Gene/Protein Disease Symptom Drug Enzyme Compound
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Query: UMLS:C0027960 (mole)
 21,279 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

Spleen cells from an unimmunized autoimmune NZB/NZW F1 female mouse were fused to the BALB/c MPC-11 drug-resistant clone 45.6 TG 1.7. One hybrid clone (D4) produced IgG-3 immunoglobulin that bound ribosomal RNA. A high concentration of this antibody was produced in the ascitic fluid of NZB/NZW male mice. DNA, tRNA, and synthetic single- and double-stranded polynucleotides could not bind significantly to the antibody. A Scatchard analysis showed that the rRNA-binding immunoglobulin is monoclonal and has a high affinity (10(9) liter/mole) for the RNA antigen.
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PMID:A hybridoma from an autoimmune NZB/NZW mouse producing monoclonal antibody to ribosomal-RNA. 735 11

Aminoacyl-tRNA protein transferases catalyze (posttranslational) aminoacylation of specific protein N-termini, using aminoacyl-tRNA as substrate. This modification targets the protein for ATP-dependent degradation; in eukaryotes, degradation occurs in the ubiquitin-mediated pathway. The eukaryotic transferase, which catalyzes Arg transfer to N-terminal Glu or Asp residues, is potently inhibited by phenylarsenoxides. The gene encoding Arg-tRNA protein transferase from the yeast Saccharomyces cerevisiae was subcloned and overexpressed in Escherichia coli to provide large amounts of homogeneous protein for a molecular analysis of this inhibition. The bifunctional reagent para-[(bromoacetyl)amino]-phenylarsenoxide is a potent and irreversible inactivator of the yeast transferase; the arsenoxide moiety of the reagent directs binding to the enzyme, while the alkyl halide moiety alkylates a residue(s) proximal to the arsenoxide site. One mole of 14C-labeled reagent was covalently incorporated during inactivation, with the side chain of Cys-315 representing the major site of alkylation. Mutation of Cys-315 to Ala yielded a fully active enzyme which was still subject to stoichiometric, irreversible inactivation by the bifunctional arsenoxide. With the C315A-enzyme, the major fraction of the 14C-labeled bifunctional reagent was associated with the side chain(s) of one or more of a stretch of Glu residues (Glu 339-341). These results show that phenylarsenoxides inhibit Arg-tRNA protein transferase by binding to a site that is either itself essential, or regulates an essential site. Inhibition appears to occur through a steric blockade mechanism.
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PMID:Inactivation of arginyl-tRNA protein transferase by a bifunctional arsenoxide: identification of residues proximal to the arsenoxide site. 781 89

In a search for tRNA-processing nucleases in Zea mays an activity was found which cleaves the precursor to Escherichia coli tyrosine tRNA in the loop of the extra arm within the mature tRNA sequence. The activity (named RNase Zma) was partially purified by ion exchange and gel filtration chromatography; the latter step enabled estimation of the molecular weight of the enzyme at 34,000. The optimal pH and Mg2+ concentration varied in an interdependent manner; 23 mM Mg2+ and pH 7.5 gave the best combination of cleavage by RNase Zma and inhibition of cleavage by (apparently) contaminating nuclease(s). Increasing concentrations of both sodium and ammonium chloride inhibited activity, in both cases by about 80% at 0.5 M. RNase Zma was also inhibited by mature tRNA (52% inhibition at 200 micrograms/ml tRNA). The activity was destroyed completely by heating at 100 degrees C for 5 min but was increasingly active over the temperature range of 23-42 degrees C; the latter experiments yielded an activation energy for the cleavage reaction of 6.2 kcal/mole. RNase Zma was also sensitive to protease digestion even though fractions which contain it consist primarily of RNA. The in vivo role of RNase Zma is unknown, but it does produce a product similar to a tRNA fragment which may be used to prime reverse transcription of copia elements in Drosophila.
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PMID:A novel tRNA precursor cleaving endoribonuclease from Zea mays. 811 2

The method of anticodon loop replacement has been used to make derivatives of yeast tRNA(Phe)GmAAY with the substitution at the 37 position (tRNA(Phe)GAAA), and at both the anticodon (tRNA(Phe)GCAG) and the 37 position. A quantitative study of the interaction of various types of yeast deacylated tRNA: tRNA(Phe)GmAAY, tRNA(Phe)GAAA, tRNA(Phe)GCAG, and tRNA(Phe)-Y with the P site of the 70S ribosome.poly(U) complex was carried out at different Mg2+ concentrations and temperatures. The replacement of the Y base on the nonmodified adenosine decreases the interaction enthalpy from 39 to 24 kcal/mole, whereas the complete removal of the Y base reduces the interaction enthalpy to 16 kcal/mole. The replacement of the second letter of the anticodon (A) with cytosine leads to a drop in the enthalpy to 6 kcal/mole, which is typical of tRNA interaction with the P site in the absence of poly(U). In the absence of poly(U) the affinity of tRNA(Phe)-Y for the P site of the 70S ribosome is 5 times lower than the affinity of tRNA(Phe)GmAAY and tRNA(Phe)GCAG. Thus, in the ribosome the modified nucleotide not only stabilizes the codon-anticodon interaction owing to the stacking interaction with the stack of codon-anticodon bases, but also lowers the free energy of binding as a result of the interaction of the modified nucleotide itself with the hydrophobic center of the P site on the ribosome.
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PMID:[Interaction of deacylated phenylalanyl tRNA from yeasts with Escherichia coli ribosomes. The role of the modified nucleotide in codon-anticodon interaction]. 814 56

We have examined multiple cofactor usage by yeast tRNA ligase in splicing in vitro. The ligase mechanism of action requires expenditure of two molar equivalents of nucleotide cofactor per mole of tRNA product. Recent evidence (Westaway, S.K., Belford, H.G., Apostol, B.L., Abelson, J., and Greer, C.L. (1993) J. Biol. Chem. 268, 2435-2443) demonstrated that the ligase-associated kinase activity is more efficient with GTP as cofactor than with ATP. Employing a ligase fusion construct with dihydrofolate reductase (Apostol, B.L., Westaway, S.K., Abelson, J., and Greer, C.L. (1991) J. Biol. Chem. 266, 7445-7455) for purposes of enzyme purification, we performed joining assays demonstrating that ATP and GTP are the most effective combination of cofactors. ATP was essential to the joining reaction, while UTP, CTP, or ATP replaced GTP inefficiently. Specific and functionally independent binding sites were confirmed for ATP and GTP by direct binding measurement. A third site was implicated in UTP- and CTP-ligase interactions. Comparison of binding constants with Kapp values determined for nucleotide-dependent joining suggested both that nucleotide triphosphate binding may be limiting in tRNA joining and that tRNA ligation occurs most efficiently using GTP for the kinase reaction and ATP as the adenylylate synthetase cofactor.
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PMID:Multiple nucleotide cofactor use by yeast ligase in tRNA splicing. Evidence for independent ATP- and GTP-binding sites. 842 19

We initiated a survey of the Streptococcus pneumoniae genome by DNA sequence sampling. More than 9,500 random DNA sequences of approximately 500 bases average length were determined. Partial sequences sufficient to identify approximately 95% of the aminoacyl tRNA synthetase genes and ribosomal protein (rps) genes were found by comparing the database of partial sequences to known sequences from other organisms. Many genes involved in DNA replication, repair, and mutagenesis are present in S. pneumoniae. Genes for the major subunits of RNA polymerase are also present, as are genes for two alternative sigma factors, rpoD and rpoN. Many genes necessary for amino acid or cofactor biosynthesis and aerobic energy metabolism in other bacteria appear to be absent from the S. pneumoniae genome. A number of genes involved in cell wall biosynthesis and septation were identified, including six homologs to different penicillin binding proteins. Interestingly, four genes involved in the addition of D-alanine to lipoteicoic acid in other gram positive bacteria were found, even though the lipoteicoic acid in S. pneumoniae has not been shown to contain D-alanine. The S. pneumoniae genome contains a number of chaperonin genes similar to those found in other bacteria, but apparently does not contain genes involved in the type III secretion commonly observed in gram negative pathogens. The G+C content of S. pneumoniae genomic DNA is approximately 43 mole percent and the size of the genome is approximately 2.0 Mb as determined by pulsed-field gel electrophoresis. Many of the genes identified by sequence sampling have been physically mapped to the 19 different SmaI fragments derived from the S. pneumoniae genome. The database of random genome sequence tags (GSTs) provides the starting material for determining the complete genome sequence, gene disruption analysis, and comparative genomics to identify novel targets for antibiotic development.
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PMID:DNA sequence sampling of the Streptococcus pneumoniae genome to identify novel targets for antibiotic development. 953 20

DNA released from neutrophils at sites of inflammation may modulate tissue proteolysis. We used tRNA and synthetic polynucleotides as models of DNA to study the influence of polynucleotides on the inhibition of neutrophil elastase by its endogenous inhibitors alpha1-proteinase inhibitor (alpha1-PI) and mucus proteinase inhibitor (MPI). Affinity chromatography showed that polynucleotides form electrostatic complexes with elastase and MPI but not with alpha1-PI, the highest affinity being for MPI. The tight-binding partial inhibition of elastase by polynucleotides was used to calculate the Kd of the elastase-polynucleotide complexes which ranged from 4 microM to 21 nM. One mole of tRNA was able to bind 9 mol of elastase. Polydeoxycytosine and tRNA significantly impaired the reversible inhibition of elastase by MPI: they moderately increased the rate of enzyme-inhibitor association, strongly enhanced the rate of complex dissociation, and lowered the enzyme-inhibitor affinity by factors of 34 and 134, respectively. The two polynucleotides also decreased the rate of the irreversible inhibition of elastase by alpha1-PI by factors of 30 and 3, respectively. Polynucleotides also changed the mechanism of inhibition of elastase by the two inhibitors from a one-step inhibition reaction to a two-step binding mechanism. Our data may help explain why proteolysis may occur at sites of inflammation despite the presence of active proteinase inhibitors.
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PMID:Effect of polynucleotides on the inhibition of neutrophil elastase by mucus proteinase inhibitor and alpha 1-proteinase inhibitor. 981 34

Four tRNA-related SINE families were isolated from the genome of the shrew Sorex araneus (SOR element), mole Mogera robusta (TAL element), and hedgehog Mesechinus dauuricus (ERI-1 and ERI-2 elements). Each of these SINEs families is specific for a single Insectivora family: SOR, for Soricidae (shrews); TAL, for Talpidae (moles and desmans); ERI-1 and ERI-2, for Erinaceidae (hedgehogs). There is a long polypyrimidine region (TC-motif) in TAL, ERI-1, and ERI-2 elements located immediately upstream of an A-rich tail with polyadenylation signals (AATAAA) and an RNA polymerase III terminator (T(4-6)) or TCT(3-4)). Ten out of 14 analyzed mammalian tRNA-related SINE families have an A-rich tail similar to that of TAL, ERI-1, and ERI-2 elements. These elements were assigned to class T+. The other four SINEs including SOR element have no polyadenylation signal and transcription terminator in their A-rich tail and were assigned to class T-. Class T+ SINEs occur only in mammals, and most of them have a long polypyrimidine region. Possible models of retroposition of class T+ and T- SINEs are discussed.
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PMID:Short interspersed elements (SINEs) from insectivores. Two classes of mammalian SINEs distinguished by A-rich tail structure. 1166 93

We have sequenced four new mitochondrial genomes to improve the stability of the tree for placental mammals; they are two insectivores (a gymnure, Echinosorex gymnurus and Formosan shrew Soriculus fumidus); a Formosan lesser horseshoe bat (Rhinolophus monoceros); and the New Zealand fur seal (Arctocephalus forsteri). A revision to the hedgehog sequence (Erinaceus europaeus) is also reported. All five are from the Laurasiatheria grouping of eutherian mammals. On this new data set there is a strong tendency for the hedgehog and its relative, the gymnure, to join with the other Laurasiatherian insectivores (mole and shrews). To quantify the stability of trees from this data we define, based on nuclear sequences, a major four-way split in Laurasiatherians. This ([Xenarthra, Afrotheria], [Laurasiatheria, Supraprimates]) split is also found from mitochondrial genomes using either protein-coding or RNA (rRNA and tRNA) data sets. The high similarity of the mitochondrial and nuclear-derived trees allows a quantitative estimate of the stability of trees from independent data sets, as detected from a triplet Markov analysis. There are significant changes in the mutational processes within placental mammals that are ignored by current tree programs. On the basis of our quantitative results, we expect the evolutionary tree for mammals to be resolved quickly, and this will allow other problems to be solved.
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PMID:Four new mitochondrial genomes and the increased stability of evolutionary trees of mammals from improved taxon sampling. 1244 98

It is essential to test a priori scientific hypotheses with independent data, not least to partly negate factors such as gene-specific base composition biases misleading our models. Seven new gene segments and sequences plus Bayesian likelihood phylogenetic methods were used to compare and test five recent placental phylogenies. These five phylogenies are similar to each other, yet quite different from Fthose of previously proposed trees, and span Waddell et al. [Syst. Biol. 48 (1999) 1] to Murphy et al. [Science 294 (2001b) 2348]. Trees for RAG1, gamma-fibrinogen, ND6, mt-tRNA, mt-RNA, c-MYC, epsilon -globin, and GHR are significantly congruent with the four main groups of mammals common to the five phylogenies, i.e., Afrotheria, Laurasiatheria, Euarchontoglires, Xenarthra plus Boreoeutheria (Laurasiatheria plus Euarchontoglires). Where these five a priori phylogenies differ, remain areas generally hard to resolve with the new sequences. The root remains ambiguous and does not reject a basal Afrotheria (the Exafroplacentalia hypothesis), Afrotheria plus Xenarthra together with basal (Atlantogenata), or Epitheria (Xenarthra basal) convincingly. Good evidence is found that Eulipotyphla is monophyletic and is located at the base of Laurasiatheria. The shrew mole, Uropsilus, is found to cluster consistently with other moles, while Solenodon may be the sister taxa to all other eulipotyphlans. Support is found for a probable sister pairing of just hedgehogs/gymnures and shrews. Relationships within Afrotheria, except the Paenungulata clade, remain hard to resolve, although there is congruent support for Afroinsectiphillia (aardvark, elephant shrews, golden moles, and tenrecs). A first-time use is made of MCMC enacted general time-reversible (GTR) amino acid and codon-based models for general tree selection. Even with ND6, a GTR amino acid model provided resolution of fine features, such as the sister group relationship of walrus to Otatriidae, and with BRCA a more reasonable rooting. An extensive analysis of GHR sequences reveals strong congruence with prior phylogenies, including strong support for Eulipotyphla, and good resolution within Rodentia. A codon model gives a worse likelihood than a nucleotide model and sometimes switches support, e.g., with RAG1+gamma-fibrinogen from a hyrax-sirenian association to support for Tethytheria. An analysis of the concatenated data is in accordance with well-resolved features of the gene trees. Taken all together, this work suggests that we are on the right path finding strong confirmation of prior phylogenies. However, with the use of robust criteria for assessing trees (i.e., not Bayesian posteriors), it is apparent parts of the tree remain hard to resolve. Since our current models are far from fitting the sequence data, we should continue with our exploratory analyses to arrive at a refined set of hypotheses for future testing using more model independent characters (e.g., rare indels, gene rearrangement, and SINE data).
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PMID:Evaluating placental inter-ordinal phylogenies with novel sequences including RAG1, gamma-fibrinogen, ND6, and mt-tRNA, plus MCMC-driven nucleotide, amino acid, and codon models. 1287 59


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