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:3.1.30.1 (S1 nuclease)
3,660 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

The nucleotide sequence of a low molecular weight RNA coded by bacteriophage T4 (and previously identified as species alpha) has been determined. The molecule is of particular biological interest for its associated biosynthetic properties. This RNA is 76 nucleotides in length, contains eight modified bases, and can be arranged in a cloverleaf configuration common to tRNAs. The anticodon sequence is UGU, which corresponds to the threonine-specific codons ACA G. The nucleotide sequence was determined primarily by nearest-neighbor analysis of RNA synthesized in vitro using [alpha-32P]nucleoside triphosphates. Using the single-strand specific nuclease S1, two in vivo labeled half-molecules were generated and analysed. This information together with restrictions imposed by nearest-neighbor data, provided a unique linear sequence of nucleotides with the features of secondary structure common to tRNA molecules.
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PMID:The nucleotide sequence of threonine transfer RNA coded by bacteriophage T4. 35 31

On in vitro transcription of total genomic DNA of the tortoise (Geoclemys reevessi), a discrete-sized RNA of 6.5S was obtained that represented a highly repetitive and transcribable sequence in the tortoise genome. Three sequences of the 6.5S RNA gene were sequenced, and a consensus sequence was deduced from these three sequences and one reported previously [Endoh, H & Okada, N. (1986) Proc. Natl Acad. Sci. USA 83, 251-255]. The 5' part of the gene showed close similaries to lysine (rabbit) and threonine (mouse) tRNAs (overall similarity 68-70%), so this tortoise sequence may have evolved from one of these tRNAs. The consensus sequence retained the expected CCA triplet at the 3' end of tRNA, but not at the 3' end of tDNA, supporting the idea that the tRNA-related region of the gene was generated via an RNA intermediate. The 5' and 3' flanking sequences of the four genes were found to be completely different from each other. Fingerprint analysis and S1 nuclease mapping analysis also showed that sequence boundaries of tortoise repetitive units exactly corresponded to RNA species. These results, together with data obtained by Southern blot hybridization, indicated that the 6.5S RNA genes are dispersed in the tortoise genome. Therefore, generation of the tRNA-related region of the gene and amplification of the whole unit of the gene are both RNA-mediated events. The existence of this tortoise sequence suggests that short interspersed sequences are more common in eukaryotic genomes than had previously been thought.
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PMID:A highly repetitive and transcribable sequence in the tortoise genome is probably a retroposon. 169 79

We have examined transcriptional start sites responsible for expression of the transposase and transposition inhibitor proteins encoded by IS50R, and determined the likely translational start site of transposase. Amino-terminal analysis of a transposase-beta-galactosidase fusion protein gave the sequence Met-Ile-Thr-Ser-Ala, which corresponds to the predicted amino acid sequence starting at position 93 of IS50. S1 nuclease mapping of IS50 RNA produced in vivo indicated that three transcripts, T1, T2 and T3, start near this position. Only T1 starts upstream from the transposase amino terminus. T2 corresponds to an in-vitro transcript described previously. Analysis of the transcripts and proteins produced from deletion derivatives of an IS50-lacZ construct suggested that the three transcripts initiate at independent but overlapping promoters clustered near the end of IS50. This analysis confirmed that only T1 can encode transposase, and that T2 is largely responsible for expression of the inhibitor protein. The coding capacity of T3 was not determined. Finally, transcripts that originate outside of IS50 are prevented from expressing transposase because of a secondary structure that is present in these transcripts only.
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PMID:Transcriptional and translational initiation sites of IS50. Control of transposase and inhibitor expression. 243 19

We have characterized RpII215, the gene encoding the largest subunit of RNA polymerase II in Drosophila melanogaster. DNA sequencing and nuclease S1 analyses provided the primary structure of this gene, its 7 kb RNA and 215 kDa protein products. The amino-terminal 80% of the subunit harbors regions with strong homology to the beta' subunit of Escherichia coli RNA polymerase and to the largest subunits of other eukaryotic RNA polymerases. The carboxyl-terminal 20% of the subunit is composed of multiple repeats of a seven amino acid consensus sequence, Tyr-Ser-Pro-Thr-Ser-Pro-Ser. The homology domains, as well as the unique carboxyl-terminal structure, are considered in the light of current knowledge of RNA polymerase II and the properties of its largest subunit. Additionally, germline transformation demonstrated that a 9.4 kb genomic DNA segment containing the alpha-amanitin-resistant allele, RpII215C4, includes all sequences required to produce amanitin-resistant transformants.
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PMID:Analysis of the gene encoding the largest subunit of RNA polymerase II in Drosophila. 249 96

Haploid cells of mating type A of the basidiomycetous yeast Rhodosporidium toruloides secrete a mating pheromone, rhodotorucine A, which is an undecapeptide containing S-farnesyl cysteine at its carboxy terminus. To analyze the processing and secretion pathway of rhodotorucine A, we isolated both genomic and complementary DNAs encoding the peptide moiety. We identified three distinct genes, RHA1, RHA2, and RHA3, encoding four, five, and three copies of the pheromone peptide, respectively. Complementary DNA clones were classified into two types. One type was homologous to RHA1, and the other type was homologous to RHA2. Transcription start sites were identified by primer extension and S1 nuclease protection, from which the site of the initiator methionine was verified. A primary precursor of rhodotorucine A was detected as a 7-kilodalton protein by immunoprecipitation of in vitro translation products. On the basis of these results, we propose similar three-precursor structures of rhodotorucine A, each containing the amino-terminal peptide sequence Met-Val-Ala. The precursors contain three, four, or five tandem repeats of the pheromone peptide, each separated by a spacer peptide, Thr-Val-Ser(Ala)-Lys, and each precursor has the carboxy-terminal sequence Thr-Val-Ala. This structure suggests that primary precursors of rhodotorucine A do not contain canonical signal sequences.
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PMID:Multiple genes coding for precursors of rhodotorucine A, a farnesyl peptide mating pheromone of the basidiomycetous yeast Rhodosporidium toruloides. 257 24

We have isolated and characterized the nuclear gene for the mitochondrial leucyl-tRNA synthetase (LeuRS) of Neurospora crassa and have established that a defect in this structural gene is responsible for the leu-5 phenotype. We have purified mitochondrial LeuRS protein, determined its N-terminal sequence, and used this sequence information to identify and isolate a full-length genomic DNA clone. The 3.7-kilobase-pair region representing the structural gene and flanking regions has been sequenced. The 5' ends of the mRNA were mapped by S1 nuclease protection, and the 3' ends were determined from the sequence of cDNA clones. The gene contains a single short intron, 60 base pairs long. The methionine-initiated open reading frame specifies a 52-amino-acid mitochondrial targeting sequence followed by a 942-amino-acid protein. Restriction fragment length polymorphism analyses mapped the mitochondrial LeuRS structural gene to linkage group V, exactly where the leu-5 mutation had been mapped before. We show that the leu-5 strain has a defect in the structural gene for mitochondrial LeuRS by restoring growth under restrictive conditions for this strain after transformation with a wild-type copy of the mitochondrial LeuRS gene. We have cloned the mutant allele present in the leu-5 strain and identified the defect as being due to a Thr-to-Pro change in mitochondrial LeuRS. Finally, we have used immunoblotting to show that despite the apparent lack of mitochondrial LeuRS activity in leu-5 extracts, the leu-5 strain contains levels of mitochondrial LeuRS protein to similar to those of the wild-type strain.
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PMID:Nuclear gene for mitochondrial leucyl-tRNA synthetase of Neurospora crassa: isolation, sequence, chromosomal mapping, and evidence that the leu-5 locus specifies structural information. 257 23

The 16S and 23S mitochondrial rRNAs of Aspergillus nidulans have been identified by Northern hybridisation and the ends of the molecules mapped onto the mitochondrial genome by S1 nuclease analysis. The results show that both the rRNA molecules are longer than originally reported, forcing a reassessment of the potential secondary structures that can form in the terminal regions. In particular, structures resembling the 5.8S- and 4.5S-like domains of the bacterial large rRNA can now be recognised within the A. nidulans 23S molecule. The new 5' termini of the 16S and 23S genes lie within conserved 18-bp sequences that may be promoters but are more likely to be processing signals that cleave the mature rRNAs from larger precursor molecules. The new end of the 23S gene abuts the 5' end of the threonine-tRNA gene.
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PMID:The mitochondrial ribosomal RNA molecules of Aspergillus nidulans. 265 6

The gene encoding the precursor polypeptide of the Marek's disease herpesvirus (MDHV) secretory glycoprotein gp57-65 (formerly identified as A antigen) has been sequenced. Previous results had localized the gene to a 4.6-kilobase (kb) segment of the BamHI B fragment in the unique long region of the MDHV genome. S1 nuclease protection experiments were used to more precisely locate the 5' initiation and approximate 3' termination points of the approximately 1.8-kb MDHV gp57-65 mRNA within this segment. These results indicated that the entire MDHV gp57-65 coding sequence is contained within a 2.35-kb PvuII-EcoRI fragment, with the direction of transcription from PvuII to EcoRI (5' to 3'). Nucleotide sequence analysis of this region revealed a single open reading frame of 1,515 base pairs. The MDHV gp57-65 coding sequence has an overall guanosine-plus-cytosine content of 41%. Translation of the single open reading frame would produce a polypeptide of 505 amino acids, with a calculated molecular weight of 56,805. The putative gp57-65 precursor polypeptide contains features common to many glycoproteins. These include a hydrophobic amino-terminal region (amino acids 1 to 27) that may function as a signal peptide and nine potential N-linked glycosylation sites (Asn-X-Ser/Thr). These two features, predicted from nucleotide sequence data, are consistent with the published data showing that gp57-65 has a signal peptide and N-linked glycosylation (R. J. Isfort, R. A. Stringer, H.-J. Kung, and L. F. Velicer, J. Virol. 57:464-474, 1986). The predicted sequence indicates that overall the polypeptide is relatively hydrophobic, with a possible 18-residue carboxyl-terminal membrane anchor sequence. This sequence appears to be less prominent than those commonly found in integral membrane glycoproteins. The lack of a strong hydrophobic anchor sequence may help to explain the predominantly secretory nature of MDHV gp57-65.
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PMID:Structure and complete nucleotide sequence of the Marek's disease herpesvirus gp57-65 gene. 283 20

The nucleotide sequence of a 2-kilobase DNA fragment of the tdc region of Escherichia coli K-12, previously cloned in this laboratory, revealed two open reading frames, tdcC and ORFX, downstream from the tdcB gene (formerly designated tdc) encoding biodegradative threonine dehydratase. A 24-base-pair sequence separated tdcC from the dehydratase coding region, and an untranslated region of 60 nucleotides, which contains a recognizable -10 consensus sequence, was found between tdcC and ORFX. The deduced amino acid sequence of tdcC showed it to be a large hydrophobic polypeptide of 431 amino acid residues, whereas ORFX coded for a small 135-residue polypeptide lacking glutamine and tryptophan. A computer-assisted sequence analysis revealed no similarity among the tdcB, tdcC, and ORFX polypeptides, and a search of the GenBank database failed to detect similarity with any other known proteins. The tdc genes and ORFX showed similar codon usage and, in analogy with other bacterial genes, showed codon usage typical for genes expressed at an intermediate level. Transcriptional analysis with S1 nuclease indicated two distinct transcription start sites upstream of the tdcB gene in regions previously identified as promoterlike elements P1 and P2. Interestingly, expression of tdcB and tdcC, but not ORFX, was contingent upon the presence of P1. These results taken together tend to suggest that the biodegradative threonine dehydratase is the second gene in a polycistronic transcription unit constituting a novel operon (tdcABC) in E. coli implicated in anaerobic threonine metabolism.
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PMID:Molecular characterization of the tdc operon of Escherichia coli K-12. 305 59

The histone H2A gene of the filamentous fungus Aspergillus nidulans has been cloned and sequenced. There is a single H2A gene in the genome of A. nidulans, and it contains three introns. The introns are 51 nucleotides (nt), 56 nt and 50 nt in length and split codons for amino acids (aa) 18, 48 and 116 of the predicted protein. The transcriptional start and termination points have been determined using an S1 nuclease protection assay. The predicted protein is 132 aa residues in length and surprisingly has a threonine after the initiator methionine instead of the usual serine. The sequence of the predicted histone H2A protein is compared to histone H2A proteins from Schizosaccharomyces pombe, Saccharomyces cerevisiae and calf thymus. Comparison of the amino acid sequence to these other H2A proteins shows that the divergence of amino acid sequences between H2A proteins is found in two clustered sites.
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PMID:The unique histone H2A gene of Aspergillus nidulans contains three introns. 331 84


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