Gene/Protein Disease Symptom Drug Enzyme Compound
Pivot Concepts:   Target Concepts:
Query: DrugBank:BIOD00001 (DNase I)
 8,324 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

By a combination of DNase I footprinting, methylation interference, and gel shift analyses we have identified multiple binding sites for nuclear proteins within the promoter region of the human neurofilament H gene. Two sites likely bind the transcription factor Sp1 while two others may be targets for previously unrecognized DNA binding proteins. One site, PAL, occurs within the 10 bp sequence GGGGAGGAGG. Two copies of the PAL sequence form an interrupted palindrome around one of the Sp1 sites. A second site, PROX, is found within the sequence GGTTGGACC. Nuclear extracts prepared from both neural and non-neural cell lines, mouse brain, and mouse liver contain proteins that recognize and bind to the PROX and PAL sequences indicating that proteins which bind to these target sequences are widespread. The appearance of these target sequences in the 5' upstream region of several neuron specific genes suggests that they play key roles in the transcription of neuron specific genes. The functional activity of these target DNA sequences was demonstrated by transfection assays using a reporter gene fused to nested deletions of the NF(H) promoter region. Interestingly, these assays revealed that maximal transient expression was obtained with DNA fusion genes containing the PAL, PROX and TATA sequences. Inclusion of the Sp1 sites into the fusion genes failed to enhance the expression of the reporter gene. To determine if the NF(H) promoter can be activated in a tissue specific manner during development transgenic mice containing the promoter region linked to a beta-galactosidase reporter gene were generated. In one line sporadic expression of the transgene occurred in the CNS and testis while in four other lines no expression occurred. Collectively these results suggest that the NF(H) gene promoter is active in a tissue specific manner only by interactions with regulatory elements that lie further upstream or downstream of the start site of initiation.
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PMID:Novel DNA binding proteins participate in the regulation of human neurofilament H gene expression. 127 52

Transcription of the corynebacteriophage diphtheria tox operon has been shown to be regulated through a corynebacterial determined factor DtxR. The dtxR gene has been recently cloned and expressed in Escherichia coli, and shown to regulate the expression of beta-galactosidase expression from a diphtheria tox promoter/operator-lacZ transcriptional fusion. Tao et al. (Tao, X., Boyd, J., and Murphy, J. R. (1992) Proc. Natl. Acad. Sci. U.S.A. 89, 5897-5901) have recently shown by gel mobility shift assay that the binding of DtxR to the tox operator requires a divalent heavy metal ion, as well as the 27-base pair interrupted palindromic sequence. We now show the activation of DtxR in the presence of Co2+, Fe2+, or Mn2+ results in the protection of a 33- and 27-nucleotide region on the coding and non-coding strand from DNase I digestion, respectively. DtxR is also activated in the presence of Ni2+; however, this metalloregulatory factor is only weakly activated by Zn2+. The diphtheria tox regulatory region protected from DNase I digestion in the presence of activated DtxR encompasses the 27-base pair interrupted palindromic sequence.
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PMID:Binding of the metalloregulatory protein DtxR to the diphtheria tox operator requires a divalent heavy metal ion and protects the palindromic sequence from DNase I digestion. 140 Apr 85

A 14-bp segment in the promoter region of the tdcABC operon of Escherichia coli shows sequence identity with the consensus binding site for the E. coli integration host factor (IHF). In an himA (IHF-deficient) strain, expression of beta-galactosidase from a tdcB'-'lacZ protein fusion plasmid was about 10% of that seen with an isogenic himA+ strain. Threonine dehydratase activity from the chromosomal tdcB gene in the himA mutant was also about 10% of the wild-type enzyme level. Two different mutations introduced into the putative IHF-binding site in the fusion plasmid greatly reduced the plasmid-coded beta-galactosidase activity in cells containing IHF. In vitro gel retardation and DNase I footprinting analyses showed binding of purified IHF to the wild-type but not to the mutant promoter. IHF protected a 31-bp region between -118 and -88 encompassing the conserved IHF consensus sequence. These results suggest that efficient expression of the tdc operon in vivo requires a functional IHF and an IHF-binding site in the tdc promoter.
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PMID:Integration host factor is required for positive regulation of the tdc operon of Escherichia coli. 172 11

The DNA sequence of the Salmonella typhimurium metA control region is presented. S1 nuclease mapping was used to determine the transcription initiation site. By measuring beta-galactosidase levels in Escherichia coli strains lysogenized with lambda phage carrying a metA-lacZ gene fusion, the MetR protein was shown to activate the metA gene. Homocysteine, an intermediate in methionine biosynthesis, plays a negative role in the MetR-mediated activation mechanism. Gel mobility shift assays and DNase I protection experiments showed that the MetR protein binds to a DNA fragment carrying the metA control region and protects a 26-bp region beginning 9 bp upstream of the -35 promoter sequence.
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PMID:Regulation of the Salmonella typhimurium metA gene by the metR protein and homocysteine. 172 33

The promoter, operator, and 5' and 3' ends of the mRNA of the Escherichia coli gene aroG (encoding the phenylalanine-sensitive 3-deoxy-arabinoheptulosonate-7-phosphate synthase) were located. Primer extension analysis and nuclease S1 mapping of in vivo transcripts were used to determine the 5' and 3' ends, respectively, of the mRNA. Both ends exhibited some heterogeneity with respect to length. The 3' end of the major molecular species was located within a region that has structural homology with known rho-independent terminators. The location of the aroG promoter was identified in both strands of the DNA by in vitro DNase I footprinting and methylation protection experiments with RNA polymerase. In these experiments, a region of up to 80 base pairs (bp) was protected by the binding of RNA polymerase. The location of the aroG operator was also identified in both strands of the DNA by in vitro DNase I footprinting with pure TyrR. TyrR protected 26 to 28 bp of DNA containing a 22-bp palindrome (TYR R box) and overlapping the -35 region of the promoter. Mutations in the aroG regulatory DNA were isolated by site-directed mutagenesis and cloned in a low-copy-number plasmid to generate aroG-lac fusions. The effects of the mutations on the regulation of aroG expression were determined by measuring the beta-galactosidase activities of the fusions in strains with tyrR, tyrR+, and multicopy tyrR+ genotypes. The results of this mutant analysis confirmed that the aroG operator contains a single TYR R box.
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PMID:Identification of the promoter, operator, and 5' and 3' ends of the mRNA of the Escherichia coli K-12 gene aroG. 197 May 63

Segmentation in Drosophila melanogaster is controlled by a network of interacting genes, many of which encode a homeodomain that confers sequence-specific binding to DNA. One of these, fushi tarazu (ftz), is a transcription factor that regulates a number of segmentation and homeotic genes, including Antennapedia (Antp). To determine the DNA binding specificity of the ftz homeodomain, we performed DNase I footprint analysis on ftz protein binding sites located near the two Antp promoters using a beta-galactosidase/ftz fusion protein synthesized in E. coli. A consensus sequence for the fusion protein's preferred binding site was derived from 19 sites. The consensus sequence contains an ATTA motif, as do the reported consensus sequences for the engrailed (en), even-skipped (eve), and bicoid (bcd) Drosophila homeodomain proteins. We propose DNA bending as an explanation for the presence of a shared motif between proteins with divergent recognition helices: according to this model, bases in ATTA would not directly contact amino acid side chains of the recognition helix but rather would be necessary for bending of the DNA around the homeodomain, perhaps facilitating important protein-DNA contacts.
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PMID:The DNA binding specificity of the Drosophila fushi tarazu protein: a possible role for DNA bending in homeodomain recognition. 198 71

A plasmid carrying a CRP-dependent promoter fused to the lac structural genes was manipulated to construct a set of spacing mutants that have varying lengths between the CRP binding site and the -35 region. The lengths of the spacer were changed over 45 bp by inserting or deleting nucleotides. DNase I footprinting analysis revealed that the spacer length did not affect the binding of cAMP-CRP to the CRP site. The effect of the spacer length on transcription activation by cAMP-CRP was tested in vivo by beta-galactosidase and quantitative S1 assays with crp+ and delta crp cells harboring plasmids. Insertions or deletions of non-integral helical turns, which displace the CRP site onto the opposite face of DNA helix compared to the original promoter, eliminated completely the activation of transcription. In contrast, changing the spacer length by integral helical turns allowed the promoter to respond to CRP, although the degree of activation varied with the length of the spacer. We conclude that stereospecific positioning of CRP and RNA polymerase on the DNA helix is strictly required for CRP action. The data support a model that CRP stimulates transcription by directly contacting RNA polymerase.
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PMID:Helical phase dependent action of CRP: effect of the distance between the CRP site and the -35 region on promoter activity. 217 26

The oxyR gene is required for the induction of a regulon of hydrogen peroxide-inducible genes in Escherichia coli and Salmonella typhimurium. The E. coli oxyR gene has been cloned and sequenced, revealing an open reading frame (305 amino acids) that encodes a 34.4-kDa protein, which is produced in maxicells carrying the oxyR clone. The OxyR protein shows homology to a family of positive regulatory proteins including LysR in E. coli and NodD in Rhizobium. Like them, oxyR appears to be negatively autoregulated: an oxyR::lacZ gene fusion produced 5-fold higher levels of beta-galactosidase activity in oxyR null mutants compared to oxyR+ controls, and extracts from an OxyR-overproducing strain were able to protect regions (-27 to +21) of the oxyR promoter from DNase I digestion. DNA sequence analysis of the oxyR2 mutation, which causes overexpression of oxyR-regulated proteins in the absence of oxidative stress, showed that the oxyR2 phenotype is due to a missense mutation (C.G to T.A transition) that changes alanine to valine at amino acid position 234 of OxyR.
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PMID:OxyR, a positive regulator of hydrogen peroxide-inducible genes in Escherichia coli and Salmonella typhimurium, is homologous to a family of bacterial regulatory proteins. 247 Nov 87

Bacterially-expressed fusion proteins containing the DNA-(region C) or hormone-binding (region E) domains of the chicken progesterone receptor (cPR) fused to the C terminus of Escherichia coli beta-galactosidase were analysed for the specificity of interaction with natural and synthetic hormone-responsive elements (HREs) and progestins, respectively. The purified fusion protein containing the progestin-binding domain bound progesterone with an apparent Kd of 1.0-1.5 nM and was specifically photocross-linked with the synthetic progestin R5020 in crude bacterial lysates. Labelling of intact bacterial cells with [3H]R5020 revealed that the majority, if not all, of the bacterially produced hormone-binding domain was active. No differences in the binding to a synthetic palindromic glucocorticoid/progestin-responsive element (GRE/PRE) were found when the bacterially produced cPR DNA-binding domain was compared in methylation interference assays with the full-length chicken progesterone receptor form A expressed in eukaryotic cells. The study of dissociation kinetics, however, revealed differences in the half-life of the complexes formed between the palindromic GRE/PRE and either the receptor form A or the fusion protein containing the cPR DNA-binding domain. DNase I protection experiments demonstrated that the bacterially produced region C of the cPR generated specific 'footprints' on the mouse mammary tumour virus long terminal repeat (MMTV-LTR) which were nearly identical to those previously reported for the rat glucocorticoid receptor.
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PMID:Expression of active hormone and DNA-binding domains of the chicken progesterone receptor in E. coli. 254 Sep 61

The oxyR-encoded regulatory protein, OxyR, acts to induce the synthesis of a family of hydrogen peroxide-inducible proteins in Salmonella typhimurium and Escherichia coli. To further define the mechanism by which oxyR regulates the production of these proteins, we identified, mapped, and characterized oxyR-regulated promoters upstream from the S. typhimurium ahp genes (encoding an alkyl hydroperoxide reductase) and the E. coli katG gene (encoding catalase). A set of ahpC promoter deletions was constructed in vitro and analysis of these deletions revealed the location of sequences that are involved in oxyR-mediated induction of the ahpC gene product. DNase I protection studies of the ahpC promoter region revealed an oxyR-dependent footprint that overlapped the sequences found to be important for oxyR control. E. coli strains containing transcriptional fusions between the katG promoter and the lacZ gene showed strongly increased synthesis of beta-galactosidase in response to hydrogen peroxide treatment. This stimulation was found to be oxyR-dependent. DNase I protection studies of the katG promoter region revealed an oxyR-dependent footprint in the same location relative to the basal promoter elements as was observed with the ahpC promoter. Although both the ahpC and katG promoters were shown to bind the same factor, no strong sequence similarities were found between the two, or between the two and a third oxyR-dependent binding site upstream from the E. coli oxyR gene itself.
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PMID:Identification and molecular analysis of oxyR-regulated promoters important for the bacterial adaptation to oxidative stress. 269 40


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