Gene/Protein Disease Symptom Drug Enzyme Compound
Pivot Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound   Target Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound

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Query: EC:2.7.7.6 (RNA polymerase)
34,946 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

1. Nucleolar RNA polymerase Ib obtained from auxin-treated lentil roots exhibits a higher transcriptional activity than the enzyme obtained from control roots. This difference is due to a change in the enzyme properties after auxin treatment. It is suggested that the hormonal effect is mediated by a factor that changes the molecular properties of nucleolar RNA polymerase. 2. Four fractions, alpha, beta, gamma and delta, that stimulate the activity of RNA polymerase Ib, have been extracted from lentil roots. Two of them, gamma and delta have been studied. Factor delta can stimulate nucleolar polymerase Ib and the nucleoplasmic enzyme II equally well, while factor gamma is specific for polymerase Ib. 3. The curve of UMP incorporation in vitro, with and without factors gamma or delta suggests that they are initiation factors. This conclusion is reinforced by the analysis of simultaneous incorporation of [gamma-32P]ATP and [3H]UMP in the RNAs synthesized in vitro. 4. Although the level of factor delta is independent of auxin treatment, that of factor gamma is doubled in auxin-treated roots. These results suggest that factor gamma is an auxin-induced protein that modulates the specific activity of the nucleolar RNA polymerase. 5. A general model of the mode of action of auxins at the molecular level is proposed. It integrates into a unified scheme the above results as well as those obtained by other workers.
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PMID:Hormonal control of transcription in higher plants. 116 23

1. The template activity of chromatin prepared from rat uterine nuclei during dioestrus, oestrus and the first 7 days of pregnancy has been examined. 2. The DNA, RNA, histone and non-histone protein contents of uterine chromatin remained constant during early pregnancy. 3. The rate of RNA synthesis on Day 1 uterine chromatin was 8.61 +/- 0.59 (mean +/- S.E.) pmol of UMP incorporated/mg DNA per 10 min. When compared with DNA prepared from rat liver nuclei, 13.20 +/- 0.27% (mean +/- S.E.) of the Day 1 chromatin DNA was available for transcription by Escherichia coli RNA polymerase. 4. Uterine chromatin from rats in early dioestrus had significantly less template activity than during oestrus. 5. Chromatin prepared from whole uterus on Day 5 and from implantation sites on Days 6 and 7 of pregnancy had a significantly higher template activity than chromatin obtained from uteri on Day 1. Chromatin from interimplantation tissue on Day 6 had a lower template activity than that from uteri on Day 1. 6. RNA - DNA hybridisation of RNA transcribed from chromatin obtained on Days 2, 5 and 7 of pregnancy showed that RNA transcribed from Day 5 chromatin obtained species not present (or present in very small amounts) in RNA transcribed by chromatin from uteri on Day 2 and from implantation tissue on Day 7 of pregnancy. 7. The results are discussed in relation to the cellular changes occurring in the stroma immediately before implantation and it is postulated that the appearance of a new species of RNA on Day 5 is related to the preparation of the stromal cells for decidualisation.
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PMID:Uterine chromatin template activity during the early stages of pregnancy in the rat. 118 77

The activation of the mouse embryo genome has been studied during early cleavage, in vivo. Individual embryos, prepared as whole mounts, were assayed for endogenous RNA polymerase activity. RNA synthesis was detected by autoradiography as the incorporation of [3H]UMP into an acid-insoluble product. No RNA polymerase activity could be detected in the pronuclei of one-cell embryos. Radioactive incorporation was first evident in the nuclei of two-cell embryos. This appeared to be confined to the nucleoplasm and could be abolished by alpha-amanitin but not by low concentrations of actinomycin D. Polymerase activity which was not affected by alpha-amanitin was first detected in the four-cell embryo, predominantly at the peripheries of the nucleoli. Nucleolar labelling increased markedly between subsequent cleavages, reaching a peak in early morulae. In one- and two-cell embryos, label incorporation could be found in the nucleus of the persisting polar body.
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PMID:The RNA polymerase activity of the preimplantation mouse embryo. 119 32

Specific activities are determined of two functional fractions of alpha-amanitin sensitive DNA-dependent RNA polymerases in nucleic from human normal and chronic lymphocytic leukemia lymphocytes. Specific activity of "free" RNA polymerase in CLL corresponds ot 0.133 pmoles (3H)-UMP/10(6) cells as compared to 0.209 in normals. Activities of the "engaged" enzymes are 0.139 in CLL and 0.132 in normals. "Free" enzymes in NL and CLL are completely inhibited by 400 ng/ml Rifamycin AF/013, while the "engaged" enzymes exhibit 70% of their original activity. 1.0 ng/ml alpha-amanitin suppress 50% of the activity of the "free" enzyme in CLL. The "free" enzyme in NL and the "engaged" enzymes in NL and CLL do not show any residual activity in the presence of 1.0 ng/ml alpha-amanitin.
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PMID:[Free and template-bound RNA polymerase in normal and leukaemic human lymphocytes (author's transl)]. 125 8

In yeast nuclear extracts, tagetitoxin inhibition of RNA polymerase III promoter-directed single- and multiple-round transcription is characterized by pausing or stalling of the elongation complex at several discrete points on the template. Paused ternary complexes isolated from tagetitoxin-inhibited reactions can be elongated to produce full-length RNA. The distribution of "tagetitoxin-enhanced" pause sites is distinct for each of the class III genes we have examined. These tagetitoxin-enhanced pause sites may also be intrinsic pause sites for the elongation complex. Tagetitoxin inhibition of in vitro transcription of the yeast SUP4 and SUP6 tRNA(Tyr) genes demonstrates template dependence and indicates that inhibition may occur after UMP incorporation. Factor-independent transcription by purified yeast RNA polymerase III can also be inhibited by tagetitoxin, and the degree of inhibition is template-dependent. Tagetitoxin may be most effective as an inhibitor under conditions where polymerase III tends to pause on the template. We propose that differences in tagetitoxin inhibition among class III genes may reflect differences in the number of stability of these pause sites.
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PMID:Tagetitoxin inhibition of RNA polymerase III transcription results from enhanced pausing at discrete sites and is template-dependent. 140 Mar 38

New spin-labeled analogs of nucleoside triphosphates, 8-amino(2,2,6,6-tetramethylpiperidine-N-oxyl)adenosine 5'-triphosphate ((8-AmTEMPO)ATP) and 5-amino(2,2,6,6-tetramethylpiperidine-N-oxyl)uridine 5'-triphosphate ((5-AmTEMPO)UTP), with the probe 4-amino(2,2,6,6-tetramethylpiperidine-N-oxyl) (4-AmTEMPO) attached to C-8 of ATP and C-5 of UTP via a secondary amine bond, were synthesized in 50 and 40% yield, respectively. These analogs showed a single spot by thin layer chromatographic analysis. The absorption spectra of (8-Am-TEMPO)ATP and (5-AmTEMPO)UTP exhibit maxima at 310 and 265 nm, respectively; their X-band EPR spectra have a typical three-line pattern with lines at 3,221, 3,239, and 3,257 Gauss. The intensity ratios for mid to high field lines of the EPR derivative lines were found to be 1.03 +/- 0.02, 1.08 +/- 0.04, and 1.15 +/- 0.07 for 4-AmTEMPO, (8-AmTEMPO)ATP, and (5-AmTEMPO)UTP, respectively. The immobilization of 4-AmTEMPO bound to C-8 of ATP or bound to C-5 of UTP was observed to be 5 and 11%, respectively, as compared with free 4-AmTEMPO. The initial velocity (s-1) of [3H]UMP incorporation into RNA in the presence of [3H]UTP, CTP, GTP, and (8-AmTEMPO)ATP or ATP was measured. The percent incorporation of (8-AmTEMPO)ATP into RNA product by Escherichia coli RNA polymerase using various DNA templates is 68, 66, and 61% for pAR1435 (plasmid containing A1 promoter from T7 DNA), calf thymus DNA, and poly(dA-dT) respectively, as compared with ATP incorporation. The polymerase-catalyzed reaction of (8-AmTEMPO)ATP with (3'-OCH3)UTP yielded 5'-triphosphate delta-amino(2,2,6,6-tetramethylpiperidine-N-oxyl)adenylyl (3'-5')3'-methoxy uridine in the presence of poly(dA-dT). The structure of this spin-labeled dinucleotide was identified by paper chromatographic analysis of the products of phosphodiesterase digestion. These analogs also can be used for the study by EPR spectroscopy of the dynamics of gene transcription catalyzed by RNA polymerases or of other nucleotide-utilizing enzymes.
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PMID:Spin-labeled nucleotide substrates for DNA-dependent RNA polymerase from Escherichia coli. 165 31

Escherichia coli RNA polymerase transcription elongation complexes have been prepared that contain a photo-cross-linking uridine analog at only the 3' end, or one or two nucleotides removed from the 3' end, in the nascent RNA chain. Additionally, complexes have been isolated in which the analog has been substituted for every UMP residue, at positions ranging from 20 to 140 nucleotides from the 3' end. The RNA has been photochemically cross-linked to the RNA polymerase to identify the subunits that form the binding site(s) for these regions in the nascent RNA. The photo-cross-linking nucleotide analog used for these studies was 5-[4-azidophenacyl)thio)uridine-5'-triphosphate (5-APAS-UTP), which acts as a 10-15 A probe. With 5-APAS-UMP positioned only at the 3' end of the RNA, or one or two nucleotides from the 3' end, only the beta subunit appeared to be contacted. When the analog was positioned throughout the RNA, both the beta and beta' subunits were contacted. No labeling of the sigma or alpha subunits was observed with any RNA length. In addition to placing this analog at specific positions in short RNAs, we have carried out transcription studies with 5-APAS-UTP to determine the optimal UTP to analog ratio for production of full length, photoreactive transcripts. Surprisingly, we found that when transcription complexes were stalled shortly after initiation, by deletion of one ribonucleoside triphosphate to synchronize transcription, changes in transcriptional pausing occurred downstream. These results suggest that events that occur early in transcription can affect the elongation and/or termination events that occur far downstream from the promoter. This effect occurred even with UTP but was greatly enhanced by replacement of UTP with either this analog or 4-thio-UTP. By enhancing the normal transcriptional pausing event, these analogs can serve as probes of the conformational changes that may exist in paused transcription complexes.
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PMID:Active site labeling of Escherichia coli transcription elongation complexes with 5-[4-azidophenacyl)thio)uridine 5'-triphosphate. 169 25

We have developed a method to determine directly the number of biotinylated (Bio) nucleotide analogs incorporated into RNA transcripts. Transcripts synthesized in vitro in the presence of [alpha 32-P]CTP and varying concentrations of Bio-4-UTP were subjected to alkaline hydrolysis and the resulting 2' and 3' nucleoside monophosphates separated by reverse-phase HPLC. The amount of 32P transferred to each monophosphate was indicative of the frequency of their incorporation into the transcript. Transcripts synthesized in the presence of equimolar concentrations of Bio-4-UTP and UTP resulted in 70 out of the 125 possible UTP sites occupied by Bio-4-UMP. This study agrees with kinetic data in suggesting that T7 RNA polymerase does not significantly discriminate between the natural and the biotinylated nucleotide. Therefore, the number of biotinylated residues that are incorporated into a transcript can be controlled by varying the ratio of Bio-4-UTP to UTP in the transcription reaction. We have shown that as few as 10 Bio-4-UMP residues per 486 nucleotide transcript still results in greater than 90% binding efficiency on a streptavidin/biotin-cellulose affinity column.
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PMID:Direct quantitation of biotin-labeled nucleotide analogs in RNA transcripts. 170 88

We have isolated Escherichia coli transcription complexes, paused in the presence and absence of Nus A, which contain RNA substituted at every UMP residue with a photocrosslinking nucleotide analog. The pause site is immediately downstream from an RNA stem-loop structure, and although pausing occurs in the absence of Nus A, it is substantially enhanced in the presence of Nus A. We have analyzed the secondary structure of this RNA and show that the analog does not interfere with the formation of the normal stem-loop structures. Additionally, the analog substrate does not alter transcriptional pausing, in the presence or absence of Nus A, indicating that Nus A recognition of the transcription complex is not affected by the presence of the crosslinking groups in the RNA. Ribonuclease digestion of the RNA in paused complexes identifies two accessible regions, two nucleotides in the loop and one near the base of the upstream side of the stem-loop. Cleavage at one loop nucleotide is enhanced by Nus A, while the nucleotide near the base of the stem-loop is partially protected. Upon irradiation of the transcription complex, Nus A is not photoaffinity labeled by the RNA, even at a high molar ration to RNA polymerase (250:1). Both the beta and beta' subunits are labeled, however, indicating that the putative stem-loop binding domain on the core polymerase involves both subunits. Because the nucleotide protected from ribonuclease by Nus A is very near two analogs, yet Nus A is not crosslinked to the RNA, it is unlikely that Nus A could be protecting this position through direct contact. Furthermore, analog is substituted at positions in both the loop and at several positions in the stem, and again, no crosslinking to Nus A is observed. We conclude that enhancement of pausing by Nus A probably does not require direct interaction with the bases in the RNA stem-loop.
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PMID:RNA-protein interactions in a Nus A-containing Escherichia coli transcription complex paused at an RNA hairpin. 170 33

We have used photoaffinity labelling to examine the chloroplast RNA polymerase components which come into contact with nascent transcripts during the in vitro transcription of plastid DNA. The transcripts were synthesized in the presence of a photoactive analogue (4-thio UTP) and alpha-32P-ATP, using enriched pea chloroplast RNA polymerase preparation and a recombinant plasmid containing the plastid 16S rRNA promoter. Brief irradiation of the transcriptional complex crosslinked the photoactive nascent RNA to proximal proteins. Labelling of the transcriptional complex was dependent on 4-thio UTP and template DNA. Two polypeptides of 51 and 54 kDa were consistently crosslinked to the nascent transcripts; about 60% of the total radioactivity of the crosslinked RNA was associated with these polypeptides. In some experiments, two additional polypeptides of 38 and 75 kDa were also found to be associated with about 13% and 17% of the total crosslinked RNA radioactivity, respectively. The UV-crosslinked transcriptional complexes were stable to either DNase or S1 nuclease hydrolysis but partially sensitive to RNase T1. Insensitivity of the complex to hydrolysis with RNase H suggested that the nascent transcripts were not crosslinked to the template. The complexes could also be hydrolysed by proteinase K and thermolysin. No crosslinkage was observed when labelled RNA molecules containing 4-thio UMP residues were added after synthesis to the polymerase preparation. This suggested that the method identified only those polypeptides which came into close contact with the transcript during its synthesis. Antibodies raised against the RNA-protein complex confirmed the presence of the polypeptides in the chloroplast RNA polymerase preparation on Western blots. Preincubation of these antibodies with the chloroplast RNA polymerase inhibited plastid DNA transcription. These data showed that the transcript-binding polypeptides were functional components of the chloroplast transcriptional complex.
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PMID:Photoaffinity labelling of the pea chloroplast transcriptional complex by nascent RNA in vitro. 171 36


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