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)

From Escherichia coli, a DNA-binding protein that preferentially recognizes a curved DNA sequence was isolated and shown to correspond to one that has recently been reported as a binding protein for the replication origin of the E. coli chromosome, named Rob. Here, a rob promoter-lacZ transcriptional fusion was constructed on the chromosome, and used to demonstrate that the expression of rob is notably enhanced at the onset of stationary phase in Luria-broth and also under certain growth conditions in a minimal medium, such as glucose- and phosphate-starvation medium. It was further shown that this growth condition-dependent expression of rob is notably reduced in a null mutant for the stationary phase-specific sigma subunit of RNA polymerase, sigma s, although sigma s-independent expression of rob was significant during the logarithmic growth phase. Furthermore the rob null mutant was found to exhibit, as compared with the wild-type, an altered profile of protein synthesis, particularly at the very late stationary phase.
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PMID:An Escherichia coli curved DNA-binding protein whose expression is affected by the stationary phase-specific sigma factor sigma S. 747 63

The pattern of transcription has been examined for a cluster of genes encoding polypeptides some or all of which are assembled into a cross-linked component of the Bacillus subtilis spore coat. Three promoters, designated PVWX, PX and PYZ, were indicated by reverse transcriptase mapping. On the basis of Northern hybridization, it appeared that the cotV, W and X genes were transcribed as a polycistronic mRNA from PVWX as well as a monocistronic cotX mRNA from Px. The cotY and cotZ genes are cotranscribed from the PYZ promoter with a smaller cotY mRNA resulting from premature termination or RNA processing. All four transcripts were synthesized late during sporulation and were not produced in mutants lacking sigma K, which directs RNA polymerase to transcribe genes in the mother-cell compartment of sporulating cells. The DNA-binding protein GerE, which affects transcription of many genes in the mother cell during the late stages of sporulation, was also shown to be involved. There was essentially no cotX mRNA in a gerE mutant and the amounts of cotVWX, cotYZ and cotY mRNAs were somewhat reduced. In vitro run-off transcription studies with sigma K RNA polymerase and GerE confirmed the presence of the three promoters, and directly showed that GerE was necessary for transcription from PX as well as enhanced transcription from the PVWX and PYZ promoters. The DNase I footprints of GerE for all three promoters were immediately upstream of the -35 regions. These GerE binding sites were compared to those in other GerE-responsive promoters and a larger consensus sequence for GerE binding was recognized. This complex transcriptional pattern of the cotVWXYZ cluster is probably necessary to ensure that an optimal amount of each protein is made for the assembly of the spore coat.
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PMID:Regulation of the transcription of a cluster of Bacillus subtilis spore coat genes. 751 71

In Streptomyces coelicolor A3(2), synthesis of the groES, groES-groEL1 and groEL2 transcripts is induced either by heat shock or by undefined physiological stress signals present at a certain stage of growth. Under all conditions tested, transcription of groES and groES-groEL1 originated from a unique start site upstream of groES, whereas transcription of groEL2 originated from a unique site upstream of groEL2. RNA polymerase isolated either from heat-shocked or control mycelia allowed in vitro transcription from the P1 promoter of groES/EL1 and the P2 promoter of groEL2. The fact that these two RNA polymerase preparations both initiated transcription with equal efficiency from the same sites suggested that a heat shock-specific sigma factor is not responsible for the temperature-induced transcription of groE genes. Instead, regulation of these genes from vegetative-type promoters may be effected by a DNA-binding protein observed in gel retardation assays, which recognizes a motif found in the groE and dnaK promoter regions of many prokaryotic genes.
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PMID:Transcriptional analysis of groEL genes in Streptomyces coelicolor A3(2). 753 Dec 76

The Escherichia coli DNA-binding protein, OmpR, is one of the best characterized of the bacterial positive regulators that enhance the transcriptional ability of RNA polymerase. OmpR, consisting of 239 amino acids, binds to specific sequences located upstream of the cognate ompC and ompF promoters. The C-terminal half of OmpR, consisting of about 120 amino acids, exhibits an inherent DNA-binding ability. To address the issue of DNA binding by OmpR, we selected a set of OmpR mutants, each of which has a single amino acid substitution in the C-terminal half of OmpR. In particular, we characterized a number of OmpR mutants which are defective in DNA binding and thereby result in an OmpF- OmpC phenotype. Among them, a putative positive control OmpR mutant was also obtained, which appears to be defective in phosphorylation-dependent transcriptional activation, but not in DNA binding. These results are discussed with general emphasis on DNA recognition by the E. coli family of OmpR-like regulatory proteins.
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PMID:Gene activation by the Escherichia coli positive regulator OmpR: a mutational study of the DNA-binding domain of OmpR. 756 3

Osmoregulated porin gene expression in Escherichia coli is controlled by the two-component regulatory system EnvZ and OmpR. EnvZ, the osmosensor, is an inner membrane protein and a histidine kinase. EnvZ phosphorylates OmpR, a cytoplasmic DNA-binding protein, on an aspartyl residue. Phospho-OmpR binds to the promoters of the porin genes to regulate the expression of ompF and ompC. We describe the use of limited proteolysis by trypsin and ion spray mass spectrometry to characterize phospho-OmpR and the conformational changes that occur upon phosphorylation. Our results are consistent with a two-domain structure for OmpR, an N-terminal phosphorylation domain joined to a C-terminal DNA-binding domain by a flexible linker region. In the presence of acetyl phosphate, OmpR is phosphorylated at only one site. Phosphorylation induces a conformational change that is transmitted to the C-terminal domain via the central linker. Previous genetic analysis identified a region in the C-terminal domain that is required for transcriptional activation. Our results indicate that this region is within a surface-exposed loop. We propose that this loop contacts the alpha subunit of RNA polymerase to activate transcription. Mass spectrometry also reveals an unusual dephosphorylated form of OmpR, the potential significance of which is discussed.
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PMID:Phosphorylation-dependent conformational changes in OmpR, an osmoregulatory DNA-binding protein of Escherichia coli. 756 33

Transcriptional control of the osmotically regulated proU operon of Salmonella typhimurium is mediated in part by a transcriptional silencer downstream from the promoter (D.G. Overdier and L.N. Csonka, Proc. Natl. Acad. Sci. USA 89:3140-3144, 1992). We carried out a fine-structure deletion analysis to determine the structure and the position of the silencer, which demonstrated that this regulatory element is located between nucleotide positions +73 to +274 downstream from the transcription start site. The silencer appears to be made up of a number of components which have cumulative negative regulatory effects. Deletions or insertions of short nucleotide sequences (< 40 bp) between the proU promoter and the silencer do not disrupt repression exerted by the silencer, but long insertions (> or = 0.8 kbp) result in a high level of expression from the proU promoter, similar to that imparted by deletion of the entire silencer. The general DNA-binding protein H-NS is required for the full range of repression of the proU operon in media of low osmolality. Although in the presence of the silencer hns mutations increased basal expression from the proU promoter three- to sixfold, in the absence of the silencer they did not result in a substantial increase in basal expression from the proU promoter. Furthermore, deletion of the silencer in hns+ background was up to 10-fold more effective in increasing basal expression from the proU promoter than the hns mutations. These results indicate that osmotic control of the proU operon is dependent of some factor besides H-NS. We propose that the transcriptional regulation of this operon is effected in media of low osmolality by a protein which makes the promoter inaccessible to RNA polymerase by forming a complex containing the proU promoter and silencer.
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PMID:Fine-structure deletion analysis of the transcriptional silencer of the proU operon of Salmonella typhimurium. 763 33

Eukaryotic transcriptional activators may stimulate RNA polymerase II activity by promoting assembly of preinitiation complexes on promoters through their interactions with one or more components of the basal machinery. On the basis of its central role in initiating transcription-complex formation upon binding to the TATA box, the general transcription factor TFIID, which includes the TATA-binding protein (TBP) and several TBP-associated factors, has been implicated as a target for activators. Consistent with this idea, an increasing number of activators have been reported to bind directly to TBP. To assess the functional importance of these in vitro interactions for transcriptional regulation in vivo, we made use of a novel strategy in yeast to show that a physical interaction with TBP is sufficient for a sequence-specific DNA-binding protein to increase initiation of transcription by RNA polymerase II. These results imply that binding of TFIID to promoter elements is a limiting step in transcription complex assembly in vivo.
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PMID:Stimulation of RNA polymerase II transcription initiation by recruitment of TBP in vivo. 772 29

We describe the identification and characterization of a gene, herein designated cotG, encoding an abundant coat protein from the spores of Bacillus subtilis. The cotG open reading frame is 195 codons in length and is capable of encoding a polypeptide of 24 kDa that contains nine tandem copies of the 13-amino-acid long, approximately repeated sequence H/Y-K-K-S-Y-R/C-S/T-H/Y-K-K-S-R-S. cotG is located at 300 degrees on the genetic map close to another coat protein gene, cotB. The cotG and cotB genes are in divergent orientation and are separated by 1.3 kb. Like the promoter for cotB, the cotG promoter is induced at a late stage of sporulation under the control of the RNA polymerase sigma factor sigma K and the DNA-binding protein GerE. The -10 and -35 nucleotide sequences of the cotG promoter resemble those of other promoters recognized by sigma K-containing RNA polymerase, and centered 70 bp upstream of the apparent start site is a sequence that matches the consensus binding site for GerE. Spore coat proteins from a newly constructed cotG null mutant lack not only CotG but also CotB, a finding that suggests that CotG may be a morphogenetic protein that is required for the incorporation of CotB into the coat.
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PMID:An additional GerE-controlled gene encoding an abundant spore coat protein from Bacillus subtilis. 781 26

The DNA-binding protein MetR belongs to the LysR family of transcriptional activators and is required for expression of the metE and metH promoters in Escherichia coli. However, it is not known if this activation is mediated by a direct interaction of MetR with RNA polymerase. In a search for RNA polymerase mutants defective in MetR-mediated activation of the metE gene, we isolated a mutation in the alpha subunit of RNA polymerase that decreases metE expression independently of the MetR protein. The mutation does not affect expression from the metH promoter, suggesting that the alpha subunit of RNA polymerase interacts differently at these two promoters. The mutation was mapped to codon 261 of the rpoA gene, resulting in a change from a glutamic acid residue to a lysine residue. Growth of the mutant is severely impaired in minimal medium even when supplemented with methionine and related amino acids, indicating a pleiotropic effect on gene expression. This rpoA mutation may identify either a site of contact with an as yet unidentified activator protein for metE expression or a site of involvement by the alpha subunit in sequence-specific recognition of the metE promoter.
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PMID:A mutation in the rpoA gene encoding the alpha subunit of RNA polymerase that affects metE-metR transcription in Escherichia coli. 783 82

SpoIIID is a sequence-specific, DNA-binding protein that activates or represses transcription of different genes by sigma K RNA polymerase in vitro. A Bacillus subtilis strain engineered to produce both sigma K and SpoIIID during growth showed effects of SpoIIID on expression of sigma K-dependent genes that were consistent with the effects of a small amount of SpoIIID on transcription of these genes in vitro, indicating that the strain provides a simple, in vivo method to screen for effects of SpoIIID on transcription of sigma K-dependent genes.
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PMID:Effects of Bacillus subtilis sporulation regulatory protein SpoIIID on transcription by sigma K RNA polymerase in vivo and in vitro. 789 17


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