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)

Three Caulobacter crescentus heat-shock proteins were shown to be immunologically related to the Escherichia coli heat-shock proteins GroEL, Lon and DnaK. A fourth heat-shock protein was detected with antibody to the C. crescentus RNA polymerase. This 37,000 Mr heat-shock protein might be related to the E. coli 32,000 Mr heat-shock sigma subunit. The synthesis of the major C. crescentus RNA polymerase sigma factor was not induced by heat shock. The E. coli GroEL protein and the related protein from C. crescentus were also induced by treatment with hydrogen peroxide. Like some of the proteins in the heat-shock protein families of Drosophila and yeast, the four heat-shock proteins in C. crescentus were found to be regulated developmentally under normal conditions. All four proteins were synthesized in the predivisional cell, but the progeny showed cell type-specific bias in the level of enhanced synthesis after heat shock. The 92,000 Mr Lon homolog and the 37,000 Mr RNA polymerase subunit were preferentially synthesized in the stalked cell, whereas the synthesis of the 62,000 Mr GroEL homolog was enhanced in the progeny swarmer cell. Furthermore, the four heat-shock proteins synthesized in the predivisional cell were partitioned in a specific manner upon cell division. The stalked cell, which initiates chromosome replication immediately upon division, received the Lon homolog, the DnaK homolog and the 37,000 Mr RNA polymerase subunit. The GroEL homolog, however, was distributed equally to both the stalked cell and the swarmer cell. These results provide access to the functions of C. crescentus heat-shock proteins under both normal and stress conditions. They also allow an investigation of the regulatory signals that modulate the asymmetric distribution of proteins and their subsequent cell type-specific expression in the initial stages of a developmental program.
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PMID:Asymmetric segregation of heat-shock proteins upon cell division in Caulobacter crescentus. 330 28

Superoxide dismutase is an enzyme which converts superoxide O2- to hydrogen peroxide. Using a single synthetic oligonucleotide 33mer, we screened the E. coli DNA library and isolated a clone containing the E. coli manganese-superoxide dismutase gene. We determined the DNA sequence. The analysis of the DNA sequence and in vivo as well as in vitro transcription has shown the following. The DNA sequence suggests two possible promoters. However, only one of them seems active during normal aerobic growth. Purified RNA polymerase initiates in vitro transcription from the same promoter. It is not clear whether the second promoter is functional. It is possible that this promoter could be activated under different growth conditions. There is an inverted repeat sequence which could form a stem-loop structure downstream of the translation stop codon TAA of the Mn-SOD gene. The results of the analysis of in vivo and in vitro RNA have shown that this is the transcription termination signal. Thus, the Mn-SOD gene constitutes a single gene operon. There is an almost perfect 19 base palindrome at the -35 region. The position and the size of the palindrome suggest that this could be a regulatory site.
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PMID:Structure and gene expression of the E. coli Mn-superoxide dismutase gene. 352 Apr 87

A point mutation in the -35 region of the promoter of the primer for initiation of DNA replication in the plasmid pMB1 was characterized. This base change causes a promoter up phenotype. The analysis of a second mutant obtained by site-directed mutagenesis allowed the exclusion of a role in the phenotype for the potential intrastrand secondary structure as well as for the methylation state of the DNA in the promoter region. The promoter up phenotype is concluded to be due to a change in the primary structure of the -35 element with the consequent production of a better cluster of hydrogen bond donors and acceptors for the RNA polymerase.
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PMID:Characterization of a promoter up mutation in the -35 region of the promoter of the primer for ColE1 replication. 355 61

U6 RNA is an abundant, capped, small nuclear RNA (snRNA) species associated with heterogeneous nuclear ribonucleoproteins in eukaryotic cells. U4 RNA and U6 RNA are hydrogen bonded in a 1:1 ratio in discrete small nuclear ribonucleoprotein particles that are required in pre-mRNA processing. Previous reports have established that the mRNAs and U1 to U5 U-snRNAs are synthesized by RNA polymerase II. Evidence is presented here for synthesis of U6 RNA by RNA polymerase III. The synthesis of U6 RNA in vitro, using Novikoff hepatoma or HeLa whole cell extracts, was not inhibited at low (1 microgram/ml) concentrations of alpha-amanitin, and only 35% inhibition occurred at 10 micrograms/ml concentration. The in vitro synthesized U6 RNA, like other RNA polymerase III transcripts, was associated with La antigen. The U6 RNA synthesized in vitro by the whole cell extracts was capped, but no other internal post-transcriptional modifications were found. Uridylic acid residues were also added post-transcriptionally to the 3'-end of U6 RNA in vitro. U6 RNA, though capped on its 5'-end, is transcribed by RNA polymerase III; this is the first report of a capped RNA molecule synthesized by RNA polymerase III.
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PMID:The capped U6 small nuclear RNA is transcribed by RNA polymerase III. 379 36

The technique of resonance Raman spectroscopy has been used to investigate the interaction of the antibiotic rifampicin with Escherichia coli RNA polymerase. Spectra were analyzed by generating the first derivative of each recorded spectrum using the Savitsky-Golay algorithm. The only band that shifted significantly in the resonance Raman spectrum of rifampicin upon the formation of the drug-core polymerase complex was the amide III band. It underwent an 8 cm-1 shift from 1306 cm-1 in aqueous solution to 1314 cm-1. A comparable shift was observed for the rifampicin-holoenzyme complex. Thus, the interaction of the sigma subunit with the core polymerase does not significantly alter the manner in which rifampicin interacts with RNA polymerase. The nature of this shift has been analyzed further by recording the resonance Raman spectrum of rifampicin in a variety of solvents with different hydrogen-bonding solvents (benzene and carbon disulfide) the amide III band was observed at approximately 1220 cm-1; in dimethyl sulfoxide, a weak hydrogen-bond acceptor, 1274 cm-1; in water, a strong hydrogen-bonding solvent, 1306 cm-1; and finally, in triethylamine, a stronger hydrogen-bonding solvent than water, it was observed at 1314 cm-1. Thus, as the hydrogen-bonding ability of the solvent increased, the amide III band shifted to higher frequency. Based on these results, the rifampicin binding site in RNA polymerase provides a stronger hydrogen-bonding environment for the amidic proton of rifampicin than is encountered when rifampicin is free in aqueous solution.
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PMID:A resonance Raman study on the interaction of rifampicin with Escherichia coli RNA polymerase. 388 50

The crystal and molecular structure of the DNA-dependent RNA polymerase inhibiting antibiotic rifamycin S (C37H45O12N) as a dihydrate has been determined, and the conformation necessary for activity has been correlated with those of other active rifamycins. The orthorhombic unit cell, space group P212121 with dimensions of a = 13.010 (2), b = 14.236 (2), c = 20.571 (4) A, contains 4 molecules. The structure was solved by a combination of vector search and direct methods and refined anisotropically to an R factor of 0.048 for 2855 reflections. The conformation of the ansa chain differs from those of rifampicin and rifamycin B but resembles that of rifamycin SV at the joining points, C(2) and C(12), of the ansa chain to the naphthoquinone chromophore. The middle part of the ansa chain, which is essential for its activity against the enzyme, has the same conformation as other active rifamycins. The effect of the 3-substitution on the ansa chain conformation is that the carboxyl (C(15) = O) group wings around the N-C(16) direction, depending upon the electronegativity of the 3-substituent. The hydrogen bonding involves O(1), O(2), O(8), O(9), O(10), and the water molecules. A possible four-stage model for the interaction of the rifamycins with the enzyme DNA-dependent RNA polymerase has been speculated.
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PMID:Correlation of structure and activity in ansamycins: structure, conformation, and interactions of antibiotic rifamycin S. 402 Aug 31

Various 5-substituted 1-beta-D-xylofuranosyluracil 5'-triphosphates (hydrogen, methyl-, ethyl-, n-propyl, n-butyl, fluoro-, chloro-, bromo-, and iodo derivatives) and some of the 3'-deoxyribofuranosyl nucleotides (3'-deoxy UTP and 3'-deoxy TTP) were synthesized chemically and their inhibitory effects on DNA-dependent RNA polymerases I and II of the cherry salmon (Oncorhynchus masou) were studied systematically. These 3'-modified UTP analogues could not be utilized as substrates in place of UTP, but they did inhibit the incorporation of UMP into RNA in vitro. In contrast, 2'-modified UTP analogues, such as 2'-dTTP and Ara TTP, were neither substrates nor inhibitors. Kinetic analysis showed that the inhibition by these compounds was essentially competitive with substrate UTP. The K1 values of RNA polymerase I for the analogues were smaller (2-6 microM) than the Km value for UTP (8 microM), but those for xylo-EtUTP, xylo-PrUTP, and xylo-BuUTP were larger (about 20 microM) than the Km for UTP. In contrast to these alkyl groups with steric and electron-donating effects, halogen groups have electron-withdrawing effects on the uracil nucleus. Therefore, it was concluded that the inhibitory activity of these analogues on RNA polymerase I was not affected by the inductive effects of substituent groups at the 5-position of uracil nucleus but by their steric effects. On the other hand, all of the K1 values of RNA polymerase II for UTP analogues were smaller (0.4-3 microM) than the Km value for UTP (4 microM). In this case, neither steric effect nor an inductive effect of substituents on UTP analogues influenced the inhibitory activity towards RNA polymerase II.
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PMID:Differential inhibitory effects of 5-substituted 1-beta-D-xylofuranosyluracil 5'-triphosphates and related nucleotides on DNA-dependent RNA polymerases I and II from the cherry salmon (Oncorhynchus masou). 406 48

1. The effect of gamma-irradiation of solutions of DNA and deoxyribonucleohistone (DNH) on their ability to prime the synthesis of RNA by DNA-dependent RNA polymerase has been studied. 2. The priming ability of both DNA and DNH decreased continuously with increasing radiation dose, but more rapidly with DNH. 3. These decreases have been compared with decreases in molecular weight and with the breakdown of the specific hydrogen-bonded structure of DNA. 4. It is concluded that a process was occurring during gamma-irradiation of DNH that, although involving a decrease in molecular weight, did not diminish and even enhanced its priming ability. This is consistent with previous physicochemical evidence that gamma-irradiation causes dissociation of histone from DNH.
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PMID:The effects of gamma-irradiation on the priming by deoxyribonucleohistone of ribonucleic acid polymerase. 486 Jun 42

Base selection by the Qbeta-replicase and E. coli transcriptase has been studied using substrate analogs. Six analogs with normal hydrogen-bonding sites were polymerized by both enzymes. Three analogs containing ring substitutions which affect the conformation at the glycosyl bond would not substitute for their normal congeners. The remaining analog was an excellent substrate for the transcriptase but not the replicase.The results imply that the base selection procedure has stringent requirements for substrate conformation. Part of the restriction may derive from the requirement that template and substrates conform to the stereochemical constraints of a double helix. In the Qbeta-replicase reaction, synthesis in the presence of substrate analogs displayed abortive kinetics, implying that the replicase reaction can be uniquely curtailed by substrate analogs.
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PMID:Q-beta-replicase and E. coli transcriptase: requirements for substrate selection as revealed by a study of base analogs. 491 89

The ethionine-induced genic derepression mechanism is visualized as a secondary process that occurs after the S-adenosyl-L methionine pool concentrations are lowered to critical levels. Although DNA methylation has been shown to be correlated with genic activity, the times observed for inducement (3 days) of the alpha-fetoprotein gene and its reversibility (within 7 days) does not make it likely that alterations in the methylated status of DNA is involved. The specific mechanism is theorized to be as follows: the adenine moiety of S-adenosyl-L-methionine base-pairs with thymine of a specific structural area of the alpha-fetoprotein gene. The process is visualized as a frequent event during moments of structural relaxation of an otherwise hyperspiralized condition of the chromatin. This weak hydrogen bonding situation allows the methylation by protein methylases of a precursor chromatin protein that after methylation by the S-adenosyl-L-methionine which is base-paired to the specific DNA site, conformationally is set or locked into place and acts as a specific repressor for the alpha-fetoprotein gene. This subsequently disallows RNA polymerase activity of the region. During turnover of this chromatin protein the replacement of the methylated repressor is normally maintained. But if the S-adenosyl-L-methionine pool concentration is lowered to a level below that required for base-pairing by the adenine moiety, then the repressed conformational condition of the alpha-fetoprotein gene is altered allowing transcription. In this manner the correlation between low S-adenosyl-L-methionine and alpha-fetoprotein synthesis can be made.
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PMID:Theoretical mechanisms for synthesis of carcinogen-induced embryonic proteins: XII mutational and non-mutational mechanism as subsets of a more general mechanism. Part A--Ethionine. 608 64


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