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

In the enteric bacterium, Escherichia coli, acyl coenzyme A synthetase (fatty acid:CoA ligase (AMP-forming) EC 6.2.1.3) activates exogenous long-chain fatty acids concomitant with their transport across the inner membrane into metabolically active CoA thioesters. These compounds serve as substrates for acyl-CoA dehydrogenase in the first step in the process of beta-oxidation. The acyl-CoA synthetase structural gene, fadD, has been identified on clone 6D1 of the Kohara E. coli gene library and by a process of subcloning and complementation analyses shown to be contained on a 2.2-kilobase NcoI-ClaI fragment of genomic DNA. The polypeptide encoded within this DNA fragment was identified following T7 RNA polymerase-dependent induction and estimated to be M(r) = 62,000 using SDS-polyacrylamide gel electrophoresis. The N-terminal amino acid sequence of acyl-CoA synthetase was determined by automated sequencing to be Met-Lys-Lys-Val-Trp-Leu-Asn-Arg-Tyr-Pro. Sequence analysis of the 2.2-kilobase NcoI-ClaI fragment revealed a single open reading frame encoding these amino acids as the first 10 residues of a protein with a molecular weight of 62,028. The initiation codon for methionine was TTG. Primer extension of total in vivo mRNA from two fadD-specific oligonucleotides defined the transcriptional start at an adenine residue 60 base pairs upstream from the predicted translational start site. Two FadR operator sites of the fadD gene were identified at positions -13 to -29 (OD1) and positions -99 to -115 (OD2) by DNase I footprinting. Comparisons of the predicted amino acid sequence of the E. coli acyl-CoA synthetase to the deduced amino acid sequences of the rat and yeast acyl-CoA synthetases and the firefly luciferase demonstrated that these enzymes shared a significant degree of similarity. Based on the similar reaction mechanisms of these four enzymes, this similarity may define a region required for the same function.
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PMID:Cloning, sequencing, and expression of the fadD gene of Escherichia coli encoding acyl coenzyme A synthetase. 146 45

The hamster histone H3.2 promoter contains an AP-1-like element (referred to as site X) that contains the sequence CGAGTCA. This site differs from the Jun/AP-1 consensus sequence by one base and is also similar to the cyclic AMP response element. Similar AP-1/cyclic AMP response element-like sites have been found in the promoters of other histone H3 genes and are known to bind proteins either in vivo or in vitro. Using site directed mutagenesis, we demonstrate that a 10-base pair region which encompasses site X is a positive control element that is necessary for the S phase dependent increase in H3.2 transcription in cells synchronized by serum stimulation or aphidicolin block. DNase I footprint analysis shows that mutating site X eliminates v-Jun and hamster cellular factor(s) binding. Further in vitro analysis with gel retardation assays reveals that the flanking sequence of this site is necessary for the formation of an H3.2 specific complex that can be distinguished from complexes formed with a collagenase or SV40 AP-1 element. Antibodies specific to the different members of the Jun and Fos family of transcription factors show that, in gel retardation assays, a Jun-like factor is a component of the H3.2 specific complex. However, the H3.2 specific complex exhibits different reactivity toward the Jun and Fos specific antibodies as compared to complexes formed with a collagenase AP-1 element. We hypothesize that a unique protein complex, containing a component related to the AP-1 family of transcription factors, binds to the AP-1-like motif of the hamster H3.2 promoter and may be involved in the S phase dependent regulation of transcription.
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PMID:Identification of a 10-base pair protein binding site in the promoter of the hamster H3.2 gene required for the S phase dependent increase in transcription and its interaction with a Jun-like nuclear factor. 147 72

We have established testis-specific in vitro transcription of the mouse protamine 1 (MP1) gene using rat testis nuclear extracts. Addition of testis nuclear extracts to brain extracts enhanced transcription from the MP1 upstream sequence-carrying adenovirus major late promoter. Moreover, the MP1 upstream region from positions -92 to -41 alone exhibited transcriptional activation in a tissue-specific manner. DNase I footprinting demonstrated the presence of a DNA-binding factor around position -60 (Tet-1) in testis nuclear extracts, but not in other tissues. Gel shift analysis also revealed the presence of testis-specific Tet-1. Since mutational analysis in transcriptional and binding assays demonstrates that the Tet-1 site is responsible for transcriptional activation, we suggest that Tet-1 is a novel tissue-specific trans-acting factor. The Tet-1-recognizing sequence was delineated to the 11-mer TGACTTCATAA at position -64. Although the first 8-mer in the Tet-1 11-mer shares homology with the cyclic AMP-responsive element, Tet-1 is demonstrated to be distinct from known cAMP-responsive element-binding factors.
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PMID:Demonstration of a testis-specific trans-acting factor Tet-1 in vitro that binds to the promoter of the mouse protamine 1 gene. 153 24

To evaluate the function of the murine ornithine decarboxylase (ODC) gene promoter, expression of chimeric ODC-chloramphenicol acetyltransferase (CAT) plasmids (pODCcat) containing 1,658 nt of the ODC promoter sequence and its various 5'-deletions was analyzed. In transient expression assays with NIH/3T3 mouse cells, pODCcat constructs exhibited fairly strong promoter activity yielding CAT values up to 40% of those obtained with the viral promoter RSV. Interestingly, 5'-deletions of the pODCcat constructs increased the promoter activity over that achieved using the entire 1.6-kb 5'-flanking region, with the highest activity being observed with about 750 nt of the ODC promoter. This finding suggests that the distal part of the promoter includes DNA elements which are involved in repressing its function. The promoter region could be deleted down to the proximal 97 nt and still be stimulated by cAMP to the same extent as the 1.6-kb promoter. DNase I footprinting and methylation interference studies showed that a specific protein binds to the region from -59 to -39, which encompasses a DNA motif resembling the consensus cyclic AMP response element (CRE). However, comparative gel retardation and Southwestern blotting experiments with the putative ODC-CRE and the somatostatin promoter CRE indicated that the 70-kDa protein interacting with the CRE-like element of the ODC promoter is different from the well-characterized nuclear CRE-binding protein CREB.
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PMID:Protein-DNA interactions in the cAMP responsive promoter region of the murine ornithine decarboxylase gene. 165 Apr 55

The cis-acting element mediating glucocorticoid inducibility of the chicken glutamine synthetase gene has been identified. Transfection studies using intact embryonic chicken retinae and L6 myoblasts demonstrate that sequences located between 1,849 and 2,120 nucleotides upstream of the glutamine synthetase transcription start site are required to achieve hormonally inducible expression of the chloramphenicol acetyltransferase gene. Moreover, a 42-nucleotide fragment from this region provides a robust hormonal induction when positioned approximately 2 kilobases from the SV40 early promoter. A sequence containing 8 nucleotides in common with the 12-nucleotide consensus glucocorticoid response element is encoded within this element. DNase I footprinting experiments confirm that this consensus sequence provides the only binding sites for the glucocorticoid receptor within the DNA required for inducibility. Removal of 8 nucleotides that map outside of the footprinting region results in attenuation of the hormonal response in L6 myoblasts and abolition of the response in embryonic retinae. This deletion eliminates the sequence 5'CAGCGTCA3', a sequence that resembles the canonical cyclic AMP response element (CRE), activating transcription factor (ATF), and AP1 binding sites. These results suggest that the glucocorticoid receptor acts in collaboration with a member of the jun/fos/ATF/CREB family of transcription factors to mediate a strong glucocorticoid induction at a site 2.1 kilobases upstream of the glutamine synthetase transcription start site.
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PMID:A single upstream glucocorticoid response element juxtaposed to an AP1/ATF/CRE-like site renders the chicken glutamine synthetase gene hormonally inducible in transfected retina. 168 91

The mitochondrial uncoupling protein gene is rapidly induced in mouse brown fat following cold exposure. To identify cis-regulatory elements, approximately 50 kb of chromatin surrounding the uncoupling protein gene was examined for its hypersensitivity to DNase I. Seven DNase I-hypersensitive sites were identified in the 5'-flanking DNA, and one site was identified in the 3'-flanking DNA. Transgenic mice with an uncoupling protein minigene were generated by microinjection of fertilized eggs with a transgene containing 3 kb of 5'-flanking DNA and 0.3 kb of 3'-flanking DNA. Expression of the transgene is restricted to brown fat and is cold inducible. Four additional transgenic lines were generated with a second transgene containing a 1.8-kb deletion in the 5'-flanking DNA, and expression of this minigene is absent in all tissues analyzed. A DNase I-hypersensitive site located in the 1.8-kb deletion contains a cyclic AMP response element that binds a brown fat tumor enriched nuclear factor. On the basis of these observations, we propose that a cis-acting regulatory sequence between -3 and -1.2 kb of the 5'-flanking region, possibly at a DNase I-hypersensitive site, is required for controlling uncoupling protein expression in vivo.
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PMID:The mitochondrial uncoupling protein gene in brown fat: correlation between DNase I hypersensitivity and expression in transgenic mice. 171 3

The tsx-p2 promoter is one of at least seven Escherichia coli promoters that are activated by the cyclic AMP (cAMP)-cAMP receptor protein (CRP) complex and negatively regulated by the CytR repressor. DNase I footprinting assays were used to study the interactions of these regulatory proteins with the tsx-p2 promoter region and to characterize tsx-p2 regulatory mutants exhibiting an altered response to CytR. We show that the cAMP-CRP activator complex recognizes two sites in tsx-p2 that are separated by 33 bp: a high-affinity site (CRP-1) overlaps the -35 region, and a low-affinity site (CRP-2) is centered around position -74 bp. The CytR repressor protects a DNA segment that is located between the two CRP sites and partially overlaps the CRP-1 target. In combination, the cAMP-CRP and CytR proteins bind cooperatively to tsx-p2, and the nucleoprotein complex formed covers a region of 78 bp extending from the CRP-2 site close to the -10 region. The inducer for the CytR repressor, cytidine, does not prevent in vitro DNA binding of CytR, but releases the repressor from the nucleoprotein complex and leaves the cAMP-CRP activator bound to its two DNA targets. Thus, cytidine interferes with the cooperative DNA binding of cAMP-CRP and CytR to tsx-p2. We characterized four tsx-p2 mutants exhibiting a reduced response to CytR; three carried mutations in the CRP-2 site, and one carried a mutation in the region between CRP-1 and the -10 sequence. Formation of the cAMP-CRP-CytR DNA nucleoprotein complex in vitro was perturbed in each mutant. These data indicate that the CytR repressor relies on the presence of the cAMP-CRP activator complex to regulate tsx-p2 promoter activity and that the formation of an active repression complex requires the combined interactions of cAMP-CRP and CytR at tsx-p2.
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PMID:The cyclic AMP (cAMP)-cAMP receptor protein complex functions both as an activator and as a corepressor at the tsx-p2 promoter of Escherichia coli K-12. 171 55

Phorbolester (PMA) and forskolin (FSK) cause a dramatic reorganization of microfilaments in cultured cells. We have incubated human blood platelets with PMA and FSK and we investigated the G-/F-actin equilibrium by the DNase I inhibition assay. PMA incubation (0.8 microM, 5 min, 37 degrees C) leads to an increase of filamentous actin (14.4 +/- 4.0%) compared to control platelets. The effect is rapid, dose-dependent and specific, since the biologically inactive derivative phorbol 12,13-didecanoate has no effect. FSK incubation (4 microM, 5 min, 37 degrees C) causes a decrease of F-actin (12.8 +/- 9.0%), the effect is rapid and dose-dependent too. Since 8-bromoadenosine 3':5' cyclic monophosphate also decreases F-actin in human blood platelets, the FSK effect seems to be mediated by cyclic AMP due to affecting the adenylate cyclase.
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PMID:[Effect of a phorbol ester (PMA) and forskolin of the G-/F-actin equilibrium in human platelets]. 196 36

The ugp operon of Escherichia coli includes genes involved in the uptake of sn-glycerol-3-phosphate and glycerophosphoryl diesters and belongs to the pho regulon which is induced by phosphate limitation. This operon has two transcriptional initiation sites, as determined by S1 nuclease mapping of the in vivo transcripts. The downstream promoter has multiple copies of the pho box, the consensus sequence shared by the pho promoters; the upstream promoter has a consensus sequence for the promoters regulated by cyclic AMP and its receptor protein, CRP. PhoB protein, which is the transcriptional activator for the pho regulon, protected the regulatory region with the pho boxes in DNase I footprinting experiments and activated transcription from the downstream promoter in vitro. Studies with transcriptional fusions between ugp and a promoterless gene for chloramphenicol acetyltransferase show that the upstream promoter is induced by carbon starvation in a manner that required the cya and crp genes. PhoB protein may act as a repressor for this upstream promoter, which also overlaps the upstream third pho box. The downstream promoter was induced by phosphate starvation and requires the PhoB protein for its activation as do the other pho regulon promoters. These results suggest that the two promoters function alternately in responding to phosphate or carbon starvation, thus providing the cell with a means to adapt to these physiological stresses.
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PMID:Dual regulation of the ugp operon by phosphate and carbon starvation at two interspaced promoters. 198 50

A transcriptional enhancer has been mapped to a region 5.5 kilobases 3' of the C beta 2 gene in the human T-cell receptor (TCR) beta-chain locus. Transient transfections allowed localization of enhancer activity to a 480-base-pair HincII-XbaI restriction enzyme fragment. The TCR beta enhancer was active on both the minimal simian virus 40 promoter and a TCR beta variable gene promoter in both TCR alpha/beta + and TCR gamma/delta + T cells. It displayed significantly less activity in Epstein-Barr virus-transformed B cells and K562 chronic myelogenous leukemia cells and no activity in HeLa fibroblasts. DNA sequence analysis revealed that the enhancer contains a consensus immunoglobulin kappa E2 motif, as well as an AP-1-binding site and a cyclic AMP response element. DNase I footprint analyses using Jurkat T-cell nuclear extracts allowed the identification of five nuclear protein-binding sites, T beta 1 to T beta 5, within the enhancer element. Deletion and in vitro mutagenesis studies demonstrated that the T beta 2- and T beta 3- and T beta 4-binding sites are each required for full transcriptional enhancer activity. In contrast, deletion of the T beta 1- and T beta 5-binding sites had essentially no effect on enhancer function. Electrophoretic mobility shift assays demonstrated that TCR alpha/beta + and TCR gamma/delta + T cells expressed T beta 2-, T beta 3-, and T beta 4-binding activities. In contrast, non-T-cell lines, in which the enhancer was inactive, each lacked expression of at least one of these binding activities. TCR alpha and beta gene expression may be regulated by a common set of T-cell nuclear proteins in that the T beta 2 element binding a set of cyclic AMP response element-binding proteins that are also bound by the T alpha 1 element of the human TCR alpha enhancer and the decamer element present in a large number of human and murine TCR beta promoters. Similarly, the T beta 5 TCR beta-enhancer element and the T alpha 2 TCR alpha-enhancer element bind at least one common T-cell nuclear protein. Taken together, these results suggest that TCR beta gene expression is regulated by the interaction of multiple T cell nuclear proteins with a transcriptional enhancer element located 3' of the C beta 2 gene and that some of these proteins may be involved in the coordinate regulation of TCR alpha and beta gene expression.
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PMID:Identification and functional characterization of the human T-cell receptor beta gene transcriptional enhancer: common nuclear proteins interact with the transcriptional regulatory elements of the T-cell receptor alpha and beta genes. 214 10


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