Gene/Protein Disease Symptom Drug Enzyme Compound
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Query: EC:3.1.30.1 (S1 nuclease)
 3,660 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

The effect of base changes at the fourth position from the 3'-terminus of Escherichia coli initiator tRNAMet has been studied to test the 'discriminator hypothesis' which proposed that the nucleotide in this position might have a role in the specificity of the aminoacylation reaction. E. coli initiator tRNA lacking the 3'-terminal tetranucleotide was prepared by partial digestion with S1 nuclease. To construct tRNA analogs with different bases in the fourth position this truncated tRNA was joined by RNA ligase to each of four chemically synthesized 2',3'-ethoxy-methylidene tetranucleotides pACCA(em), pCCCA(em), pGCCA(em), and pUCCA(em). In vitro aminoacylation studies showed that all four molecules accepted methionine, albeit with different Vmax values.
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PMID:E. coli initiator tRNA analogs with different nucleotides in the discriminator base position. 629 8

The nucleotide sequence of the Bacillus megaterium protein C gene, encompassing the coding region and 341 base pairs of flanking regions, has been determined. The gene codes for a 72-residue protein whose predicted amino acid sequence is identical to that previously determined for protein C with the exception of an amino-terminal methionine predicted from the gene sequence, but not found in the mature protein. The translational initiation codon is preceded by an 11-base pair sequence highly complementary to the 3' terminus of B. megaterium 16S rRNA. Protection against S1 nuclease digestion by hybridization of a protein C gene fragment to RNA containing high levels of protein C mRNA localized the transcription initiation site 108 base pairs upstream from the translation start site. Upstream from the transcription initiation site there are no obvious homologies with conserved regions of promoters for previously described B. subtilis vegetative or sporulation genes.
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PMID:Complete nucleotide sequence and start sites for transcription and translation of the Bacillus megaterium protein C gene. 632 39

We have sequenced a methionine tRNA from mosquito mitochondria, and examined its structure using nucleases S1 and T1 under non-denaturing conditions. The sequence is highly homologous to a putative initiator methionine tRNA gene from Drosophila mitochondria. Its anticodon stem contains a run of three G-C base pairs that is characteristic of conventional initiator tRNAs; however, nuclease S1 analysis suggested an anticodon loop configuration characteristic of conventional elongator tRNAs. We propose that this tRNA can assume both initiator and elongator roles.
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PMID:Sequence and structure of a methionine transfer RNA from mosquito mitochondria. 632 14

We previously characterized and cloned a unique human hepatic dihydrodiol dehydrogenase (DDH) that exhibits high affinity binding for bile acids (Stolz, A., Hammond, L., Lou, H., Takikawa, H., Ronk, M., and Shively, J. E. (1993) J. Biol. Chem. 268, 10448-10457). This hepatic dihydrodiol dehydrogenase demonstrates significant sequence homology with the cytosolic rat bile acid binder 3 alpha-hydroxysteroid dehydrogenase and other members of the monomeric oxidoreductase gene family. We now report the genomic organization and chromosomal localization of the human hepatic DDH in order to further define its physiological role and provide additional insight into the development of this gene family. The 15-kilobase human hepatic DDH gene was contained in an overlapping cosmid and lambda genomic clones and is composed of nine exons. A major transcriptional start site was determined to be 30 base pairs upstream from the ATG initiation methionine by both primer extension and S1 nuclease mapping studies. The human hepatic DDH gene was mapped by chromosomal in situ hybridization and analysis of human-mouse somatic cell hybrids to the tip of the short arm of chromosome 10 at p14. Strict conservation of the intron-exon junctions in the human hepatic DDH and two other members of the monomeric oxidoreductase gene family, aldose reductase and mouse major vas deferens protein suggests evolution from a common ancestral gene. Human hepatic DDH mRNA was identified in both human hepatoma Hep G2 and human lung carcinoma cell line NCI-H322 by RN'ase protection; thus, these cell lines will be useful in examining the regulation of the gene.
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PMID:Genomic organization and chromosomal localization of a novel human hepatic dihydrodiol dehydrogenase with high affinity bile acid binding. 813 67

The microfibril-associated glycoprotein (MAGP) was recently established as a discrete constituent of 10-nm microfibrils. We have characterized the primary structure of the mouse transcript, the structure and chromosomal localization of the murine gene, and the developmental pattern of gene expression. The transcript consists of 1,037 base pairs as determined by cDNA cloning, Northern blot analysis, S1 nuclease mapping, and primer extension mapping. Using a cDNA fragment as a probe, we isolated a single genomic clone that contained the entire mouse gene. Analysis of this clone indicated that Magp is fragmented into 9 exons, with the initiator Met codon located in exon 2. As determined by analysis of somatic cell hybrid lines and by fluorescence in situ hybridization, the mouse gene was mapped to chromosome 4 at a location corresponding to region D3-E1. Genomic sequence immediately upstream of the transcription start site was found to be GC-rich but lacked TATA or CCAAT boxes as well as other cis-acting motifs known to regulate transcription. Promoters of this type are usually found in genes that exhibit broad temporal and spatial patterns of expression. Consistent with this idea, the Magp transcript appeared to be the widespread product of mesenchymal/connective tissue cells throughout mouse development. This study presents the first comprehensive evaluation of microfibril gene expression during mammalian development.
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PMID:Structure, chromosomal localization, and expression pattern of the murine Magp gene. 826 79

Genomic clones encoding the mouse cell-surface antigen, Ly-49, were isolated, and the gene organization was analyzed. The gene spanned approximately 19 kb, and contained seven exons and six introns. The lengths of introns ranged from 1.3 to 8 kb. A 1067-bp sequence in the 5'-flanking region was determined. Primer extension analysis and S1 nuclease mapping revealed a cap site at 158 bp upstream from the ATG coding the N-terminal Met of Ly-49. The 5'-flanking sequence contained a possible promoter sequence, a potential binding site for the T cell-specific transcription factor (TCF-1 alpha/LEF-1), and three sites for the basic helix-loop-helix-binding basic proteins (bHLH). However, no CAAT box-like sequence was present. These results provide important clues for understanding the mechanism of gene expression of lymphocyte antigens.
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PMID:The gene encoding mouse lymphocyte antigen Ly-49: structural analysis and the 5'-flanking sequence. 829 25

The synthesis of estrogens from androgens is catalyzed by a microsomal cytochrome P450 termed aromatase (P450arom). The expression of this enzyme is highly regulated in both a developmental and cell-type specific fashion. We have chosen to examine the molecular basis of aromatase gene regulation by studying two models of aromatase expression: the Sebright bantam chicken and the R2C rat Leydig tumor cell line. In the first model, affected (Sebright) chickens express aromatase in many extragonadal tissues, while normal Leghorn chickens express aromatase only in the ovary and hypothalamus. Our studies have demonstrated that in normal chickens the site of transcription initiation is located approx. 147 nucleotides upstream of the initiator methionine. While Sebright animals also express aromatase mRNA initiated at an analogous initiation site in the ovary, a distinctive species of aromatase mRNA is also detected and is present in ovary and extragonadal tissues. This mRNA contains an identical coding sequence, but contains an alternatively spliced 5' noncoding exon that is derived from a distinctive promoter. The second model, the R2C Leydig tumor cell line, provides ample contrast. This cell line expresses high basal levels of aromatase (150-200 pmol/h/mg protein) that is suppressed with administration of 8 bromo cAMP or forskolin but the activity is not altered by glucocorticoids or epidermal growth factor treatment. Despite this distinctive pattern of regulation, at least three species of aromatase mRNA are detected in Northern blots, each of which is also detected in rat ovary. Primer extension and S1 nuclease assays indicate that both granulosa cells and R2C cells utilize a promoter that is located approx. 97 nucleotides upstream of the initiator methionine. These studies suggest that the "ovarian" promoter is evolutionarily conserved in both rats and chickens. These results further imply that the genetic mechanisms controlling the diversity of aromatase expression among tissues and among different species are likely to fall into two groups: those that employ distinctive promoters and alternative splicing and those that effect different patterns of regulation through a common ("ovarian") promoter.
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PMID:Diverse mechanisms of control of aromatase gene expression. 847 47

Multiple AE2 Cl-/HCO3- exchanger mRNAs have been identified in rat. To determine the genetic basis for these mRNAs and whether they encode different variants of the exchanger, we used both rapid amplification of cDNA ends and S1 nuclease protection protocols and examined the organization of the gene. mRNAs encoding three N-terminal variants of AE2 (AE2a, AE2b, and AE2c) were identified and shown to be transcribed from alternative promoters. The AE2a transcription unit consists of 23 exons, with exons 1 and 2 containing 5'-untranslated sequence and the first 17 codons. The first exon of AE2b is located in intron 2; it contains 5'-untranslated sequence and an alternative 3-amino acid N-terminal coding sequence and is spliced to exon 3. The first exon of AE2c is located in intron 5; it consists of 5'-untranslated sequence and is spliced to exon 6, which contains the translation initiation codon corresponding to Met-200 of AE2a. Northern analysis shows that AE2a is expressed in all tissues, AE2b exhibits a more restricted distribution with highest levels in stomach, and AE2c is expressed only in stomach. Thus, the use of alternative promoters leads to the production of three N-terminal variants of AE2 that exhibit tissue-specific patterns of expression.
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PMID:Three N-terminal variants of the AE2 Cl-/HCO3- exchanger are encoded by mRNAs transcribed from alternative promoters. 863 28

The dsz gene cluster of Rhodococcus erythropolis IGTS8 comprises three genes, dszA, dszB, and dszC, whose products are involved in the conversion of dibenzothiophene (DBT) to 2-hydroxybiphenyl and sulfite. This organism can use DBT as the sole sulfur source but not as a carbon source. Dsz activity is repressed by methionine, cysteine, Casamino Acids, and sulfate but not by DBT or dimethyl sulfoxide. We cloned 385 bp of the DNA immediately 5' to dszA in front of the reporter gene lacZ of Escherichia coli. We showed that this region contains a Rhodococcus promoter and at least three dsz regulatory regions. After hydrazine mutagenesis of this DNA, colonies that were able to express beta-galactosidase in the presence of Casamino Acids were isolated. Sequencing of these mutants revealed two possible regulatory regions. One is at -263 to -244, and the other is at -93 to -38, where -1 is the base preceding the A of the initiation codon ATG of dszA. An S1 nuclease protection assay showed that the start of the dsz promoter is the G at -46 and that transcription is repressed by sulfate and cysteine but not by dimethyl sulfoxide. The promoter encompasses a region of potential diad symmetry that may contain an operator. Immediately upstream of the promoter is a protein-binding domain between -146 and -121. Deletion of this region did not affect repression, but promoter activity appeared to be reduced by threefold. Thus, it could be an activator binding site or an enhancer region.
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PMID:Genetic analysis of the dsz promoter and associated regulatory regions of Rhodococcus erythropolis IGTS8. 893 95

The sequence of the S-adenosyl-L-methionine:trans-caffeoyl-CoA O-methyltransferase (CCoAOMT, EC2.1.1.104) gene, including the 5'-flanking region of 5 kb, was determined from parsley (Petroselinum crispum) plants. The enzyme appears to be encoded by one or two genes, and the ORF is arranged in five exons spaced by introns from 107 to 263 bp in length. The genomic sequence matches the ORF of the cDNA previously reported from elicited parsley cell cultures, showing only three base changes that do not affect the enzyme polypeptide sequence. S1 nuclease protection assays and primer extension analyses with genomic and cDNA templates revealed the transcription start site 67 bp upstream of the translation start codon, indicating a shorter 5'-UTR than reported previously for the transcript. Promoter regulatory consensus elements such as two 'CAAT' boxes and one 'TATA' box were identified at -196, -127 and -31, respectively, relative to the transcription start site, and an SV 40-like enhancer element is located 347 bp upstream. Most notably, three putative cis-regulatory elements were recognized by sequence alignments, which represent motifs recurring in the promoters of several genes of the stress-inducible phenylpropanoid pathway (boxes P, A and L). Transient expression assays with a set of 5'-truncated promoter-GUS fusions show that significant promoter activity is retained in a 354 bp promoter fragment. In vitro DNase 1 footprint experiments and electrophoretic mobilty shift assays (EMSA) identified in this fragment a unique sequence motif with elicitor-inducible trans-factor binding activity, which was unrelated to boxes P, A, or L. This novel cis-regulatory element, designated box E, appears to be conserved in the TATA-proximal regions of other stress-inducible phenylpropanoid genes, and in vitro binding of nuclear protein was confirmed in EMSA assays for such an element from the PAL-1 promoter (-54 to -45). Moreover, the deletion of box E reduced the activity and erased the elicitor-responsiveness of the CCoAOMT promoter in transient expression assays. The results corroborate the proposed physiological function of CCoAOMT in elicited plant cells and may shed new light on the sequential action of trans-active factors in the regulation of phenylpropanoid genes.
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PMID:Structure of the parsley caffeoyl-CoA O-methyltransferase gene, harbouring a novel elicitor responsive cis-acting element. 903 50


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