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)

DnaA protein is a DNA-binding protein which recognizes a 9-bp consensus sequence called the DnaA box. By binding to DnaA boxes, DnaA protein regulates initiation of chromosomal replication and transcription of several genes. The dnaA gene contains two DnaA boxes, one located in the regulatory region and one within the structural gene. In this paper, we explore the role of the internal DnaA box in dnaA expression because it has been proposed that the DnaA box-DnaA protein complex can block transcribing RNA polymerase. Firstly, we analyzed the degree of derepression of the dnaA gene, measured as beta-galactosidase activity of a dnaA-lacZ fusion inserted onto the bacterial chromosome, produced by an extra copy number of the dnaA DnaA boxes carried by multicopy plasmids. Secondly, we analyzed repression produced by elevated levels of DnaA protein on single-copy dnaA-lacZ fusions containing or not containing the internal DnaA box. Our results indicate that the internal DnaA box does not play a regulatory role in dnaA expression.
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PMID:Transcription termination in the Escherichia coli dnaA gene is not mediated by the internal DnaA box. 789 19

Upstream binding factor (UBF) is an important transactivator of RNA polymerase I and is a member of a family of proteins that contain nucleic acid binding domains named high-mobility-group (HMG) boxes because of their similarity to HMG chromosomal proteins. UBF is a highly sequence-tolerant DNA-binding protein for which no binding consensus sequence has been identified. Therefore, it has been suggested that UBF may recognize preformed structural features of DNA, a hypothesis supported by UBF's ability to bind synthetic DNA cruciforms, four-way junctions, and even tRNA. We show here that full-length UBF can also bend linear DNA to mediate circularization of probes as small as 102 bp in the presence of DNA ligase. Longer probes in the presence of UBF become positively supercoiled when ligated, suggesting that UBF wraps the DNA in a right-handed direction, opposite the direction of DNA wrapping around a nucleosome. The dimerization domain and HMG box 1 are necessary and sufficient to circularize short probes and supercoil longer probes in the presence of DNA ligase. UBF's sequence tolerance coupled with its ability to bend and wrap DNA makes UBF an unusual eukaryotic transcription factor. However, UBF's ability to bend DNA might explain how upstream and downstream rRNA gene promoter domains interact. UBF-induced DNA wrapping could also be a mechanism by which UBF counteracts histone-mediated gene repression.
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PMID:The RNA polymerase I transactivator upstream binding factor requires its dimerization domain and high-mobility-group (HMG) box 1 to bend, wrap, and positively supercoil enhancer DNA. 793 71

Transcription of the core (C) gene of hepatitis B virus DNA (HBV-DNA) was studied by an in vitro transcription system using nuclear extracts of human liver cell (HepG2) and non-liver cell (HeLa) origins. RNA polymerase II-dependent run-off transcription of 3.5-kb (C) mRNA was observed in both nuclear extracts; but the efficiency was much higher in the HepG2 nuclear extract. Analysis of run-off transcripts using upstream deletion mutants of HBV-DNA demonstrated that there are two transcription start sites located at approximately nucleotide numbers (nt) 1,797 +/- 5 and 1,815 +/- 5. This analysis also suggested that the minimum core promoter sequence and a cis-acting and liver-specific element for C mRNA transcription are located in the downstream region from -80 and -110 (HincII site) of transcription start sites, respectively. DNA-binding protein assays using synthetic double-stranded oligonucleotide probes corresponding to three regions in the upstream region (nt from 1,401 to 1,760) of transcription start sites revealed that there are some liver cell-specific and non-specific DNA-binding proteins in both nuclear extracts. The amount of those proteins was generally higher in the HepG2 nuclear extract. However, no obvious correlation was observed in the present study between the presence of DNA-binding proteins and transcription activity of nuclear extracts in our system. The possible causes of this discrepancy are discussed.
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PMID:Analysis of upstream region of hepatitis B virus core gene using in vitro transcription system. 796 51

Mother-cell-specific gene expression during sporulation of Bacillus subtilis is controlled by sigma E and sigma K RNA polymerases. sigma E is required for the expression of genes during stage III (engulfment of the forespore), while sigma K is required for the expression of genes during stage IV (formation of the spore cortex) and stage V (formation of the spore coat). Previous studies indicated that SpoIIID could influence transcription by sigma K RNA polymerase in vitro. We demonstrate here that SpoIIID is a DNA-binding protein that recognizes specific sequences in the promoter regions and open reading frames of both sigma E- and sigma K-dependent genes. We also show that SpoIIID can activate or repress transcription by both forms of RNA polymerase. These results support the idea that the appearance and subsequent disappearance of SpoIIID plays a major role in controlling the mother-cell pattern fo gene expression during stages III to V of sporulation.
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PMID:Sporulation regulatory protein SpoIIID from Bacillus subtilis activates and represses transcription by both mother-cell-specific forms of RNA polymerase. 796 71

The EVI1 gene encodes a zinc-finger, DNA-binding protein originally described as the transforming gene associated with a common ecotropic viral insertion site in myeloid leukemias. Previous studies demonstrated EVI1 expression in human leukemias in cases with 3q26 translocations, but not in normal blood or bone marrow. These studies also suggested an association between EVI1 expression and chromosome 7 deletion (del). Because of this association, we examined expression of EVI1 using RNA polymerase chain reaction (PCR) in patients with myelodysplastic syndromes (MDS) and acute leukemia with and without 3q26 translocations. EVI1 RNA was expressed in 29% of 34 (95% confidence interval, 20% to 50%) patients with the MDS subtypes refractory anemia (RA), refractory anemia with excess blasts (RAEB), or refractory anemia with excess blasts in transformation (RAEB-T). The vast majority of these cases occurred in patients with RAEB and RAEB-T. EVI1 expression was not detected in patients with chronic myelomonocytic leukemia (CMML), normal bone marrow or cord blood, or a variety of other hematologic malignancies. EVI1 RNA was detected in three of 18 patients with acute myelogenous leukemia (AML) and in two of four patients with acute promyelocytic leukemia (APL). Karyotypes showed that only one AML patient had karyotype 3q26 abnormalities, indicating that EVI1 expression is associated with cases that do not have structural abnormalities involving chromosome 3q26. These studies document for the first time the abnormal expression of EVI1 RNA by patients with MDS, and suggest an important role for EVI1 in the pathogenesis or progression of some myeloid malignancies.
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PMID:Expression of EVI1 in myelodysplastic syndromes and other hematologic malignancies without 3q26 translocations. 804 40

Eukaryotic ribosomal gene transcription units are bordered at their 3' ends by short DNA sequences which specify site-specific termination by RNA polymerase I (polI). PolI terminators from yeast through to mammals appear to follow similar rules: they contain a site for a sequence-specific DNA-binding protein; they function only in one orientation; 3' ends are formed upstream of the binding site; and 5' flanking sequences influence the position and efficiency of 3' end formation. Recent progress in understanding the mechanism of RNA chain elongation by other polymerases suggests a model for polI termination in which termination is seen as one of the several outcomes possible when a polymerase encounters a pause site.
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PMID:The mechanism of transcription termination by RNA polymerase I. 805 32

Ad4BP, a zinc finger DNA-binding protein, was identified as a transcription factor regulating steroidogenic P-450 genes in a cAMP-dependent manner. Immunochemical and immunohistochemical studies with steroidogenic tissues, adrenal, ovary, and testis, were performed using the antiserum to Ad4BP. Ad4BP was expressed to the same extent in the three zones of the adrenal cortex. Immunohistochemical examination of ovarian follicle and corpus luteum showed the expression of Ad4BP. The granulosa and thecal cells, the two distinct types of the steroidogenic cells in the follicle, gave Ad4BP signals, which were stronger than in the latter cells than in the former. Immunoblot analyses of mature and regressed corpora lutea indicated a parallel expression of Ad4BP and side-chain cleavage P-450, and both proteins significantly decreased in the regressed tissues. Leydig cells surrounding seminiferous tubules gave clear immunostaining signals for Ad4BP. ELP, a mammalian counterpart of Drosophila FTZ-F1 detected in EC cells, and are isoforms transcribed from the same gene. The Ad4BP and ELP forms recognize same nucleotide sequences. Reverse transcriptase-polymerase chain reaction with specific primers for ELP revealed that steroidogenic tissues contained ELP as well as Ad4BP. The effects of the two proteins on the transcription of the CYP11B gene were compared using the expression vectors of Ad4BP and ELP. ELP did not activate transcription and showed a weak inhibitor effect on the Ad4BP-dependent transactivation of the CYP11B gene promoter when transfected simultaneously. A gel shift analysis using in vitro synthesized Ad4BP and ELP revealed that the binding activity of ELP is significantly weaker than that of Ad4BP.
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PMID:Functional difference between Ad4BP and ELP, and their distributions in steroidogenic tissues. 805 72

Yolk protein factor 1 (YPF1) is a heterodimeric DNA-binding protein from Drosophila melanogaster. In this report, we describe evidence that YPF1 is a homolog of Ku, a human autoimmune antigen that is the DNA-binding subunit of a DNA-dependent protein kinase. In vitro this kinase phosphorylates several transcription factors and, at the time of transcription initiation, the carboxyl-terminal domain of RNA polymerase II. We find that a cDNA clone for the smaller subunit (beta) of YPF1 encodes a 72-kDa protein that has extensive homology to the smaller subunit of the heterodimeric Ku protein (24% identity, 51% similarity over the entire 631 amino acid length). Further, the larger YPF1 subunit (alpha) shares immunological epitopes with the larger subunit of Ku. YPF1 and Ku also appear to bind DNA similarly. Southwestern blot experiments demonstrate that, like the Ku protein, the smaller YPF1 subunit binds DNA in the absence of the larger subunit. Further, cross-linking experiments indicate that, once again like the Ku protein, both subunits make contact with DNA when YPF1 binds as a heterodimer. YPF1 beta transcripts occur at low levels in all stages of Drosophila development except during oogenesis and early embryogenesis when they increase 25-fold. In situ hybridization localizes the beta gene to position 34C on the left arm of chromosome 2.
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PMID:Yolk protein factor 1 is a Drosophila homolog of Ku, the DNA-binding subunit of a DNA-dependent protein kinase from humans. 815 78

The transcription factor sigma-54 (sigma 54) is a sequence-specific DNA-binding protein that directs RNA polymerase to a particular class of promoter. The interaction of sigma 54 with promoter DNA has been analysed by protein-DNA crosslinking and enzymatic and chemical proteolysis. Direct physical evidence for a DNA-contacting surface within the carboxy-terminal one-third of the protein has been obtained. This region of sigma 54 is likely to be close to the surface of the protein, and contacts DNA when either sigma 54 or the sigma 54-holoenzyme bind specifically to promoter DNA. The amino-terminal region of sigma 54 appears to be highly susceptible to proteolysis, and its integrity influences the accessibility towards proteolysis of a second region of sigma 54, which includes the DNA-contacting surface. Thus the amino-terminal region of sigma 54 may have a role in influencing its DNA-binding properties, the major determinants of which appear to reside in the carboxy-terminal one-third of the protein.
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PMID:Identification of a DNA-contacting surface in the transcription factor sigma-54. 817 Mar 85

The phage Mu gene C encodes a 16.5-kDa site-specific DNA-binding protein that functions as a trans-activator of the four phage "late" operons, including mom. We have overexpressed and purified C and used it for DNase I footprinting and transcription analyses in vitro. The footprinting results are summarized as follows. (i) As shown previously (V. Balke, V. Nagaraja, T. Gindlesperger, and S. Hattman, Nucleic Acids Res. 12:2777-2784, 1992) in vivo, Escherichia coli RNA polymerase (RNAP) bound the wild-type (wt) mom promoter at a site slightly upstream from the functionally active site bound on the C-independent tin7 mutant promoter. (ii) In the presence of C, however, RNAP bound the wt promoter at the same site as tin7. (iii) C and RNAP were both bound by the mom promoter at overlapping sites, indicating that they were probably on different faces of the DNA helix. The minicircle system of Choy and Adhya (H. E. Choy and S. Adhya, Proc. Natl. Acad. Sci. USA 90:472-476, 1993) was used to compare transcription in vitro from the wt and tin7 promoters. This analysis showed the following. (i) Few full-length transcripts were observed from the wt promoter in the absence of C, but addition of increasing amounts of C greatly stimulated transcription. (ii) RNA was transcribed from the tin7 promoter in the absence of C, but addition of C had a small stimulatory effect. (iii) Transcription from linearized minicircles or restriction fragment templates was greatly reduced (although still stimulated by C) with both the wt and tin7 promoters. These results show that C alone is capable of activating rightward transcription in vitro by promoting RNAP binding at a functionally active site. Additionally, DNA topology plays an important role in transcriptional activation in vitro.
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PMID:In vitro transcriptional activation of the phage Mu mom promoter by C protein. 818 89


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