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Buzan JM, Low RL. Preference of human mitochondrial RNA polymerase for superhelical templates with mitochondrial promoters. Biochem Biophys Res Commun 1988; 152:22-9. [PMID: 3358762 DOI: 10.1016/s0006-291x(88)80674-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
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.
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Affiliation(s)
- J M Buzan
- Department of Pathology, Washington University School of Medicine, St. Louis, Missouri 63110
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2
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Aoyama T, Takanami M. Supercoiling response of E. coli promoters with different spacer lengths. BIOCHIMICA ET BIOPHYSICA ACTA 1988; 949:311-7. [PMID: 3349085 DOI: 10.1016/0167-4781(88)90157-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The effect of negative supercoiling on a series of synthetic Escherichia coli promoters has been investigated. These promoters carry perfect consensus sequences at the -35 and -10 regions, but with different spacer lengths (Aoyama, T. et al. (1983) Nucleic Acids Res. 11, 5855-5864). Topoisomeric plasmids carrying these synthetic promoters were constructed, and their activities were compared by detecting in vitro transcripts with the probe-hybridization method. In the relaxed state, the one with 17 basepairs (bp) spacing showed the highest activity, and the activity steeply decreased both sides of the optimal spacing. Similar results have been observed by run-off transcription. By introducing negative superhelicity, the 17 bp spacing promoter showed a relatively little response to supercoiling. In contrast, the activities of those with 16 and 18 bp spacings were markedly stimulated by supercoiling, with the mean, negative superhelical density (-sigma) which gave the maximum activity being about the same for the 16-18 bp spacing promoters (-sigma = 0.03 to 0.04). The promoter with 19 bp spacing, which showed no activity in the relaxed state, exhibited a significant activity at higher superhelicities (-sigma = 0.06). Even the 20 bp spacing promoter showed some activity by increasing superhelicity, while the 15 bp spacing promoter did not. On the basis of these observations, possible mechanisms by which negative supercoiling of DNA stimulates the protomer activity are discussed.
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Affiliation(s)
- T Aoyama
- Institute for Chemical Research, Kyoto University, Uji, Japan
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3
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Boeuf H, Zajchowski DA, Tamura T, Hauss C, Kédinger C. Specific cellular proteins bind to critical promoter sequences of the adenovirus early EIIa promoter. Nucleic Acids Res 1987; 15:509-27. [PMID: 2950379 PMCID: PMC340449 DOI: 10.1093/nar/15.2.509] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
As an approach to the identification of essential factors required for specific expression of the adenovirus type 2 EIIaE early (EIIaE) promoter, an in vitro system was established. Under appropriate conditions, using crude extracts of non-infected HeLa cells, efficient and accurate EIIaE expression has been reproduced. As in vivo, this transcription was strongly dependent upon the integrity of two non-consensus TATA-like elements, T1 and T2, corresponding to the major (EIIaE1) and minor (EIIaE2) start sites, respectively, as well as upon intact upstream elements (A, between -40 and -50 and B, between -70 and -90) common to both overlapping promoters. The implication of specific DNA-binding proteins in the transcriptional effects mediated by these elements was demonstrated by DNAse I footprinting analyses. Both crude nuclear extracts and partially purified fractions confer specific protection against DNAse I digestion to the T1 and B promoter elements defined above, and to a far upstream region (element C, between -110 and -150), which has previously been identified as a weaker promoter element by in vivo transcriptional studies. Separation of the T1 recognition factor from those which bind to the upstream elements B and C by chromatographic fractionation of the extracts has also been achieved.
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MESH Headings
- Adenovirus Early Proteins
- Adenoviruses, Human/genetics
- Adenoviruses, Human/metabolism
- Antigens, Viral, Tumor/genetics
- Base Sequence
- DNA, Viral/genetics
- DNA, Viral/metabolism
- Genes
- Genes, Viral
- HeLa Cells/metabolism
- Humans
- Nucleoproteins/isolation & purification
- Nucleoproteins/metabolism
- Oncogene Proteins, Viral/genetics
- Promoter Regions, Genetic
- Protein Binding
- Transcription, Genetic
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Dietrich J, Teissere M, Job C, Job D. Effect of salts on abortive and productive elongation catalysed by wheat germ RNA polymerase II. Nucleic Acids Res 1986; 14:1583-97. [PMID: 3513126 PMCID: PMC339530 DOI: 10.1093/nar/14.4.1583] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Modification of the ionic conditions in reaction assays containing wheat germ RNA polymerase II and poly(dAT) as template markedly alters the catalytic properties of the transcription complexes. These effects have been studied by measuring the rate of abortive initiation and the extent of productive RNA synthesis. Using combinations of metal ions or various salts, a marked inhibition of abortive initiation was always associated with an increased length of RNA chains. These results are discussed in terms of modulation of the stability of transcription complexes induced by salts or divalent cations. The behavior exhibited by wheat germ RNA polymerase II is also discussed in comparison with previously reported results for procaryotic and eucaryotic RNA polymerases.
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Blair DG. Comparison of the effects of polyamines on the activities of RNA polymerases from murine normal tissues and transplantable tumors. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. B, COMPARATIVE BIOCHEMISTRY 1986; 85:833-44. [PMID: 3816157 DOI: 10.1016/0305-0491(86)90183-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Nuclear DNA-dependent RNA polymerases I, II and III were purified from kidney, liver and spleen from Swiss mice (Mus musculis) and from seven transplantable murine tumors. In the presence of the optimal concentration of (NH4)2SO4 for each polymerase, 1-8 mM spermidine or spermine stimulated most polymerases several fold, and generally, enzyme I was stimulated more than either enzyme II or III. Spermine was more efficacious than spermidine as a stimulant of polymerase activity except for polymerase III from three tumors. Tumor polymerases I (or II) and the corresponding normal tissue enzymes responded similarly to the polyamines. Stimulation of a RNA polymerase by a polyamine could not be correlated with the growth rate of the tissues of polymerase origin or with the tissue's RNA polymerase or RNA synthetic activities.
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Moussatché N. Polyamines stimulate DNA-dependent RNA synthesis catalyzed by vaccinia virus. BIOCHIMICA ET BIOPHYSICA ACTA 1985; 826:113-20. [PMID: 4052428 DOI: 10.1016/0167-4781(85)90116-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The RNA synthesis in purified vaccinia virus can occur in the presence of either Mg2+ or Mn2+ if polyamine (spermidine or spermine) is present in the assay system. Under our assay conditions transcription was linear up to 30 min and the RNAs synthesized had a sedimentation coefficient of about 8 to 12 S. We also prepared a virus extract from purified vaccinia virus and tested for in vitro transcription. The soluble transcription system was dependent on the addition of exogenous DNA and single-stranded DNA was a more effective template than double-stranded. In the presence of polyamine and Mg2+ or Mn2+ the viral RNA polymerase was active in the transcription of total native vaccinia DNA and a small fragment cloned in pBR322.
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Brahms JG, Dargouge O, Brahms S, Ohara Y, Vagner V. Activation and inhibition of transcription by supercoiling. J Mol Biol 1985; 181:455-65. [PMID: 2582135 DOI: 10.1016/0022-2836(85)90419-x] [Citation(s) in RCA: 59] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Stimulation of transcriptional activity in vitro is observed at low and moderate negative superhelical densities up to the level of the natural superhelical form of the plasmid pBR322. We have isolated and identified three specific transcription products: ampicillinR RNA, tetracyclineR RNA and "Rep" RNA. Their enhancement of transcription occurs at different levels of superhelicity, suggesting a sequence-dependent structural alteration of promoters upon changes of axial writhe, which may generate kink formation. The activation of transcription is drastically inhibited at higher specific linking differences exceeding that of the natural superhelical form of pBR322, which is correlated with a transition from the right-handed B to a left-handed DNA form of particular sequences induced by supercoiling. We have identified a new stop point in the beta-lactamase coding sequence composed of eight alternating purine-pyrimidine residues which, at higher torsional stress, causes transcription to stop, leading to the synthesis of a short RNA of about 55 nucleotides instead of AmpR RNA (about 580 nucleotides). In the "Rep" promoter, two alternating purine-pyrimidine segments are found, which conformational change at higher superhelical densities may be implicated in repression of "Rep" RNA synthesis. The enhancement and inhibition of transcription by supercoiling support the role of energetic and structural changes in topologically constrained DNA as elements of a control mechanism.
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Blair DG. Activation of mammalian RNA polymerases by polyamines. THE INTERNATIONAL JOURNAL OF BIOCHEMISTRY 1985; 17:23-30. [PMID: 3888717 DOI: 10.1016/0020-711x(85)90081-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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9
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Mishoe H, Brady JN, Lancz G, Salzman NP. In vitro transcription initiation by purified RNA polymerase II within the adenovirus 2 major late promoter region. J Biol Chem 1984. [DOI: 10.1016/s0021-9258(17)43343-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Blair DG. Stimulation of RNA polymerases I and II from mouse L1210 leukemia and Ehrlich ascites carcinoma cells by spermine and spermidine and its modification by ammonium sulfate. THE INTERNATIONAL JOURNAL OF BIOCHEMISTRY 1984; 16:1415-22. [PMID: 6530025 DOI: 10.1016/0020-711x(84)90250-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Nuclear RNA polymerases from murine L1210 leukemia and Ehrlich carcinoma cells were stimulated more effectively by spermine than by spermidine. Optimal stimulatory concentrations of spermine and spermidine for Ehrlich polymerases Ia and Ib decreased to physiological values and maximal stimulation increased as the concentration of (NH4)2SO4 was reduced from 0.08 to 0 M. In the presence of 0.062-0.074 M (NH4)2SO4 L1210 polymerases Ia, IIa and IIb were stimulated significantly by both polyamines, whereas, at (NH4)2SO4 concentrations of 0.11-0.17 M, stimulation was suppressed and high concentrations of the polyamines were inhibitory. Similarly, stimulation of Ehrlich solubilized polymerase by polyamines was inhibited by 0.064 M (NH4)2SO4.
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Blair DG. Stimulation of RNA polymerases from mouse spleen by polyamines and its modification by ammonium sulfate. THE INTERNATIONAL JOURNAL OF BIOCHEMISTRY 1984; 16:747-56. [PMID: 6468735 DOI: 10.1016/0020-711x(84)90185-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Nuclear RNA polymerases Ia, Ib, II and III purified from spleen of Swiss albino mice (Mus musculus) were stimulated significantly by the polyamines, spermine and spermidine, in the presence of ammonium sulfate in vitro. In the absence of ammonium sulfate, the optimal stimulating concentrations of both the polyamines for the RNA polymerases were generally diminished and more physiological. 8 mM spermine stimulated both RNA polymerases Ia and II in the presence of sulfate ions, but inhibited both enzymes significantly in the absence of sulfate ions. Stimulation of mouse spleen RNA polymerase II by spermine affects elongation of RNA chains whereas inhibition by spermine affects initiation of RNA synthesis.
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Hale P, Woodward RS, Lebowitz J. Carbodiimide inactivation of Escherichia coli RNA polymerase promoters on supercoiled simian virus 40 and ColE1 DNAs occurs by a one-hit process at salt concentrations in the physiological range. J Biol Chem 1983. [DOI: 10.1016/s0021-9258(18)32254-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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13
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Voets R, Lagrou A, Hilderson H, Van Dessel G, Dierick W. Characterization and transcription of bovine thyroid chromatin. THE INTERNATIONAL JOURNAL OF BIOCHEMISTRY 1983; 15:87-94. [PMID: 6825907 DOI: 10.1016/0020-711x(83)90015-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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14
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Gundelfinger E, Stein H. Rna polymerase I from Drosophila hydei pupae-purification and partial characterization. FEBS Lett 1982; 142:7-11. [PMID: 7106288 DOI: 10.1016/0014-5793(82)80207-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Studies of in vitro transcription by calf thymus RNA polymerase II using a novel duplex DNA template. J Biol Chem 1982. [DOI: 10.1016/s0021-9258(18)34669-6] [Citation(s) in RCA: 141] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Lavialle C, Reuveni Y, Thoren M, Salzman N. Molecular interaction between simian virus 40 DNA and Escherichia coli RNA polymerase. Mapping of the initiation sites on supercoiled and linear DNA. J Biol Chem 1982. [DOI: 10.1016/s0021-9258(19)68227-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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18
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Lewis MK, Burgess RR. 5 Eukaryotic RNA Polymerases. ACTA ACUST UNITED AC 1982. [DOI: 10.1016/s1874-6047(08)60277-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
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19
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Luchnik AN, Bakayev VV, Zbarsky IB, Georgiev GP. Elastic torsional strain in DNA within a fraction of SV40 minichromosomes: relation to transcriptionally active chromatin. EMBO J 1982; 1:1353-8. [PMID: 6327265 PMCID: PMC553216 DOI: 10.1002/j.1460-2075.1982.tb01322.x] [Citation(s) in RCA: 78] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
After treatment of SV40 minichromosomes with DNA topoisomerase I, the superhelicity in the bulk of the DNA extracted from minichromosomes is known to remain unchanged. However, we found that the DNA extracted from a small fraction of SV40 minichromosomes (2-5%), was almost completely relaxed, and covalently closed as shown by agarose gel electrophoresis. Thus, the DNA in these 2-5% of SV40 minichromosomes was probably torsionally strained (TS). The proportion of such TS minichromosomes is close to the estimated proportion of transcriptionally active minichromosomes. The distribution of the TS minichromosomes in sucrose gradient coincided with the distribution of transcriptionally active complexes. Both sedimented faster than the majority of minichromosomes. Furthermore, after treatment with topoisomerase I the relaxed minichromosomes could be quantitatively separated from the bulk of material by recentrifugation in a sucrose gradient. A major part of the endogenous RNA polymerase activity was recovered in the relaxed fraction. These data suggest that TS-minichromosomes correspond to transcriptionally active chromatin. After relaxation with topoisomerase I the TS minichromosomes lacked histones.
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Crepin M, Triadou P, Lelong JC, Gros F. Identification of transcription initiation sites for bacterial RNA polymerase and eukaryotic RNA polymerase B on the 5' end of the mouse beta-Globin gene. EUROPEAN JOURNAL OF BIOCHEMISTRY 1981; 118:371-7. [PMID: 7285930 DOI: 10.1111/j.1432-1033.1981.tb06412.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Using a recombinant phage containing the mouse beta-Globin gene with lambda gtWES bacteriophage DNA, transcription initiation sites for Escherichia coli RNA polymerase and calf thymus RNA polymerase B were mapped at the 5' and 3' ends of the mouse beta-Globin gene. The bacterial enzyme was capable of initiating RNA synthesis at the 3' end site located at about 700 residues from the 3' end of the beta-Globin restriction enzyme map. Initiation at this site was more efficient than initiation at the known early lambda promotors (PL, PR). Calf thymus RNA polymerase B initiated transcription at the same sites as the bacterial enzyme but in this case maximum efficiency was at the 5' end site as compared to the 3' end site. Initiation of transcription occurs in the region of the d(T-A-T-A-A) sequence. Initiation efficiency at the 5' end site, as probed by the maximum rate of transcription, was shown to depend partly upon the presence of the adjacent sequences upstream and downstream of the 5' initiation site.
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O'Hare K, Benoist C, Breathnach R. Transformation of mouse fibroblasts to methotrexate resistance by a recombinant plasmid expressing a prokaryotic dihydrofolate reductase. Proc Natl Acad Sci U S A 1981; 78:1527-31. [PMID: 6262811 PMCID: PMC319164 DOI: 10.1073/pnas.78.3.1527] [Citation(s) in RCA: 119] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
A recombinant plasmid has been constructed for the expression of inserted DNA sequences coding for polypeptide chains using the simian virus 40 early promoter and splicing and polyadenylylation signals from the rabbit beta-globin gene. The coding regions for two prokaryotic methotrexate-resistant dihydrofolate reductases were introduced into the expression vector. When mouse fibroblasts were exposed to these recombinant plasmids, it was possible to select methotrexate-resistant clones that had integrated the plasmids and produced a chimeric RNA coding for the prokaryotic enzyme.
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Chandrasekaran E, Mendicino A, Garver F, Mendicino J. Structures of sialylated O-glycosidically and N-glycosidically linked oligosaccharides in a monoclonal immunoglobulin light chain. J Biol Chem 1981. [DOI: 10.1016/s0021-9258(19)69839-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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23
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Das GC, Niyogi SK. Structure, replication, and transcription of the SV40 genome. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1981; 25:187-241. [PMID: 6261296 DOI: 10.1016/s0079-6603(08)60485-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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24
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Benoist C, Chambon P. Deletions covering the putative promoter region of early mRNAs of simian virus 40 do not abolish T-antigen expression. Proc Natl Acad Sci U S A 1980; 77:3865-9. [PMID: 6253995 PMCID: PMC349727 DOI: 10.1073/pnas.77.7.3865] [Citation(s) in RCA: 99] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
A recombinant plasmid was constructed by insertion of the early genes of simian virus 40 (SV40) into pBR322. When it was introduced into eukaryotic cells, the SV40 early genes were expressed. We have made deletion mutants of this plasmid, from which the major cap sites of SV40 early mRNAs have been removed along with some of the sequences upstream. The deleted sequences appear to be dispensable for early gene expression, but this does not necessarily imply that they serve no function in the initiation of transcription on wild-type SV40.
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Abstract
The regulatory effects of host cellular histones on the transcription of simian virus 40 (SV40) DNA were investigated by using reconstituted and native SV40 nucleoprotein complexes (NPCs). Reconstituted NPCs were prepared from SV40 DNA and the combination fraction of five histones, H1, H2A, H2B, H3, and H4, isolated from the nuclei of permissive (CV-1) or nonpermissive (BALB/c 3T3, rat liver, and calf thymus) cells. Native NPCs were prepared by alkali disruption of purified SV40 virions. Nuclease digestion of these NPCs gave regular patterns of bands similar to those of SV40 NPCs from SV40-infected CV-1 cells, suggesting the presence of a nucleosomal structure. Transcription of NPCs was analyzed in vitro by using Escherichia coli DNA-dependent RNA polymerase. Both histone H1 and the fraction consisting of all five histones inhibited transcription of SV40 DNA by about 90 to 95%. The fraction consisting of four histones lacking H1 reduced the transcription by 30 to 35%, to a level similar to that of transcription with native NPCs. Transcription was inhibited regardless of whether the origin of histones was permissive or nonpermissive cells. Gel electrophoretic patterns of RNA products transcribed from SV40 DNA and reconstituted and native NPCs showed several identical peaks between 13S and 28S. The patterns were identical whether NPCs reconstituted with H1 alone, all five histones, or four histones lacking H1 were used.
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Saragosti S, Croissant O, Yaniv M. Localization of the binding sites of prokaryotic and eukaryotic RNA polymerases on simian virus 40 DNA. EUROPEAN JOURNAL OF BIOCHEMISTRY 1980; 106:25-31. [PMID: 6280998 DOI: 10.1111/j.1432-1033.1980.tb05993.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The binding sites of calf thymus RNA polymerase (B) II, wheat germ RNA polymerase B and of the Escherichia coli RNA polymerase were mapped on the simian virus 40 genome by observation of enzyme-linear DNA complexes by electron microscopy. Three to four major sites and several minor sites are observed for each enzyme; common binding sites for the three enzymes are found in positions 0.17, 0.53 and 0.90 of the viral physical map. Initiation complexes with these enzymes can be stabilized with specific ribodinucleotides and a single ribonucleoside triphosphate. Whereas ApA and ATP greatly enhances the binding of the E. coli enzyme at position 0.17, they stabilize the binding of the eukaryotic enzyme at many sites, some of them located in close proximity of the origin of replication.
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Lewis M, Burgess R. Transcription of simian virus 40 DNA by wheat germ RNA polymerase II. Priming of RNA synthesis by the 3'-hydroxyl of DNA at single strand nicks. J Biol Chem 1980. [DOI: 10.1016/s0021-9258(19)85584-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Hale P, Woodward RS, Lebowitz J. E. coli RNA polymerase promoters on superhelical SV40 DNA are highly selective targets for chemical modification. Nature 1980; 284:640-4. [PMID: 6245374 DOI: 10.1038/284640a0] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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29
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Ballario P, Di Mauro E, Giuliani C, Pedone F. Purification of sea-urchin RNA polymerase II. Characterization by template requirements and sensitivity to inhibitors. EUROPEAN JOURNAL OF BIOCHEMISTRY 1980; 105:225-34. [PMID: 7379783 DOI: 10.1111/j.1432-1033.1980.tb04493.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The purification of RNA polymerase II from gastrulae of Paracentrotus lividus is described. The enzyme obtained is homogeneous as judged by electrophoresis under non-denaturing conditions. It is able to transcribe both native high-Mr P. lividus DNA and Psammechinus miliaris h22 histone DNA, although single-stranded and nicked DNAs are better templates. P. lividus RNA polymerase II forms with homologous native DNA stable binary complexes that are able to initiate RNA chains after exposure to heparin. Heparin-resistant complexes do not form on nicks of DNA molecules. Sensitivity of sea-urchin RNA polymerase II to rifamycin derivatives and alpha-amanitin has been determined.
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Wasylyk B, Chambon P. Transcription by eukaryotic RNA polymerases A and B of chromatin assembled in vitro. EUROPEAN JOURNAL OF BIOCHEMISTRY 1979; 98:317-27. [PMID: 226362 DOI: 10.1111/j.1432-1033.1979.tb13191.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Chromatin was assembled in vitro from simian virus 40 DNA form I and the calf-thymus four histones H2A, H2B, H3 and H4. Transcription with calf thymus RNA polymerases A and B (I and II) was greatly inhibited. Nucleosomes were found to inhibit both RNA chain initiation and elongation. The inhibition of elongation could be relieved by increasing ionic strength, suggesting that electrostatic interactions between histone octamer and DNA have to be broken for RNA polymerase to transcribe DNA organised into nucleosomes.
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31
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Teissère M, Durand R, Ricard J, Cooke R, Penon P. Transcription in vitro of cauliflower mosaic virus DNA by RNA polymerase I, II, and III purified from wheat embryos. Biochem Biophys Res Commun 1979; 89:526-33. [PMID: 486178 DOI: 10.1016/0006-291x(79)90661-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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32
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Gariglio P, Llopis R, Oudet P, Chambon P. The template of the isolated native simian virus 40 transcriptional complexes is a minichromosome. J Mol Biol 1979; 131:75-105. [PMID: 226716 DOI: 10.1016/0022-2836(79)90302-4] [Citation(s) in RCA: 70] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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33
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Pays E, Donaldson D, Gilmour RS. Specificity of chromatin transcription in vitro. Anomalies due to RNA-dependent RNA synthesis. BIOCHIMICA ET BIOPHYSICA ACTA 1979; 562:112-30. [PMID: 373804 DOI: 10.1016/0005-2787(79)90131-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In the presence of Mn2+, globin mRNA can be transcribed into a partial RNA copy by Escherichia coli RNA polymerase. This process also occurs when the mRNA is transcribed together with chromatin. A fraction, at least, of the newly synthesized RNA copy (anti-globin RNA) can serve as a template for the synthesis of globin sequences of the same polarity as the original mRNA. This process is sufficient to explain the specific synthesis of a subset of the globin RNA on mouse foetal liver chromatin. It also accounts for the synthesis of double-stranded RNA sequence by E. coli RNA polymerase, on chromatin as well as on pure mRNA. Results are presented suggesting that the poly(A) tract of the mRNA could be preferentially transcribed. In the presence of Mg2+, the RNA-dependent transcription is strongly inhibited, as well as the synthesis of double-stranded RNA. Under these conditions, the transcription on chromatin appears to be largely DNA dependent, and the synthesis of globin sequences is completely asymmetric. Spermine (0.3 mM) seems to improve the specificity of transcription. The transcription of chromatin in vitro is thus largely dependent on the nature of the divalent cation present in the in the incubation mixture.
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Wasylyk B, Thevenin G, Oudet P, Chambon P. Transcription of in vitro assembled chromatin by Escherichia coli RNA polymerase. J Mol Biol 1979; 128:411-40. [PMID: 220426 DOI: 10.1016/0022-2836(79)90095-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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35
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Lebowitz P, Weissman SM. Organization and transcription of the simian virus 40 genome. Curr Top Microbiol Immunol 1979; 87:43-172. [PMID: 232871 DOI: 10.1007/978-3-642-67344-3_3] [Citation(s) in RCA: 64] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
MESH Headings
- Antigens, Viral/genetics
- Base Sequence
- Cell Transformation, Neoplastic
- Cell Transformation, Viral
- DNA, Circular/analysis
- DNA, Circular/genetics
- DNA, Viral/analysis
- DNA, Viral/genetics
- Genes, Viral
- Genetic Code
- Hybridization, Genetic
- Nucleotides/analysis
- RNA, Messenger/analysis
- RNA, Messenger/genetics
- RNA, Viral/analysis
- RNA, Viral/genetics
- Simian virus 40/analysis
- Simian virus 40/genetics
- Templates, Genetic
- Transcription, Genetic
- Viral Proteins/analysis
- Viral Proteins/genetics
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36
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Hossenlopp P, Sümegi J, Chambon P. Transcription in vitro of adenovirus-2 DNA by RNA polymerases class C purified from uninfected and adenovirus-infected HeLa cells. EUROPEAN JOURNAL OF BIOCHEMISTRY 1978; 90:615-31. [PMID: 710451 DOI: 10.1111/j.1432-1033.1978.tb12642.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
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.
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37
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Lescure B, Chestier A, Yaniv M. Transcription of polyoma virus DNA in vitro. II. Transcription of superhelical and linear polyoma DNA by RNA polymerase II. J Mol Biol 1978; 124:73-85. [PMID: 213607 DOI: 10.1016/0022-2836(78)90148-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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38
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Lescure B, Dauguet C, Yaniv M. Transcription of polyoma virus DNA in vitro. III. Localization of calf thymus RNA polymerase II binding sites. J Mol Biol 1978; 124:87-96. [PMID: 213608 DOI: 10.1016/0022-2836(78)90149-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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39
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Luse DS, Beer M. In vitro transcription of Drosophila ribosomal genes using Drosophila RNA polymerases. Biochem Biophys Res Commun 1978; 82:964-70. [PMID: 666850 DOI: 10.1016/0006-291x(78)90618-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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40
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Rjalakshmi S, Rao PM, Sarma DS. Modulation of carcinogen chromatin-DNA interaction by polyamines. Biochem Biophys Res Commun 1978; 81:936-40. [PMID: 666803 DOI: 10.1016/0006-291x(78)91441-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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41
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Pierce DA, Fausto N. Mechanism of stimulation of chromatin transcription by putrescine: effects on rate of elongation and number of initiation sites utilized. Biochemistry 1978; 17:102-9. [PMID: 338031 DOI: 10.1021/bi00594a014] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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42
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Van Keulen H, Retèl J. Transcription specificity of yeast RNA polymerase A. Highly specific transcription in vitro of the homologous ribosomal transcription units. EUROPEAN JOURNAL OF BIOCHEMISTRY 1977; 79:579-88. [PMID: 923568 DOI: 10.1111/j.1432-1033.1977.tb11842.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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43
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Karpetsky TP, Hieter PA, Frank JJ, Levy CC. Polyamines, ribonucleases, and the stability of RNA. Mol Cell Biochem 1977; 17:89-99. [PMID: 333273 DOI: 10.1007/bf01743432] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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44
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Sümegi J, Breedveld D, Hossenlopp P, Chambon P. A rapid procedure for purification of EcoRI endonuclease. Biochem Biophys Res Commun 1977; 76:78-85. [PMID: 194592 DOI: 10.1016/0006-291x(77)91670-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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45
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Gross RH, Luse DS, Beer M. Selective in situ transcription of Drosophila polytene chromosomes by Drosophila RNA polymerases. Exp Cell Res 1977; 106:412-7. [PMID: 405229 DOI: 10.1016/0014-4827(77)90192-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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46
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Holland MJ, Hager GL, Rutter WJ. Transcription of yeast DNA by homologous RNA polymerases I and II: selective transcription of ribosomal genes by RNA polymerase I. Biochemistry 1977; 16:16-24. [PMID: 318852 DOI: 10.1021/bi00620a003] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Purified yeast DNA was transcribed by homologous RNA polymerases I and II and Escherichia coli RNA polymerase. Transcripts synthesized in vitro were analyzed by molecular hybridization with complementary DNA (cDNA) synthesized from yeast poly(A)-containing mRNA with viral reverse transcriptase and ribosomal DNA labeled in vitro by nick translation with E. coli DNA polymerase I. RNA synthesized by polymerase I and II in the presence of Mn2+ contained sequences complementary to cDNA and rDNA at a frequency consistent with random transcription of the template. Similarly, E. coli RNA polymerase synthesized an apparently random transcript in the presence of either Mn2+ or Mg2+. In contrast to these results, RNA polymerase I but not polymerase II transcripts were markedly enriched in sequences complementary to rDNA when transcription was carried out in the presence of Mg2+. The observed enrichment was 15-30-fold higher than observed for polymerase II or E. coli polymerase transcripts and is consistent with the transcript being comprised of 6-10% ribosomal sequences. These data strongly suggest that RNA polymerase I plays a critical role in selective transcription of ribosomal cistrons.
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Sasaki Y, Goto H, Ohta H, Kamikubo T. Template activity of synthetic deoxyribonucleotide polymers in the eukaryotic DNA-dependent RNA polymerase reaction. EUROPEAN JOURNAL OF BIOCHEMISTRY 1976; 70:369-75. [PMID: 1009936 DOI: 10.1111/j.1432-1033.1976.tb11026.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
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.
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48
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Bellard M, Oudet P, Germond JE, Chambon P. Subunit structure of simian-virus-40 minichromosome. EUROPEAN JOURNAL OF BIOCHEMISTRY 1976; 70:543-53. [PMID: 188649 DOI: 10.1111/j.1432-1033.1976.tb11046.x] [Citation(s) in RCA: 130] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Electron microscopic evidence indicates that Simian virus 40 (SV40) minichromosomes extracted from infected cells consist of 20 +/- 2 nucleosomes, each containing 190 -- 200 base pairs of DNA. About 50% of the nucleosomes are not close together, but connected by segments of DNA of irregular lengths which correspond to about 15% of the viral genome, irrespective of the ionic strength. Micrococcal nuclease digestion studies show that there is about 200 base pairs of DNA in the biochemical unit of SV40 chromatin. Therefore, the visible internucleosomal DNA of the SV40 minichromosome does not arise from an unfolding of a fraction of the 190 - 200 base pairs of DNA initially wound in the nucleosome. These results support the chromatin model which proposes that the same DNA length is contained in the nucleosome and the biochemical unit. Results from extensive micrococcal nuclease digestion suggest that an SV40 nucleosome consists of a 'core' containing a DNA segment of about 135 base pairs associated to a DNA fragment more susceptible to nuclease attack. The addition of histone H1 results in a striking condensation of the SV40 minichromosome, which supports the assumption that histone H1 is involved in the folding of chromatin fibers.
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49
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Lescure B, Oudet P, Chambon P, Yaniv M. Transcription of polyoma virus DNA in vitro. Localization of Escherichia coli RNA polymerase initiation sites. J Mol Biol 1976; 108:83-97. [PMID: 187757 DOI: 10.1016/s0022-2836(76)80096-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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50
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Long E, Dina D, Crippa M. DNA-dependent RNA polymerase C from Xenopus laevis ovaries. Ability to transcribe intact double-stranded DNA. EUROPEAN JOURNAL OF BIOCHEMISTRY 1976; 66:269-75. [PMID: 947751 DOI: 10.1111/j.1432-1033.1976.tb10516.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
DNA-dependent RNA polymerase C, partially purified from Xenopus laevis ovaries, has been resolved by DEAE-Sephadex chromatography in two forms, eluting at 0.2 M and 0.3 M ammonium sulfate, respectively. Both are sensitive to high concentrations of alpha-amanitin (200 mug/ml). Their ionic strength dependence and divalent cation requirements are indistinguishable. Quantitatively, RNA polymerase C represents the major form of RNA polymerase activity solubilized from the ovaries. Both RNA polymerases C are able to transcribe efficiently either high-molecular-weight Xenopus DNA or intact adenovirus DNA, as compared to nicked DNA. In contrast, RNA polymerase A has little activity on an intact DNA template. The salt dependence of the RNA polymerases C activity is different on the two kinds of template. Nicked DNA is efficiently transcribed up to a salt concentration of 100 mM ammonium sulfate. On intact DNA, optimal transcription is obtained at 40 mM ammonium sulfate and is inhibited by higher salt concentrations.
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