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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)

The possible involvement of anionic phospholipids in the transcriptional process was studied in isolated rat liver nuclei synthesizing RNA in the presence of phosphatidylserine, which was employed in the form of multillamellar liposomes as a means of delivering the lipid to the nuclei in aqueous medium. The divalent ion requirement for RNA synthesis and the properties of the incubation mixture were not significantly modified by the phospholipid, which increased the rate and the extent of the incorporation of 3H-UMP without changing the endogeneous degradation pattern of the product or affecting the activity of a particular RNA polymerase, as indicated by the sensitivity to amanitin. The thin layer chromatography analysis of the alkaline hydrolysates of the RNA showed that the stimulation involved an increase of the total polyribonucleotide elongation rate. The size of the product was essentially unchanged in the presence of phosphatidylserine, as demonstrated by the qualitative overlapping of the sedimentation profiles of control and lipid treated samples in formamide-sucrose gradients. The release of the H1 fraction from intact nuclei occurring with phosphatidylserine indicated that the DNA template availability was increased by a partial removal of the restrictions imposed by histones, as suggested also by the comparison with heparin and Sarkosyl. These evidences, together with the data accumulated on the occurrence of lipids in chromatin and nuclear matrix, and on their changes related to cell growth, differentiation and malignant transformation, allow a better definition of the role that phospholipids might play in regulating the DNA template availability in the cell.
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PMID:Influence of phosphatidylserine on endogeneous RNA synthesis in isolated rat liver nuclei. 244 70

A general method of gene isolation has been developed that involves the chemical linkage of RNA to cellulose by a water-soluble carbodiimide, and the continuous circulation of DNA containing specific sequences complementary to the RNA. The temperature of the cellulose matrix is maintained at 37 degrees (50% formamide, 0.3 M NaCl-0.03 M Na(3) citrate) to allow efficient DNA-RNA interaction in the stationary phase, while unreacted and any reassociated DNA is denatured at 90 degrees and then recirculated into the hybridization chamber. Between 40 and 45% of fragmented (32)P-labeled simian virus (SV)40 DNA was removed from the circulating solution when cellulosebound SV40-specific RNA, assymmetrically transcribed in vitro with Escherichia coli RNA polymerase, was used. In the presence of 10(4)-fold excess of sheared E. coli DNA, nearly half of the [(32)P]SV40 DNA was recovered from the mixture as a DNA-RNA hybrid with negligible contamination by bacterial DNA. The isolation procedure is almost quantitative for the complementary DNA. The efficiency and selectivity of this method permit the isolation of a defined DNA sequence from a large and complex genome.
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PMID:A general method of gene isolation. 435 49

We have developed a novel technique to map restriction sites on large duplex DNAs by electron microscopy. In this method, the sample DNA is first cut with a restriction enzyme. The resulting fragments are briefly digested with Escherichia coli exonuclease III, and treated with wheat germ RNA polymerase II to fill-in with RNA the resulting gaps. These small RNAs, complementary to sequences immediately adjacent to either side of the restriction site, are isolated from the DNA template and R-looped to the full-length DNA. When this material is prepared by the formamide-cytochrome spreading technique, small bubbles are visible wherever there is a restriction site on the DNA. Improved methods of mapping are outlined.
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PMID:Mapping restriction sites on large DNAs by electron microscopy. 631 36

Both bacteriophage T7 and the related bacteriophage T3 have strong termination sites for bacterial RNA polymerase located near 20% on the standard genome map. These termination sites are used with 90% efficiency in vivo, even in cells which contain a defective p protein. Under normal reaction conditions in vitro, Escherichia coli RNA polymerase terminates with 90% efficiency at the T7 terminator site but shows little or no termination at the corresponding T3 locus. Thus, the two templates form an ideal in vitro test system with which to study the parameters that govern transcriptional termination. Termination at these sites has been monitored by following the time course of RNA synthesis under conditions where only a single transcriptional cycle is carried out and by following the size distribution of RNA chains by gel electrophoresis. Termination of the T7 termination site is unaffected by a large variety of changes in reaction conditions, by quantitative cleavage of the nascent RNA during the reaction with a mixture of single- and double-stranded specific ribonucleases, or by a number of different mutations in the subunits of RNA polymerase, including sigma. Similarly, a large variety of changes in reaction conditions fail to enhance termination at the T3 terminator site, including changes in temperature, MgCl2 concentration, and glycerol concentration or the addition of dimethyl sulfoxide, ethanol, or spermidine to the reaction. However, in the presence of elevated salt concentrations, at low ribonucleoside triphosphate concentrations, and in the presence of formamide, efficient in vitro utilization of the T3 terminator is seen. Changes in the RNA polymerase protein can also enhance utilization of the T3 site. A class of rifampicin-resistant rpoB mutants has been identified which produce a rifampicin-resistant RNA polymerase which is able to utilize the T3 terminator site in vitro. Similarly, the normal Bacillus subtilits RNA polymerase utilizes the T3 terminator site in vitro with high efficiency.
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PMID:Termination of transcription by Escherichia coli ribonucleic acid polymerase in vitro. Effect of altered reaction conditions and mutations in the enzyme protein on termination with T7 and T3 deoxyribonucleic acids. 699 5

Using DNA ejection in vitro as a model, we have studied the DNA injection defect caused by alkylation and depurination of T7 bacteriophage. Phage was alkylated with 0.02 M methyl methanesulfonate for 2 h at 37 degrees C; alkylated phage was then incubated 24 h at 30 degrees C to induce depurination. These samples were treated with formamide to cause DNA ejection without dissociation of the phage capsid. After ejection, the phage preparations were analyzed by electron microscopy. DNA lengths in capsid-DNA complexes were measured; relative numbers of full, empty, and partially empty phage heads were determined. To establish the direction of DNA ejection, E. coli RNA polymerase was bound to capsid-DNA complexes. The results showed that DNA was partially ejected from both alkylated and depurinated phages. In the alkylated sample, RNA polymerase was bound to the DNA end distal to the capsid; this showed that ejection started from the genetic left end. We interpret these results to show, in confirmation of earlier results obtained by marker rescue, that alkylation causes T7 phage to partially inject its DNA, starting from the genetic left end. For depurinated phage, our results suggest that partial DNA injection is responsible, in this case as well, for the already documented injection defect.
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PMID:Injection defect in alkylated and depurinated T7 bacteriophage: analysis by DNA ejection. 704

Primers for vertebrate mitochondrial leading-strand DNA replication are products of transcription synthesized by mitochondrial RNA polymerase. The precursor primer RNA exists as a persistent RNA-DNA hybrid, known as an R-loop, formed during transcription through the replication origin (Xu, B., and Clayton, D. A. (1996) EMBO J. 15, 3135-3143). In an effort to examine the precise structure of this primer RNA intermediate, we have used two methods to reconstitute model R-loops containing the mouse mitochondrial DNA origin sequence. First, we demonstrate that bacteriophage SP6 RNA polymerase can efficiently catalyze the formation of an R-loop at the mouse mtDNA origin sequence. Second, the R-loop can be assembled by annealing presynthesized RNA and supercoiled DNA template in the presence of formamide. R-loop formation by either method is dependent on specific template sequences. The reconstituted R-loop is exceptionally stable and exhibits an unexpected structure. Structural studies indicate that the RNA strand is organized within the RNA-DNA base-paired region, suggesting that the heteroduplex interaction occurs through a specific conformation. We propose that the organized structure of the R-loop is critical for primer RNA function in vivo with important implications for the RNA processing and DNA replication machinery.
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PMID:Properties of a primer RNA-DNA hybrid at the mouse mitochondrial DNA leading-strand origin of replication. 879 72

Cells must rapidly sense and respond to a wide variety of potentially cytotoxic external stressors to survive in a constantly changing environment. In a search for novel genes required for stress tolerance in Saccharomyces cerevisiae, we identified the uncharacterized open reading frame YER139C as a gene required for growth at 37 degrees C in the presence of the heat shock mimetic formamide. YER139C encodes the closest yeast homolog of the human RPAP2 protein, recently identified as a novel RNA polymerase II (RNAPII)-associated factor. Multiple lines of evidence support a role for this gene family in transcription, prompting us to rename YER139C RTR1 (regulator of transcription). The core RNAPII subunits RPB5, RPB7, and RPB9 were isolated as potent high-copy-number suppressors of the rtr1Delta temperature-sensitive growth phenotype, and deletion of the nonessential subunits RPB4 and RPB9 hypersensitized cells to RTR1 overexpression. Disruption of RTR1 resulted in mycophenolic acid sensitivity and synthetic genetic interactions with a number of genes involved in multiple phases of transcription. Consistently, rtr1Delta cells are defective in inducible transcription from the GAL1 promoter. Rtr1 constitutively shuttles between the cytoplasm and nucleus, where it physically associates with an active RNAPII transcriptional complex. Taken together, our data reveal a role for members of the RTR1/RPAP2 family as regulators of core RNAPII function.
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PMID:Rtr1 is the Saccharomyces cerevisiae homolog of a novel family of RNA polymerase II-binding proteins. 1840 53


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