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)

CD and UV spectroscopy were employed to study at different temperatures the conformational states of the DNA-dependent RNA polymerase core- and holo-enzymes, as well as of its alpha and beta subunits. Both core- and holo-enzyme were shown to have a higher percentage of regular structures than the separate subunits. CD and fluorescence methods were used to monitor the complex formation between rifamycin SV or its derivative, rifampicin, with the RNA polymerase from the E. coli wild and mutant (Rpo B255) types, the former enzyme being sensitive and the latter being resistant to these antibiotics. Complexation led to concomitant changes in the conformation of antibiotics and local structural rearrangements of the protein in vicinity of the binding site which comprises at least one tryptophan residue in a hydrophobic microenvironment.
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PMID:[Physico-chemical properties of DNA-dependent RNA-polymerase from Escherichia coli and its subunits]. 638 81

Termination of transcription at the end of the tryptophan (trp) operon of E. coli at the trp t site is very efficient in vivo, but is only 25% efficient in vitro. To try to resolve this discrepancy, we have altered numerous parameters and report here on the modifications that bring the in vitro results into closer agreement with the in vivo ones. Lowering the concentration of UTP (but not ATP, CTP or GTP) in the transcription mix can greatly improve termination at trp t. With three other terminators structurally similar to trp t, there is no detectable effect of reducing the concentration of any of the four triphosphates. This response at trp t to low UTP is therefore both nucleotide-specific and terminator-specific, suggesting that apparently minor structural differences may still have profound effects upon termination. Increased specificity and sensitivity may also be provided by the NusA protein, which causes RNA polymerase to pause at trp t and at the 1:2 stem of the trp attenuator. NusA protein also enhances termination at trp t, an effect similar to the low UTP response. Further, termination can be slightly improved by including rho factor, resulting in an overall efficiency of almost 100% at trp t.
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PMID:Effects of NusA protein on transcription termination in the tryptophan operon of Escherichia coli. 675 52

Adult rat hepatocytes in primary culture were used to study the effect of tryptophan pyrolysis products on the transcriptional process. Hepatocytes were treated with 1, 5 and 10 micrograms/ml of 3-amino-1,4-dimethyl-5H-pyrido-[4,3-b]-indole (Trp-P-1) or 3-amino-1-methyl-5H-pyrido-[4,3-b]-indole (Trp-P-2) for 2 and 4 h. The ultrastructural study revealed the appearance of nucleolar microsegregation accompanied by a reduction in peri- and interchromatin fibrils and granules in hepatocytes exposed to 10 micrograms/ml of each pyrolysate for 1 or 2 h. Biochemical investigation showed that the incorporation of [3H]uridine into nuclear RNA of treated hepatocytes was strongly decreased. Time- and concentration-related inhibition have been established; however, the inhibitory effect of Trp-P-1 was always superior to that of Trp-P-2. The determination of Mg2+-dependent RNA polymerase activity in an in vitro system functioning with isolated rat liver nuclei incubated in the presence of Trp-P-1 or Trp-P-2 showed a 40% inhibition of this activity. After a 1-h exposure of hepatocytes to 5 and 10 micrograms/ml of Trp-P-1, the recovery of RNA synthesis capacity was complete by 2 h and that of normal ultrastructural aspect was achieved within 4 h. All these results indicated that Trp-P-1 and Try-P-2 acted at the nucleolar level by a blockade of pre-rRNA synthesis and at the extranucleolar by decreasing the ultrastructural RNP responsible for hnRNA synthesis.
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PMID:Ultrastructural and biochemical alterations induced by tryptophan pyrolysis products on rat hepatocytes in primary culture. I. Action on the transcriptional process. 683 20

Rifampin-resistant mutants of Escherichia coli were isolated which had altered patterns of resistance or sensitivity to the inhibitory compounds 5-methyltryptophan and 5-methylanthranilate. The levels of tryptophan (trp) operon polypeptides in different rifampin-resistant mutants were elevated or reduced, in a manner consistent with their sensitivity to the two analogs. Complementation tests established that the mutations were in rpoB, the structural gene for the beta subunit of ribonucleic acid polymerase. Introduction of these rpoB mutations into mutant strains which terminate transcription abnormally at the trp operon attenuator established that the rpoB mutations alter trp operon expression by increasing or decreasing transcription termination at the attenuator. The rpoB mutations affected transcription termination at the attenuator only in strains which were able to form what is thought to be a ribonucleic acid termination structure. These findings suggest that alteration of the beta subunit of ribonucleic acid polymerase directly or indirectly affects ribonucleic acid polymerase's recognition of the transcription termination signal at the trp operon attenuator.
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PMID:Rifampin resistance mutations that alter the efficiency of transcription termination at the tryptophan operon attenuator. 700 79

Termination of transcription by RNA polymerase at rho-independent sites appears to depend primarily upon two structural features, a region of GC-rich dyad symmetry in the DNA preceding the stop point and a stretch of uridines at the 3' end of the transcript. The possibility that the former might be responsible for slowing elongation prompted us to perform a kinetic analysis of transcription across the leader and terminator regions of the E. coli tryptophan (trp) operon. Regions where the elongation rate is dramatically slowed or stopped are identifiable because they generate discrete transcript hands on a gel. Species derived from pause sites, unlike those resulting from termination sites, are transient and detectable only within the first two minutes of transcription, since polymerase eventually resumes elongation. At two mutant trp attenuator sites (trp a135 and trp a1419), where termination is incomplete or absent in vitro, a substantial pause is nevertheless observed. Likewise, a significant pause occurs at trp t, the termination site at the end of the operon. Our experiments also reveal a major pause site at about position 90 in the trp leader sequence, just past a region of dyad symmetry. The RNA hairpin corresponding to this site is U-rich, and pausing is strongly enhanced by incorporation of BrUTP. In contrast, this analog does not affect pausing at the attenuator or terminator sites with hairpins that are GC-rich. These results strongly support the hypothesis that pausing of the polymerase is an obligatory prelude to rho-independent termination. Moreover, the termination event evidently results from consecutive but discrete responses to separate structural features of these sites.
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PMID:Rho-independent termination: dyad symmetry in DNA causes RNA polymerase to pause during transcription in vitro. 701 94

The nucleotide sequence of trpR of Escherichia coli was determined. This gene codes for a polypeptide (Mr 12,356) that is 108 amino acid residues in length. NH2-terminal, COOH-terminal, and total amino acid analyses of purified aporepressor agree with the deduced amino acid sequence and establish the translation start and stop codons of the structural gene. The transcription start site for trpR mRNA synthesis in vitro was shown to be 56 base pairs prior to the translation start site. The nucleotide sequence on either side of the transcription start site is homologous to the trp operon operator. Purified trp aporepressor, when activated by L-tryptophan, protects restriction sites in this region, the presumed trpR operator, from cleavage by the respective restriction endonucleases. Bound RNA polymerase protects the same restriction sites. These findings and the additional observation that trp repressor inhibits transcription initiation in vitro establish that there is a functional overlap of operator and promoter sequences in the regulatory region of the trpR operon. These findings indicate that expression of trpR is autoregulatory.
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PMID:Nucleotide sequence and expression of Escherichia coli trpR, the structural gene for the trp aporepressor. 701 34

E. coli ribosomal protein L12, because of its unique features, has been studied in more detail than perhaps any of the other ribosomal proteins. Unlike the other ribosomal proteins that are generally present in stoichiometric amounts, there are four copies of L12 per ribosome, some of which are acetylated on the N-terminal serine. The acetylated species, referred to as L7, has not been shown, as yet, to possess any different biological activity than L12. A specific enzyme that acetylates L12 to form L7, using acetyl-CoA as the acetyl donor, has been purified from E. coli extracts. L12 is also unique in that it does not contain cysteine, tryptophan, histidine, or tyrosine, is very acidic (pI: 4.85) and has a high content of ordered secondary structure (approximately 50%). The protein is normally found in solution as a dimer and also forms a tight complex with ribosomal protein L10. There are three methionine residues in L12, located in the N-terminal region of the protein, one or more of which are essential for biological activity. Oxidation of the methionines to methionine sulfoxide prevents dimer formation and inactivates the protein. The four copies of L12 are located in the crest region(s) of the 50S ribosomal subunit. There is good evidence that the soluble factors, such as IF-2, EF-Tu, EF-G and RF, interact with L12 on the ribosome during the process of protein synthesis. This interaction is essential for the proper functioning of each of the factors and for GTP hydrolysis associated with the individual partial reactions of protein synthesis. The L12 gene is located on an operon that contains the genes for L10 and beta beta' subunits of RNA polymerase at about 88 min on the bacterial chromosome. DNA-directed in vitro systems have been used to study the unique regulation of the expression of these genes. Autogenous regulation, translational control, and transcription attenuation are regulatory mechanisms that function to control the synthesis of these proteins.
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PMID:Chemistry and biology of E. coli ribosomal protein L12. 701 80

Termination of transcription by Escherichia coli RNA polymerase in vitro appears to depend primarily on two structural features of the termination site--a G+C-rich region of dyad symmetry and a series of terminal uridine residues in the transcript. To determine whether these two features are sufficient to specify rho-independent termination in vitro, we have introduced new sequences within a tryptophan (trp) operon structural gene to create two sites with these characteristics. Transcription with wild-type RNA polymerase in vitro demonstrates that discrete termination occurs at one of these new sites, although at a low level. Use of the mutant RNA polymerase rpo203, which is more sensitive to certain weak terminators than is the wild-type enzyme, increases termination at both sites. We have compared the activity of our synthetic terminators with those of several termination sites in the E. coli trp operon. Under normal conditions of transcription in vitro, termination becomes more efficient with an increase in the length of the stem in the RNA hairpin or an increase in the number of consecutive uridine residues. Transcription with the rpo203 polymerase and with ribonucleotide analogs gives changes consistent with these general trends. These results support a model for termination involving separate but essential roles for the RNA hairpin and the stretch of uridines in the transcript.
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PMID:Synthetic sites for transcription termination and a functional comparison with tryptophan operon termination sites in vitro. 702 54

We have overproduced the leader peptidase from Escherichia coli in a high yield by using a T7 RNA polymerase/promoter system and purified the enzyme. This leader peptidase showed an apparent pH optimum of about 10 toward a synthetic peptide substrate, and was stable at temperatures below 40 degrees C. Kinetic studies indicated that one of the active site residues in the enzyme has a pKa value of approximately 7.5. The enzyme was rapidly inactivated by reaction with N-bromosuccinimide (NBS). When approximately two tryptophan residues were oxidized with NBS, the activity was almost completely lost and this inactivation was markedly prevented by a substrate. These NBS-reactive tryptophan residues were identified as Trp300 and Trp310 by a peptide mapping analysis. This indicates that Trp300 and/or Trp310 are critically important for the activity of the leader peptidase. On the other hand, the enzyme was scarcely inhibited by treatment with N-acetylimidazole, iodoacetic acid, 5,5'-dithiobis(2-nitrobenzoic acid), succinic anhydride, or 2,4,6-trinitrobenzenesulfonate. Diethylpyrocarbonate inhibited the enzyme; however, this inhibition did not seem to result from the modification of histidine residues. Thus, there seem to be no functionally important tyrosine, cysteine, or histidine residues or amino groups among the residues which readily react with these reagents. However, the enzyme was inactivated significantly by treatment with phenylglyoxal or 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide. Therefore, some of the arginine residues and the carboxyl groups appear to be important for the enzyme activity.
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PMID:Leader peptidase from Escherichia coli: overexpression, characterization, and inactivation by modification of tryptophan residues 300 and 310 with N-bromosuccinimide. 762 19

We have reconstituted Bacillus subtilis trp attenuation in vitro. Purification of the mtrB gene product (TRAP) to near homogeneity allowed us to demonstrate that addition of this protein plus L-tryptophan to template, RNA polymerase, and nucleoside triphosphates caused transcription termination in the trpEDCFBA leader region. TRAP acts by binding to the nascent transcript and preventing formation of an RNA antiterminator structure, thereby allowing terminator formation and transcription termination. Oligonucleotides complementary to segments of the antiterminator were used to demonstrate that formation of this RNA hairpin was responsible for transcription read-through. TRAP was found to be a 60-kDa multimeric protein composed of identical 6- to 8-kDa subunits, and its elution profile on a chromatographic column did not change in the presence of tryptophan.
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PMID:Reconstitution of Bacillus subtilis trp attenuation in vitro with TRAP, the trp RNA-binding attenuation protein. 767 34


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