Cibacron Blue inhibition of prokaryotic and eukaryotic DNA-dependent RNA polymerases

1990 ◽  
Vol 55 (11) ◽  
pp. 2769-2780
Author(s):  
Aleš Cvekl ◽  
Květa Horská
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Wheat Germ ◽  
Rna Polymerase Iii ◽  
Enzymic Activity ◽  
Rna Polymerases ◽  
Cibacron Blue ◽  
E Coli ◽  
Polymer Formation ◽  
Calf Thymus

A comparison was drawn between the action of Cibacron Blue F3GA on the enzymic activity of DNA-dependent RNA polymerases from different sources, e.g. Escherichia coli, calf thymus and wheat germ (polymerase II). Sensitivity towards this inhibitor was determined for polymer formation and primed abortive synthesis of trinucleotide UpApU. In case of E. coli polymerase and wheat germ polymerase II the dye inhibits both polymer formation and abortive synthesis. Calf thymus polymerase II is inhibited only in the polymerisation step. The primed initiation reaction was found to be resistant towards the dye. In case of E. coli polymerase and wheat germ polymerase II the sensitive step is the formation of internucleotide bond whereas in case of calf thymus polymerase II the translocation of the enzyme is influenced. An analysis of kinetic data indicates more than one binding site for the dye on RNA polymerase II from calf thymus and wheat germ. Cibacron blue does not inhibit specific transcription catalyzed by RNA polymerase III from human HeLa cells and mouse leukemia L1210 cells.

scholarly journals The Perinucleolar Compartment and Transcription

1998 ◽  
Vol 143 (1) ◽  
pp. 35-47 ◽  
Author(s):  
Sui Huang ◽  
Thomas J. Deerinck ◽  
Mark H. Ellisman ◽  
David L. Spector
Keyword(s):  
Nucleic Acids ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Rna Polymerase Iii ◽  
Selective Inhibition ◽  
Rna Polymerases ◽  
Double Labeling ◽  
Polypyrimidine Tract Binding Protein ◽  
Cell Biol ◽  
Perinucleolar Compartment

The perinucleolar compartment (PNC) is a unique nuclear structure localized at the periphery of the nucleolus. Several small RNAs transcribed by RNA polymerase III and two hnRNP proteins have been localized in the PNC (Ghetti, A., S. Piñol-Roma, W.M. Michael, C. Morandi, and G. Dreyfuss. 1992. Nucleic Acids Res. 20:3671–3678; Matera, A.G., M.R. Frey, K. Margelot, and S.L. Wolin. 1995. J. Cell Biol. 129:1181– 1193; Timchenko, L.T., J.W. Miller, N.A. Timchenko, D.R. DeVore, K.V. Datar, L. Lin, R. Roberts, C.T. Caskey, and M.S. Swanson. 1996. Nucleic Acids Res. 24: 4407–4414; Huang, S., T. Deerinck, M.H. Ellisman, and D.L. Spector. 1997. J. Cell Biol. 137:965–974). In this report, we show that the PNC incorporates Br-UTP and FITC-conjugated CTP within 5 min of pulse labeling. Selective inhibition of RNA polymerase I does not appreciably affect the nucleotide incorporation in the PNC. Inhibition of all RNA polymerases by actinomycin D blocks the incorporation completely, suggesting that Br-UTP incorporation in the PNC is due to transcription by RNA polymerases II and/or III. Treatment of cells with an RNA polymerase II and III inhibitor induces a significant reorganization of the PNC. In addition, double labeling experiments showed that poly(A) RNA and some of the factors required for pre-mRNA processing were localized in the PNC in addition to being distributed in their previously characterized nucleoplasmic domains. Fluorescence recovery after photobleaching (FRAP) analysis revealed a rapid turnover of polypyrimidine tract binding protein within the PNC, demonstrating the dynamic nature of the structure. Together, these findings suggest that the PNC is a functional compartment involved in RNA metabolism in the cell nucleus.

Trinucleotide AUA and UAU formation catalyzed by wheat germ RNA polymerase II

1989 ◽  
Vol 54 (3) ◽  
pp. 811-818 ◽  
Author(s):  
Aleš Cvekl ◽  
Květa Horská ◽  
Karel Šebesta ◽  
Ivan Rosenberg ◽  
Antonín Holý
Keyword(s):  
Ionic Strength ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Wheat Germ ◽  
Catalytic Mechanism ◽  
Bond Formation ◽  
E Coli ◽  
Substrate Properties ◽  
Rna Polymerase Holoenzyme ◽  
Analogous Mechanism

The elongation of dinucleotides ApU and UpA to trinucleotides ApUpA and UpApU by wheat germ RNA polymerase II was studied at a medium ionic strength (60 mM-KCl). The catalytic mechanism of the first internucleotide bond formation consists in the binding of the primer dinucleotide followed by the binding of NTP ("ordered bibi" reaction), i.e. by an analogous mechanism as found for RNA polymerase holoenzyme from E. coli. In further experiments phosphonate analogues of dinucleotides ApU and UpA were used as the priming dinucleotides. It was shown that analogues U(c)pA and Up(c)A are very poor primers for the synthesis of corresponding trinucleotides; the elongation of analogues A(c)pU and Ap(c)U was not observed at all. The comparison of kinetic constants Kia, KmA, KmB and Vmax as well as the substrate properties of phosphonate analogues indicates the increased specifity of the wheat germ RNA polymerase initiation binding site in comparison with the E. coli holoenzyme.

The yeast alpha 2 protein can repress transcription by RNA polymerases I and II but not III

1993 ◽  
Vol 13 (7) ◽  
pp. 4029-4038
Author(s):  
B M Herschbach ◽  
A D Johnson
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Rna Polymerase Iii ◽  
Rna Polymerases ◽  
Rna Polymerase I ◽  
Cell Type ◽  
Yeast Saccharomyces Cerevisiae ◽  
Cell Type Specific ◽  
Polymerase I ◽  
Rna Polymerase Ii Transcription

The alpha 2 protein of the yeast Saccharomyces cerevisiae normally represses a set of cell-type-specific genes (the a-specific genes) that are transcribed by RNA polymerase II. In this study, we determined whether alpha 2 can affect transcription by other RNA polymerases. We find that alpha 2 can repress transcription by RNA polymerase I but not by RNA polymerase III. Additional experiments indicate that alpha 2 represses RNA polymerase I transcription through the same pathway that it uses to repress RNA polymerase II transcription. These results implicate conserved components of the transcription machinery as mediators of alpha 2 repression and exclude several alternate models.

scholarly journals Sen1 is required for RNA Polymerase III transcription termination in an R-loop independent manner

2019 ◽  
Author(s):  
Julieta Rivosecchi ◽  
Marc Larochelle ◽  
Camille Teste ◽  
Frédéric Grenier ◽  
Amélie Malapert ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Fission Yeast ◽  
Rna Polymerase Ii ◽  
Genome Stability ◽  
Transcription Termination ◽  
Rna Polymerase Iii ◽  
Rna Polymerases ◽  
Independent Manner ◽  
Polymerase Iii

ABSTRACTR-loop disassembly by the human helicase Senataxin contributes to genome stability and to proper transcription termination at a subset of RNA polymerase II genes. Whether Senataxin-mediated R-loop disassembly also contributes to transcription termination at other classes of genes has remained unclear. Here we show in fission yeast that SenataxinSen1promotes efficient termination of RNA Polymerase III (RNAP3) transcriptionin vivo. In the absence of SenataxinSen1, RNAP3 accumulates downstream of the primary terminator at RNAP3-transcribed genes and produces long exosome-sensitive 3’-extended transcripts. Importantly, neither of these defects was affected by the removal of R-loops. The finding that SenataxinSen1acts as an ancillary factor for RNAP3 transcription terminationin vivochallenges the pre-existing view that RNAP3 terminates transcription autonomously. We propose that Senataxin is a cofactor for transcription termination that has been co-opted by different RNA polymerases in the course of evolution.

scholarly journals Studies on sex-organ development. Changes in the oestrogenic response of the chick Müllerian duct as measured by chromatin template and ribonucleic acid initiation capacity

1979 ◽  
Vol 182 (2) ◽  
pp. 257-269 ◽  
Author(s):  
G K Andrews ◽  
C S Teng
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Wheat Germ ◽  
Average Rate ◽  
Developmental Trend ◽  
Mullerian Duct ◽  
Müllerian Duct ◽  
E Coli ◽  
Chromatin Template

Assays of transcription in vitro, with Escherichia coli RNA polymerase or wheat-germ RNA polymerase II, were used to characterize chromatin templates isolated from the left Müllerian duct of the chick embryo during normal development, and during development in the presence of diethylstilboestrol. Control Müllerian-duct template capacity with E. coli RNA polymerase decreased from 6.42% on day 10 to 4.34% by day 15 of development. Similar results were found with wheat-germ RNA polymerase II. In the presence of rifampicin and heparin, the prokaryotic enzyme transcribed a number-average RNA chain of 670 nucleotide residues, at an average rate of 110 nucleotide residues/min, from Müllerian-duct chromatin of all developmental stages. From day 10 to day 15 there was a 44% decrease in the number of initiation sites for E. coli RNA polymerase on Müllerian-duct chromatin. A 47% decline was observed when these chromatins were transcribed with excess RNA polymerase II in the presence of rifamycin Af/013. Signs of increasing responsiveness to oestrogen developed between days 10 and 16. Embryos exposed to maximally responsive doses of diethylstilboestrol for 2 days showed increases in Müllerian-duct chromatin template capacity, RNA-chain initiation sites, wet weight, protein and RNA. The changes seen in the oviduct of the 1-week-old chick injected for 2 days with diethylstilboestrol were defined as 100% responses. By comparison, the Müllerian duct, after exposure to diethylstilboestrol from day 10 to day 12, from day 13 to day 15 or from day 16 to day 18, showed a 15%, 39% and 72% template response respectively, and a 42%, 56% and 85% initiation-site change respectively. A similar developmental trend was observed in all parameters. It is concluded that oestrogenic responsiveness in the developing Müllerian duct increases from day 10 to nearly maximal values by day 16 of development, and that this transition is paralleled by a progressive restriction of genomic activity.

STRUCTURAL AND FUNCTIONAL PROPERTIES OF THREE MAMMALIAN NUCLEAR DNA-DEPENDENT RNA POLYMERASES

1972 ◽  
Vol 71 (2_Suppla) ◽  
pp. S222-S246 ◽  
Author(s):  
P. Chambon ◽  
F. Gissinger ◽  
C. Kedinger ◽  
J. L. Mandel ◽  
M. Meilhac ◽  
...  
Keyword(s):  
Molecular Weight ◽  
Rna Polymerase ◽  
Rat Liver ◽  
Nuclear Dna ◽  
Active Role ◽  
Rna Polymerases ◽  
E Coli ◽  
Structural And Functional Properties ◽  
Calf Thymus ◽  
Derivatives Of

ABSTRACT Three DNA-dependent RNA polymerases AI, BI and BII were purified from calf thymus. These enzymes were characterized by their sensitivity to amanitin, their subunit pattern and their template specificities. Enzyme AI is resistant to amanitin, while B enzymes are inhibited by this poison. Each of these enzymes contains two subunits of high molecular weight: A1 (M.W. 197 000) and A2 (M.W. 126 000) for enzyme AI, Bl (M.W. 214 000) and B3 (M.W. 140 000) for enzyme BI, B2 (M.W. 180 000) and B3 for enzyme BII. In addition, each enzyme contains several subunits of lower molecular weight. Purification of B enzymes from rat liver showed the presence of two enzymes similar to calf thymus RNA polymerases BI and BII and suggested the existence of an additional B enzyme in rat liver. The number of RNA polymerase form B molecules was determined in a variety of animal tissues by binding of labelled amanitin. The values ranged from 1 × 104 to 6.5 × 104 molecules per haploid genome. Studies with derivatives of rifamycin indicated that calf thymus B enzymes were able to recognize specific initiation sites on calf thymus DNA, which were different from those recognized by enzyme AI or E. coli RNA polymerase. These results favour the hypothesis that the multiplicity of animal RNA polymerases could play an active role in the control of transcription.

scholarly journals Studies on sex-organ development. Changes in chromatin structure during spermatogenesis in maturing rooster testis as demonstrated by the initiation pattern of ribonucleic acid synthesis in vitro

1978 ◽  
Vol 170 (2) ◽  
pp. 203-210 ◽  
Author(s):  
C Mezquita ◽  
C S Teng
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Wheat Germ ◽  
Acid Synthesis ◽  
Chromatin Interaction ◽  
E Coli ◽  
Double Stranded Dna ◽  
The Stability ◽  
Kinetics Of

To probe the structural change in the genome of the differentiating germ cell of the maturing rooster testis, the chromatin from nuclei at various stages of differentiation were transcribed with prokaryotic RNA polymerase from Escherichia coli or with eukaryotic RNA polymerase II from wheat germ. The transcription was performed under conditions of blockage of RNA chain reinitiation in vitro with rifampicin or rifampicin AF/013. With the E. coli enzyme, the changes in (1) the titration curve for the enzyme-chromatin interaction, (2) the number of initiation sites, (3) the rate of elongation of RNA chains, and (4) the kinetics of the formation of stable initiation complexes revealed the unmasking of DNA in elongated spermatids and the masking of DNA in spermatozoa. In both cases the stability of the DNA duplex in the initiation region for RNA synthesis greatly increased. In contrast with the E. coli enzyme, the wheat-germ RNA polymerase II was relatively inefficient at transcribing chromatin of elongated spermatids. Such behaviour can be predicted if unmasked double-stranded DNA is present in elongated spermatids.

Immunological analyses of selected eukaryotic RNA polymerases II

1985 ◽  
Vol 63 (12) ◽  
pp. 1217-1230 ◽  
Author(s):  
Michael F. Bettiol ◽  
Randall T. Irvin ◽  
Paul A. Horgen
Keyword(s):  
Molecular Weight ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
High Molecular Weight ◽  
Wheat Germ ◽  
Polyclonal Antibodies ◽  
Sodium Dodecyl ◽  
Cross Reactivity ◽  
Rna Polymerases ◽  
Antibody Preparations

Polyclonal antibodies to native RNA polymerase II of Achlya ambisexualis and Agaricus bisporus were produced in rabbits and in mice. Monoclonal antibodies were produced against the α-amanitin resistant RNA polymerase II of the mushroom A. bisporus. These antibodies were used in comparative cross-reactivity studies with five purified RNA polymerases II (A. bisporus, A. ambisexualis, Saccharomyces cerevisiae, wheat germ, and calf thymus). A method for quantitatively comparing cross-reactivity was developed utilizing an enzyme-linked immunosorbant assay (ELISA). ELIS A comparisons indicated that the two filamentous fungi cross-reacted effectively with one another and depending upon the preparation reacted less effectively with yeast and wheat germ RNA polymerases II. Cross-reactivity measurements were also made by immunoblotting sodium dodecyl sulfate – polyacrylamide separated RNA polymerases II. The mouse anti-A. bisporus RNA polymerase II immunoglobulin G (IgG) and the monoclonal antibody preparations did not react with high molecular subunits of A. bisporus RNA polymerase II. The sera did, however, cross-react with high molecular weight subunits of A. ambisexualis. Similarily, rabbit anti-A. ambisexualis RNA polymerase II IgG reacted only with low molecular weight subunits of A. bisporus RNA polymerase II, but reacted with high molecular weight subunits of A. ambisexualis and wheat germ. Our results indicate differences in the cross-reactivity of native and denatured RNA polymerases II and suggest differences in the tertiary and quaternary organization of the enzymes examined.

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