4.5S RNA molecule with extensive homology to the Alu family of interspersed repetitive DNA sequences has been found physically associated with polyadenylated nuclear and cytoplasmic RNAs (W. Jelinek and L. Leinwand, Cell 15:205-214, 1978; S. Haynes et al., Mol. Cell. Biol. 1:573-583, 1981). In this report, we describe a 4.5S RNA molecule in rat cells whose RNase fingerprints are identical to those of the equivalent mouse molecule. We show that the rat 4.5S RNA is part of a small family of RNA molecules, all sharing sequence homology to the Alu family of DNA sequences. These RNAs are synthesized by RNA polymerase III and are developmentally regulated and short-lived in the cytoplasm. Of this family of small RNAs, only the 4.5S RNA is found associated with polyadenylated RNA.

Liver and kidney nuclear RNA synthesis and modifications in dimethylnitrosamine-treated rats

RNA synthesis was measured in nuclei isolated from rat liver and kidney 22 h post injection of 30 mg dimethylnitrosamine/kg body weight. In nuclear preparations were shown by electron microscopy to consist of clean hepatocytes and the liver nuclei showed no apparent necrosis at that time. In vitro RNA synthesis and methylation were proportional to time and nuclear concentration, as well as dependent on exogenous nucleoside triphosphates and S-adenosylmethionine. 60-70% of the in vitro synthesis was inhibited by 1 microgram/ml alpha-amanitin. Total liver nuclear RNA synthesis was increased after dimethylnitrosamine exposure, but, unlike RNA synthesis in nuclei after partial hepatectomy, both alpha-amanitin-sensitive and -resistant synthesis were increased. Differences were found between dimethylnitrosamine-treated liver and kidney nuclear RNA synthesis which was sensitive to inhibition by 1-10 microgram/ml alpha-amanitin, presumably a product of RNA polymerase III. Nuclear RNA methylation with S-adenosylmethionine, which was dependent on new RNA synthesis, differed between dimethylnitrosamine-treated rat liver and kidney nuclei. The endogenous RNA methyl substituents labeled in vitro showed differences in levels of methylation of bases, the 2'-O position of ribose and caps in comparison between control and dimethylnitrosamine-treated nuclei from both liver and kidney. Significant differences were obtained in both nuclear RNA transcription and methylation in vitro between the two tissues in response to pretreatment of the rat in vito dimethylnitrosamine.

An alpha-amanitin-resistant DNA-dependent RNA polymerase II from the fungus Aspergillus nidulans

An alpha-amanitin-resistant DNA-dependent RNA polymerase II has been purified from the lower eukaryote Aspergillus nidulans to apparent homogeneity by extraction of the enzyme at low salt concentration, polymin P (polyethylene imine) fractionation, binding to ion-exchangers and density gradient centrifugation. By this procedure 0.4 mg of RNA polymerase II can be purified over 6,000-fold from 500 g (wet weight) of starting material with a yield of 25% and a specific activity of 550 units/mg. The subunit composition has been resolved by polyacrylamide gel electrophoresis in the presence of sodium dodecylsulphate and by two-dimensional gel electrophoresis using a non-denaturing gel in the first dimension and a dodecylsulphate slab gel in the second dimension. The putative subunits have molecular weights of 170,000, 150,000, 33,000, 27,000, 24,000, 19,000, 18,000 and 16,000. Only one form of RNA polymerase II could be resolved by electrophoresis. The chromatographic and catalytic properties and the subunit composition of the purified RNA polymerase II are clearly different from RNA polymerase I from A. nidulans but throughout comparable with other class II enzymes. It differs from all other class II enzymes by its insensitivity towards the toxin alpha-amanitin, even at concentrations up to 400 micrograms/ml, and appears to be unable to bind O-[14C]methyl-gamma-amanitin at a concentration of 10 micrograms/ml of the toxin. We conclude that the purified RNA polymerase from A. nidulans is a real, but exceptional, type of the class II RNA polymerases.

RNA polymerase III from Drosophila hydei pupae. Purification and partial characterization

DNA-dependent RNA polymerase III, which is usually highly resistant to alpha-amanitin, has been purified from Drosophila hydei pupae. The enzyme is insensitive to alpha-amanitin concentrations up to 0.1 microM; at 100 microM alpha-amanitin the enzyme activity is inhibited by approximately 10%. The enzyme was extracted at low ionic strength and purified to homogeneity by six purification steps; 0.1--0.2 mg enzyme/kg pupae could be obtained. The subunit composition of the enzyme was determined after sucrose-gradient centrifugation by sodium dodecyl sulphate electrophoresis in polyacrylamide gels. The enzyme was resolved into putative subunits of molecular weight 154 000, 135 000, 62 000, 58 000, 38 000, 32 000, 31 000, 27 200, 26 500, 21 500 and 17 500. This subunit composition is in general accord with that of eucaryotic class III enzymes. The catalytic properties (salt-activation profile, ratio of activity with denatured DNA to that with native DNA) and the order of elution of the enzyme from DEAE-cellulose with respect to RNA polymerase II agree with the classification of the isolated enzyme as an RAN polymerase III.

RNA polymerase from the fungus, Aspergillus nidulans. Large-scale purification of DNA-dependent RNA polymerase I (or A)

The DNA-dependent RNA polymerase I (or A) from the lower eukaryote Aspergillus nidulans has been purified on a large scale to apparent homogeneity by homogenizing the fungal hyphae in liquid nitrogen, extraction of the enzyme at high salt concentration, precipitation of RNA polymerase activity with polymin P (a polyethylene imine), elution of the RNA polymerase from the polymin P precipitate, ammonium sulphate precipitation, molecular sieving on Bio-Gel A-1.5m, binding to ion-exchangers and DNA-cellulose affinity chromatography. By this procedure 1.6 mg of RNA polymerase I can be purified over 2000-fold from 500 g wet weight of starting material with a yield of 30--35%. The isolated RNA polymerase I is stable for several months at -20 degrees C. The subunit compostion has been resolved by polyacrylamide gel electrophoresis on two-dimensional gels, using either non-denaturing of 8 M urea (pH 8.7) cylindrical gels in the first dimension and sodium dodecyl sulphate slab gels in the second dimension. The putative subunits have molecular weights of 190,000, 135,000, 63,000, 62,000, 43,000, 29,000, (28,000), 16,000 and probably 13,000 and 12,000. Two distinct forms of RNA polymerase I (Ia and Ib) have been resolved by DEAE-Sephadex A-25 chromatography showing ample differences in enzymatic properties and subunit pattern. Additional information is given on RNA polymerase II (or B) which appears to be highly insensitive to alpha-amanitin at concentrations up to 400 micrograms/ml.

Large species differences in the pattern of snPI RNA which can distinguish ape from human

The snPI RNA species are a recently described set of molecules whose sizes range from 5S to 10S. They can be labeled in vitro in isolated nuclei and are apparently formed by an RNA polymerase I type of activity. However, in contrast to ribosomal precursor RNA, the usual polymerase I product, they are not found in the nucleolus but rather are located in the nucleoplasm. The snPI RNAs have been found in all mammalian cell types studied. The spectrum seen in gel electrophoresis is unique to each animal species studied but is essentially the same in different cell types within a species. The differences in snPI patterns are quite large between even closely related species and are clearly distinguishable in gorilla and human cells.

Amatoxins, phallotoxins, phallolysin, and antamanide: the biologically active components of poisonous Amanita mushrooms

This review gives a comprehensive account of the molecular toxicology of the bicyclic peptides obtained from the poisonous mushrooms of the genus Amanita. The discussion of the biochemical events will be preceded by a consideration of the chemistry of the toxic peptides. The structural features essential for biological activities of both the amatoxins and the phallotoxins will be discussed, also including the most important analytical data. Similar consideration will be given to antamanide, a cyclic peptide, which counteracts phalloidin. In addition, the phallolysins, three cytolytic proteins from Amanita phalloides will be discussed. The report on the biological activity of the amatoxins will deal with the sensitivity of the different RNA-polymerases towards the toxins and with their action on various cell types. Consideration will also be given to systems in which alpha-amanitin was used and can be used as a molecular tool; in the past, many investigators used the inhibitor in molecular biology, genetics, and even in physiological research. As for the phallotoxins, discussion of the affinity of these toxins for actin is provied. Further discussion attempts to understand the course of intoxication by filling in the gap between the first molecular event, formation of microfilaments, and the various lesions in hepatocytes during the intoxication.

Transcription in vitro of adenovirus-2 DNA by RNA polymerases class C purified from uninfected and adenovirus-infected HeLa cells

DNA-dependent RNA polymerase class C (or III) has been solubilized from either uninfected or adenovirus-2-infected HeLa cells and purified by chromatography on phosphocellulose, DNA-cellulose, CM-Sephadex and DEAE-Sephadex. The last column separated the enzyme into three forms CI, CII and CIII, which were completely free of RNA polymerases class A and B and of DNase and RNase. The total and the relative amount of these different enzyme C forms did not vary whether purified from uninfected or infected cells. Irrespective of the stage of purification, the three enzyme forms transcribed deproteinized adenovirus-2DNA very efficiently. This transcription was highly sensitive to elevated ionic strength (especially in the presence of Mg2+) and was accompanied by continuous reinitiation as shown by adding poly(rI), a potent inhibitor of initiation. In addition heparin-resistant initiation complexes could be formed at elevated temperature. The RNA synthesized in vitro on deproteinized intact adenovirus-2 DNA by the different forms of RNA polymerase class C, has been characterized. Analysis of the transcripts by gel electrophoresis, RNA self-annealing, hybridization to separated adenovirus-2 DNA strands and to restriction endonuclease (BamHI, HindIII), adenovirus-2 DNA fragments have demonstrated that restriction endonuclease (BamHI, HindIII), adenovirus-2 DNA fragments have demonstrated that the various regions of the adenovirus-2 genome were randomly transcribed. In addition, hybridization of RNA transcripts labelled at their 5' end by either [gamma32P]ATP or [gamma-32P]GTP indicated that not only elongation but also initiation occurred randomly through the entire adenovirus-2 genome, irrespective of the form of the enzyme and of the origin of the cells (normal or infected). The results are discussed in terms of the components which are possibly involved in specific transcription.

Evidence for the existence of two forms of RNA polymerases I and II in insect wing epidermis

DNA-dependent RNA polymerases were solubilized from developing wings of the oak silkmoth, Antheraea pernyi, and partially purified by ion-exchange chromatography and sucrose gradient sedimentation. Four enzyme species were resolved on the basis of chromatographic behavior, divalent cation requirements, ionic strength optima, template preference and alpha-amanitin sensitivity. Each class (i.e. RNA polymerase I and II) was present in two forms termed IA, IB and IIA, IIB on the basis of their elution pattern from the column. Both class I enzymes were sensitive to high concentrations of alpha-amanitin but this may be due to general toxicity rather than specific inhibition. The intraclass variants did not differ significantly in enzymatic properties although form IIB was more sensitive to alpha-amanitin (50% inhibition at 2 . 10(-9) M) than form IIA (3 . 10(-8)M).

Synthesis of histone messenger RNAs by RNA polymerase II in nuclei from S phase HeLa S3 cells

Nuclei were isolated from synchronized HeLa S3 cells and transcribed utilizing their endogenous RNA polymerases. Our data suggest that S phase nuclei are capable of synthesizing histone mRNA sequences while nuclei from G1 phase cells are not. Transcription of histone mRNA sequences by S phase nuclei can be abolished completely by low levels of alpha-amanitin (1.0 microgram/ml, a concentration which completely inhibits RNA polymerase II). From these results it appears that transcription of the histone mRNA sequences occurs during the S phase but not during the G1 phase of the cell cycle and that RNA polymerase II is responsible for histone gene readout.

Synthesis of ribonucleotides and their participation in ribonucleic acid synthesis by Coxiella burnetii

Synthesis of ribonucleic acid (RNA) by the deoxyribonucleic acid-dependent RNA polymerase of Coxiella burnetii required adenosine, uridine, guanosine, and cytidine 5'-triphosphates. Cell-free preparations of this obligate intracellular procaryotic parasite had competence to phosphorylate ribonucleoside mono- and diphosphates in the presence of exogenous adenosine and guanosine 5'-triphosphates to the corresponding di- and triphosphates. C. burnetii contained about 2 nmol of adenosine 5'-triphosphate per mg of protein, which could serve as a approximately P donor for in vivo synthesis of nucleoside triphosphates. The latter were then used as substrates in the synthesis of RNA in a coordinated metabolic system with C. burnetii RNA polymerase. It is suggested that during infection the rickettsiae might obtain the nucleotides necessary for RNA synthesis from the vacuoles in which C. burnetii proliferates.

Purification and properties of RNA polymerase I from Ehrlich ascites cells

DNA-dependent RNA polymerase I (or A) (nucleoside triphosphate:RNA nucleotidyltransferase, EC 2.7.7.6) was purified from Ehrlich ascites cells after solubilization from isolated nuclei. The purification was accomplished by a procedure involving initial precipitation with ammonium sulfate, following by chromatographies on DEAE-Sephadex and phosphocellulose ion exchange resins and gel filtration on Sepharose 6B. A chromatographically homogeneous enzyme was obtained which was purified about 2300-fold relative to nuclear extracts. The specific activity of the most purified enzyme fraction was 230 nmol of [3H]UTP incorporated into RNA per mg of protein in 10 min at 37 degrees C, which is similar to those reported for the highly purified RNA polymerase I from mouse myeloma and calf thymus. The elution position on Sepharose 6B gel filtration indicated a molecular weight of approx. 580 000. Analysis of the purified enzyme by polyacrylamide gel electrophoresis under nondenaturing conditions revealed only one protein band. Certain heterogeneity in the RNA polymerase I fractions was found in the early chromatographic steps, but not in the most purified fractions.

Enzymatic properties of viral replication complexes isolated from adenovirus type 2-infected HeLa cell nuclei

When HeLa cell nuclei, isolated 17 h after infection with adenovirus type 2 (Ad2), were extracted with 200 mM ammonium sulfate, Ad2 nucleoprotein complexes were selectively released. These complexes contained a DNA polymerase activity that corresponded to DNA polymerase molecules actively engaged in Ad2 DNA replication. Under our high-salt (200 mM ammonium sulfate) incubation conditions, where no reinitiation occurred, full-length Ad2 DNA chains were synthesized by elongation of chains that had been initiated in vivo. This conclusion was further supported by density labeling experiments indicating that the in vitro DNA synthesis was semiconservative. Evidence is presented suggesting that at least part of the DNA polymerase molecules engaged in Ad2 DNA replication belong to the gamma class.