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)

The synthesis, isolation, and characterization of a new photo-cross-linking uridine 5'-triphosphate analogue are described. This nucleotide analogue, 5-[(4-azidophenacyl)thio]uridine 5'-triphosphate (5-APAS-UTP), contains an aryl azide group approximately 10 A from the uridine ring. The azide is photoactivated by irradiation at 300 nm, resulting in covalent attachment of the nucleotide to adjacent molecules. The nucleotide can be desulfurated with Raney nickel to cause molecular cleavage between the base and the aryl azide. Desulfuration yields uridine 5'-triphosphate and p-azidoacetophenone. If the analogue is cross-linked to another molecule, desulfuration leaves the analogue's acetophenone group attached to that molecule. This effectively leaves behind a molecular tag on molecules that interact with the uridine analogue either as monomeric nucleotide or as part of an RNA molecule. This nucleotide analogue can be incorporated into internal positions in RNA by transcription in vitro with Escherichia coli RNA polymerase. It can therefore be used to examine interactions between RNA and other molecules (e.g., proteins or nucleic acids). Because the sulfur atom can be selectively removed, the covalent bonds formed between analogue-containing RNA and other molecules can be cleaved, when desired, to facilitate identification of the cross-linked molecules and RNA nucleotides in the cross-linked complex.
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PMID:Synthesis and characterization of 5-[(4-Azidophenacyl)thio]uridine 5'-triphosphate, a cleavable photo-cross-linking nucleotide analogue. 247 76

The effects of 14 metal ions (chlorides) on the transcription of calf thymus DNA and phage T4 DNA with Escherichia coli RNA polymerase were tested. These assays were conducted under improved conditions of lower pH and in the absence of 2-mercaptoethanol to permit greater stability of the metal ions in solution. Among the divalent metal ions tested, the concentration-dependent order of inhibition of overall transcription is Pb2+ greater than Zn2+ greater than Cu2+ greater than Be2+ greater than Cd2+ greater than Ni2+ greater than Ca2+ greater than Co2+ greater than Mn2+ greater than Mg2+ greater than Sr2+ and is the same with either template. At pH 7.4 and in the absence of 2-mercaptoethanol, considerably lower concentrations of several of the divalent metal ions are needed for inhibition of overall transcription than at pH 8.1 and in the presence of 2-mercaptoethanol. Ca2+, Mg2+, Sr2+, Zn2+, Li+, Na+, and K+--considered to be non-mutagenic and non-carcinogenic--decrease chain initiation (measured with T4 DNA) at concentrations that inhibit overall transcription. Pb2+, Cd2+, Co2+, Be2+, and Mn2+--all mutagenic or carcinogenic--stimulate chain initiation (although at widely different rates) at concentrations that inhibit overall transcription. Cu2+ and Ni2+--both carcinogenic--stimulate initiation only at very low concentrations, followed by a progressive decrease in initiation at concentrations that inhibit overall transcription.
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PMID:Selective effects of metal ions on RNA synthesis rates. 617 51

By use of poly(dA-dT) as template and Escherichia coli RNA polymerase, several metal ions were tested for their effect on the efficiency of transcription and on the misincorporation of CMP into the poly(rA-rU) product. In the presence of 10 mM MgCl2, Mn2+ has a stimulatory effect on the transcription, Co2+ has very little effect on the reaction, Cu2+ and Zn2+ are strongly inhibitory, and Cd2+ and Ni2+ are less inhibitory. The background misincorporation of CMP in the presence of MgCl2 is about 1 nucleotide per 2000 correct nucleotides incorporated and is independent of Mg2+ concentration. Zn2+, Ca2+, Sr2+, Li+, Na+, and K+--all nonmutagenic and noncarcinogenic--do not increase misincorporation. Mn2+ causes a concentration-dependent threefold increase in the misincorporation that can be slightly reversed at higher MgCl2 concentrations. Cd2+ causes a dramatic increase in the misincorporation with increasing CdCl2 concentration that can be substantially overcome by higher concentrations of Mg2+. Cu2+ also increases the misincorporation, Ni2+ slightly increases it, and Co2+ does not increase it at all. Several control experiments indicate that the misincorporation of CMP is dependent on the template-directed synthesis of poly(rA-rU). Nearest-neighbor analysis indicates that CMP is incorporated in place of UMP into the poly(rA-rU) product. The increase in misincorporation appears to be related both to the "hard-soft" character of the metal ions and to their carcinogenic potential.
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PMID:Effect of several metal ions on misincorporation during transcription. 702 4

A series of plasmid vectors, pRSET A, B, and C, have been developed for high-level protein expression in prokaryotes and have been characterized. Based upon the T7 RNA polymerase-driven pET system, the pRSET vectors encode recombinant proteins as fusions with a multifunctional leader peptide containing a hexahistidyl sequence for purification on Ni(2+)-affinity resins, a tyrosine residue for radioiodination, and an enterokinase proteolytic cleavage site for leader peptide removal. Monoclonal antibodies (MAbs) to two epitopes on the leader peptide, which also contains amino acids 1-12 of the T7 gene 10 major capsid protein, were developed and provide for universal immunological detection of pRSET-expressed fusion proteins. Subcloning of protein-encoding DNA is facilitated by an 11-site polylinker which is offset for all three ribosomal reading frames, and an f1(+) origin of DNA replication permits single-stranded DNA synthesis for site-directed mutagenesis protocols. Representative fusion proteins overexpressed in Escherichia coli were successfully purified under both denaturing and nondenaturing conditions by single-step Ni2+ affinity chromatography. Purification was independent of recombinant protein solubility in sonicated or freeze-thawed E. coli lysates. Isolation of MAbs for selective recognition of either of two leader peptide epitopes was demonstrated by immunoprecipitation, but this selectivity was less evident under conditions for Western blotting. In combining the utility of T7 RNA polymerase-directed expression with several recent advances in protein purification and detection, the pRSET vectors will serve as a powerful resource for a variety of studies in protein biochemistry.
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PMID:A multifunctional prokaryotic protein expression system: overproduction, affinity purification, and selective detection. 768 11

We have isolated milligram quantities of active single chain antibody from the insoluble fraction of Escherichia coli cultures. The system relies on high-level expression from a T7 RNA polymerase-directed gene construct, 8 M urea to dissolve the desired protein out of the insoluble fraction, presumably inclusion bodies, isolation and concentration of the desired protein by nickel chelate [IDA-Ni(II)] immobilized metal-ion affinity chromatography (IMAC), and removal of urea from column fractions by dialysis directly into storage buffer. Routinely, about 50% of the protein loaded onto an IMAC column is recovered as single chain Fv at a concentration of approximately 0.7 mg/mL. As little as 3 days are required to obtain 10 mg of final product when starting with an overnight inoculum.
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PMID:Rapid, high-yield recovery of a recombinant digoxin binding single chain Fv from Escherichia coli. 776 85

Transcription factor Sp1, which has a DNA binding domain composed of three zinc fingers, binds to GC box (consensus sequence, G/T-GGGCGG-G/A-G/A-C/T) and activates the transcription by RNA polymerase II. Metal substitution of nickel(II) for zinc(II) in Sp1 causes no differences in the mode of protein-DNA interaction. However, sequence preference of Ni(II)Sp1 changes from 5'-GGGGCGGGGC to 5'-GGGGCGTGGC, and is distinct from that of Zn(II)Sp1. The result indicates an important effect of metal-induced folding on sequence-specific recognition of DNA by zinc-finger proteins.
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PMID:Alteration of DNA binding specificity by nickel (II) substitution in three zinc (II) fingers of transcription factor Sp1. 835 9

RAP30 and RAP74 are subunits of RAP30/74 (TFIIF), a general initiation and elongation factor for transcription by RNA polymerase II. Complementary DNA (cDNA) clones have previously been reported encoding human RAP30 and RAP74. Here we report expression of these cDNAs using a T7 RNA polymerase system in Escherichia coli. Production of human RAP30 was very efficient using the expression vector pET11d. RAP30 accumulated within inclusion bodies and was solubilized using guanidine hydrochloride. After removal of the denaturant, RAP30 was soluble and active in accurate transcription. Approximately 44 mg of highly purified and soluble RAP30 was obtained from a 1-liter culture of cells. Production of RAP74 was more problematic, because a mixture of full length RAP74 and RAP74 fragments was produced in E. coli. Most RAP74 fragments were shortened by deletion of the COOH-terminus of the protein and probably resulted from premature translation termination. RAP74 was most successfully produced using a pET23d construct, in which the RAP74 peptide was fused to a short polyhistidine stretch at its COOH-terminus. Addition of the polyhistidine sequence allowed purification using a Ni2+ affinity resin. Full length RAP74 carrying this polyhistidine extension was purified in a single step by Ni2+ affinity chromatography in 4 M urea; the yield of RAP74 was approximately 3 mg from a 1-liter culture of cells. RAP74 derivatized with a polyhistidine stretch at its NH2-terminus, on the other hand, remained contaminated with RAP74 fragments after Ni2+ affinity chromatography.(ABSTRACT TRUNCATED AT 250 WORDS)
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PMID:Production of human RAP30 and RAP74 in bacterial cells. 839 Aug 79

Human SPARC has been cloned by the polymerase chain reaction from an endothelial cell cDNA library and expressed in Escherichia coli as a biologically active protein. Transcriptional expression of the insert cDNA was dependent on the activation of the T7 RNA polymerase promoter by isopropylgalactopyranoside. Two forms of recombinant SPARC (rSPARC) protein were recovered from BL21 (DE3) E. coli after transformation with the plasmid pSPARCwt: a soluble, monomeric form of rSPARC and an insoluble, aggregated form sequestered in inclusion bodies. The isolation of the soluble form of rSPARC was accomplished by anion-exchange, nickel-chelate affinity, and gel filtration chromatographies. The isolated protein was an intact, full-length polypeptide of 293 amino acids by the following criteria: N-terminal amino acid sequence, reaction with anti-SPARC immunoglobulins specific for N-terminal and C-terminal sequences, and interaction of the C-terminal histidine tag of rSPARC with a nickel-chelate affinity resin. Circular dichroism and intrinsic fluorescence spectroscopy indicated that the conformation of rSPARC was dependent on interaction with Ca2- ions. The recombinant protein inhibited cell spreading and bound specifically to bovine aortic endothelial cells. Levels of bacterial endotoxin (< 18 pg/microgram rSPARC) present in rSPARC preparations were below the threshold that affects the behavior of these endothelial cells. These conformational and biological properties of rSPARC are consistent with previously described characteristics of the native protein. The purification of biologically active rSPARC, as well as mutated forms of the protein, will provide sufficient quantities of protein for the determination of structure/function relationships.
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PMID:Expression of biologically active human SPARC in Escherichia coli. 855 46

The SUG1 gene of Saccharomyces cerevisiae encodes a putative ATPase. Mutations in SUG1 were isolated as suppressors of a mutation in the transcriptional activation domain of GAL4. Sug1 was recently proposed to be a subunit of the RNA polymerase II holoenzyme and to mediate the association of transcriptional activators with holoenzyme. We show here that Sug1 is not a subunit of the holoenzyme, at least in its purified form, but of the 26S proteasome, a large complex of relative molecular-mass 2,000K that catalyses the ATP-dependent degradation of ubiquitin-protein conjugates. Sug1 co-purifies with the proteasome in both conventional and nickel-chelate affinity chromatography. Our observations account for the reduced ubiquitin-dependent proteolysis in sug1 mutants and suggest that the effects of sug1 mutations on transcription are indirect results of defective proteolysis.
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PMID:Identification of the gal4 suppressor Sug1 as a subunit of the yeast 26S proteasome. 862 1

All pairwise interactions of RNA polymerase II and general transcription factors (TF) IIB, E, F, and H have been quantitated by surface plasmon resonance with the use of a Ni2+ chelate on the sensor surface where necessary to attain higher sensitivity. Only 4 of 10 possible interactions were found above the detection limit: TFIIB, -E, and -F binding to RNA polymerase II and TFIIE binding to TFIIH. These four interactions constitute a minimal set for the formation of a transcription initiation complex and may represent the primary interactions involved in assembly of the complex. Point mutations in TFIIB that alter the location of transcription start sites in vivo markedly diminished the affinity of TFIIB binding to RNA polymerase II. Protein blotting revealed an interaction between the largest subunit of TFIIE and third largest subunit of TFIIH, which may be responsible for TFIIE binding to TFIIH.
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PMID:A minimal set of RNA polymerase II transcription protein interactions. 870 41


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