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 insertion of the blood retrotransposon into the untranslated region of exon 7 of the sn-glycerol-3-phosphate dehydrogenase-encoding gene (Gpdh) in Drosophila melanogaster induces a GPDH isozyme-GPDH-4-and alters the pattern of expression of the three normal isozymes-GPDH-1 to GPDH-3. The process of transcript terminus formation inside the retrotransposon insertion reduces the level of the Gpdh transcript that contains exon 8 and increases the level of the transcript that contains exons 1-7. The induced GPDH-4 isozyme is a translation product of the three transcripts that contain fragments of the blood retrotransposon. The mechanism of mutagenesis by the blood insertion is postulated to involve the pause or termination of transcription within the blood sequence, which in turn is caused by the interference of a DNA-binding protein with the RNA polymerase. Thus, we show the formation of a new functional GPDH protein by the insertion of a transposable element and discuss the evolutionary significance of this phenomenon.
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PMID:Retrotransposon insertion induces an isozyme of sn-glycerol-3-phosphate dehydrogenase in Drosophila melanogaster. 861 45

Transcription and DNA supercoiling are known to be linked by a cause-effect relationship that operates in both directions. It is proposed here that this two-way relationship may be exploited by the E. coli genome to facilitate constitutive transcription of supercoil-sensitive genes by polymerase batteries made up of uniformly spaces RNA polymerase elongation complexes. Specifically, it is argued that (1) polymerases transcribing DNA in tandem cooperate to relax each other's transcription-driven positive supercoils; and (2) negative supercoils driven upstream by elongation complexes tend to be 'harnessed' and used to cooperatively (and periodically) initiate fresh transcription from promoters. Harnessing of transcription-driven negative supercoils is thought to be achieved through the erection of protein barriers to the rotational upstream propagation of supercoils from transcription events. The possible relevance of such cooperation amongst polymerases to the activation of transcription by DNA-binding protein factors is emphasized. Some testable predictions are made and implications are discussed.
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PMID:Cooperative relaxation of supercoils and periodic transcriptional initiation within polymerase batteries. 896 1

We report on the characterization of three new transcription units expressed during sporulation in Bacillus subtilis. Two of the units, cse15 and cse60, were mapped at about 123 degrees and 62 degrees on the genetic map, respectively. Their transcription commenced around h 2 of sporulation and showed an absolute requirement for sigmaE. Maximal expression of both cse15 and cse60 further depended on the DNA-binding protein SpoIIID. Primer extension results revealed -10 and -35 sequences upstream of the cse15 and cse60 coding sequences very similar to those utilized by sigmaE-containing RNA polymerase. Alignment of these and other regulatory regions led to a revised consensus sequence for sigmaE-dependent promoters. A third transcriptional unit, designated csk22, was localized at approximately 173 degrees on the chromosome. Transcription of csk22 was activated at h 4 of sporulation, required the late mother-cell regulator sigmaK, and was repressed by the GerE protein. Sequences in the csk22 promoter region were similar to those of other sigmaK-dependent promoters. The cse60 locus was deduced to encode an acidic product of only 60 residues. A 37.6-kDa protein apparently encoded by cse15 was weakly related to the heavy chain of myosins, as well as to other myosin-like proteins, and is predicted to contain a central, 100 residue-long coiled-coil domain. Finally, csk22 is inferred to encode a 18.2-kDa hydrophobic product with five possible membrane-spanning helices, which could function as a transporter.
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PMID:cse15, cse60, and csk22 are new members of mother-cell-specific sporulation regulons in Bacillus subtilis. 899 Feb 90

Transcription is coupled to repair in Escherichia coli and in humans. Proteins encoded by the mfd gene in E. coli and by the ERCC6/CSB gene in humans, both of which possess the so-called helicase motifs, are required for the coupling reaction. It has been shown that the Mfd protein is an ATPase but not a helicase and accomplishes coupling, in part, by disrupting the ternary complex of E. coli RNA polymerase stalled at the site of DNA damage. In this study we overproduced the human CSB protein using the baculovirus vector and purified and characterized the recombinant protein. CSB has an ATPase activity that is stimulated strongly by DNA; however, it neither acts as a helicase nor does it dissociate stalled RNA polymerase II, suggesting a coupling mechanism in humans different from that in prokaryotes. CSB is a DNA-binding protein, and it also binds to XPA, TFIIH, and the p34 subunit of TFIIE. These interactions are likely to play a role in recruiting repair proteins to ternary complexes formed at damage sites.
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PMID:Human transcription-repair coupling factor CSB/ERCC6 is a DNA-stimulated ATPase but is not a helicase and does not disrupt the ternary transcription complex of stalled RNA polymerase II. 899 76

The Bacillus subtilis spoVD gene encodes a penicillin-binding protein required for spore morphogenesis. SpoIIID is a sequence-specific DNA-binding protein that activates or represses the transcription of many different genes. We have defined the spoVD promoter region and demonstrated that it is recognized by sigmaE RNA polymerase in vitro and that SpoIIID represses spoVD transcription. Two strong SpoIIID-binding sites were mapped in the spoVD promoter region, one overlapping the -35 region and the other encompassing the -10 region and the transcriptional start site.
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PMID:Bacillus subtilis SpoIIID protein binds to two sites in the spoVD promoter and represses transcription by sigmaE RNA polymerase. 900 59

The coiled body is a phylogenetically conserved nuclear organelle whose function is not known. Probes for detection of p80-coilin, an 80 kDa protein enriched in the coiled body, have made possible studies determining the behavior of the coiled body during the cell cycle, in proliferating cells, as well as reports suggesting some relationship of the coiled body to mRNA splicing and to the nucleolus. The objective of this study is to examine the distribution of p80-coilin and nucleolar proteins in cells infected with adenovirus in vitro. HeLa cells grown as monolayers were infected with successive dilutions of type 5 human adenovirus culture and fixed in methanol/acetone at different time points. Single and double indirect immunofluorescence was performed with human autoantibodies to p80-coilin, fibrillarin, NOR-90/hUBF, RNA polymerase I, PM-Scl, and To, as well as rabbit polyclonal serum to p80-coilin (R288) and mouse monoclonal antibody to adenovirus 72-kDa DNA-binding protein. Indirect immunofluorescence (IIF) with anti-p80-coilin antibodies showed that the usual bright dot-like coiled body staining pattern was replaced in infected cells by 1-5 clusters of tiny dots at the periphery of the nucleus. This phenomenon was first detected within 12 h of infection and affected more severely cells with increased length and load of infection. Cells subjected to heat shock presented no such alteration. Double IIF showed cells with abnormal coiled body appearance expressed the viral 72-kDa DNA-binding protein. Nucleolar proteins RNA polymerase I and NOR-90/hUBF became associated with the p80-coilin-enriched clusters and were no longer detected in the nucleolus. Other nucleolar proteins, like PM-Scl and To, remained associated to the nucleolus and were not detected in the newly formed clusters. Fibrillarin had a heterogeneous behavior, being restricted to the nucleolus in some infected cells while in some others it was associated with the p80-coilin-enriched clusters. Thus our results showed that in vitro adenovirus infection induced radical redistribution of nucleolar and coiled body constituents into newly formed structures characterized by clusters of tiny dots in the periphery of the nucleus. The fact that three major proteins involved in rRNA synthesis and processing colocalized with p80-coilin in these clusters may bring additional support to the idea that the coiled body and p80-coilin may be implicated in functions related to the nucleolus.
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PMID:The behavior of the coiled body in cells infected with adenovirus in vitro. 911 27

The sigma-N (sigmaN) subunit of the bacterial RNA polymerase is a sequence specific DNA-binding protein. The RNA polymerase holoenzyme formed with sigmaN binds to promoters in an inactive form and only initiates transcription when activated by enhancer-binding positive control proteins. We now provide evidence to show that the DNA-binding activity of sigmaN involves two distinct domains: a C-terminal DNA-binding domain that directly contacts DNA and an adjacent domain that enhances DNA-binding activity. The sequences required for the enhancement of DNA binding can be separated from the sequences required for core RNA polymerase binding. These results provide strong evidence for communication between domains within a transcription factor, likely to be important for the function of sigmaN in enhancer-dependent transcription.
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PMID:Two domains within sigmaN (sigma54) cooperate for DNA binding. 914 80

Eukaryotic transcriptional activators may function by stimulating formation of RNA polymerase II preinitiation complexes at the core promoter of genes. In this case, their mode of action will intrinsically depend on how these complexes assemble on promoters in living cells, an issue that remains largely unexplored. Here we show that in yeast the basal transcription machinery is brought to the promoter in the form of at least two subcomplexes, TFIID and a complex comprising TFIIB and other essential components. Individual recruitment of either complex by artificial contact with a transcriptionally inactive, sequence-specific DNA-binding protein suffices to trigger transcriptional activation from a wild-type core promoter bearing the appropriate binding site. In contrast, activation from a promoter containing a weakened TATA element is only observed upon recruitment of TFIID. Tethering TFIIB on that promoter remains without effect, but the simultaneous recruitment of both components leads to strong synergistic activation. These findings suggest a simple mechanism whereby two activators that contact distinct subcomplexes of the basal machinery may stimulate transcription synergistically and differentially depending on the nature of the promoter.
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PMID:Synergistic and promoter-selective activation of transcription by recruitment of transcription factors TFIID and TFIIB. 922 10

Regulation of gene expression in the mother cell compartment of sporulating Bacillus subtilis involves sequential activation and inactivation of several transcription factors. Among them are two sigma factors, sigmaE and sigmaK, and a DNA-binding protein, SpoIIID. A decrease in the level of SpoIIID is thought to relieve its repressive effect on transcription by sigmaK RNA polymerase of certain spore coat genes. Previous studies showed that sigmaK negatively regulates the level of spoIIID mRNA. Here, it is shown that sigmaK does not affect the stability of spoIIID mRNA. Rather, sigmaK appears to negatively regulate the synthesis of spoIIID mRNA by accelerating the disappearance of sigmaE RNA polymerase, which transcribes spoIIID. As sigmaK begins to accumulate by 4 h into sporulation, the sigmaE level drops rapidly in wild-type cells but remains twofold to fivefold higher in sigK mutant cells during the subsequent 4 h. In a strain engineered to produce sigmaK 1 h earlier than normal, twofold less sigmaE than that in wild-type cells accumulates. SigmaK did not detectably alter the stability of sigmaE in pulse-chase experiments. However, beta-galactosidase expression from a sigE-lacZ transcriptional fusion showed a pattern similar to the level of sigmaE protein in sigK mutant cells and cells prematurely expressing sigmaK. These results suggest that the appearance of sigmaK initiates a negative feedback loop controlling not only transcription of spoIIID, but the entire sigmaE regulon, by directly or indirectly inhibiting the transcription of sigE.
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PMID:A feedback loop regulates the switch from one sigma factor to the next in the cascade controlling Bacillus subtilis mother cell gene expression. 932 64

Evidence obtained in both eukaryotes and prokaryotes indicates that arbitrary contacts between DNA-bound proteins and components of the transcriptional machinery can activate transcription. Here we demonstrate that the Escherichia coli omega protein, which copurifies with RNA polymerase, can function as a transcriptional activator when linked covalently to a DNA-binding protein. We show further that omega can function as an activation target when this covalent linkage is replaced by a pair of interacting polypeptides fused to the DNA-binding protein and to omega, respectively. Our findings imply that the omega protein is associated with RNA polymerase holoenzyme in vivo, and provide support for the hypothesis that contact between a DNA-bound protein and any component of E. coli RNA polymerase can activate transcription.
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PMID:Conversion of the omega subunit of Escherichia coli RNA polymerase into a transcriptional activator or an activation target. 949 8


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