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:2.7.7.6 (RNA polymerase)
34,946 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

Recent studies on the contamination of groundwater with human enteric viruses have focused on public water systems, whereas little is known about the occurrence of viruses in private household wells. The objective of the present study was to estimate the incidence of viruses in Wisconsin household wells located near septage land application sites or in rural subdivisions served by septic systems. Fifty wells in seven hydrogeologic districts were sampled four times over a year, once each season. Reverse transcriptase PCR (RT-PCR), followed by Southern hybridization, was used to detect enteroviruses, rotavirus, hepatitis A virus (HAV), and Norwalk-like viruses (NLVs). In addition, cell culture was used to detect culturable enteroviruses. Companion water samples were collected for total coliforms, Escherichia coli, fecal enterococci, F-specific RNA coliphages, nitrate, and chloride analyses. Among the 50 wells, four (8%) were positive for viruses by RT-PCR. Three wells were positive for HAV, and the fourth well was positive for both rotavirus and NLV in one sample and an enterovirus in another sample. Contamination was transient, since none of the wells was virus positive for two sequential samples. Culturable enteroviruses were not detected in any of the wells. Water quality indicators were not statistically associated with virus occurrence, although some concordance was noted for chloride. The present study is the first in the United States to systematically monitor private household wells for virus contamination and, combined with data for public wells, provides further insight on the extent of groundwater contamination with human enteric viruses.
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PMID:Incidence of enteric viruses in groundwater from household wells in Wisconsin. 1257 Oct 44

Metalaxyl is a systemic fungicide used to control plant diseases caused by Oomycete fungi. Its formulations include granules, wettable powders, dusts, and emulsifiable concentrates. Application may be by foliar or soil incorporation, surface spraying (broadcast or band), drenching, and seed treatment. Metalaxyl registered products either contain metalaxyl as the sole active ingredient or are combined with other active ingredients (e.g., captan, mancozeb, copper compounds, carboxin). Due to its broad-spectrum activity, metalaxyl is used world-wide on a variety of fruit and vegetable crops. Its effectiveness results from inhibition of uridine incorporation into RNA and specific inhibition of RNA polymerase-1. Metalaxyl has both curative and systemic properties. Its mammalian toxicity is classified as EPA toxicity class III and it is also relatively non-toxic to most nontarget arthropod and vertebrate species. Adequate analytical methods of TLC, GLC, HPLC, MS, and other techniques are available for identification and determination of metalaxyl residues and its metabolites. Available laboratory and field studies indicate that metalaxyl is stable to hydrolysis under normal environmental pH values, It is also photolytically stable in water and soil when exposed to natural sunlight. Its tolerance to a wide range of pH, light, and temperature leads to its continued use in agriculture. Metalaxyl is photodecomposed in UV light, and photoproducts are formed by rearrangement of the N-acyl group to the aromatic ring, demethoxylation, N-deacylation, and elimination of the methoxycarbonyl group from the molecule. Photosensitizers such as humic acid, TiO2, H2O2, acetone, and riboflavin accelerate its photodecomposition. Information is provided on the fate of metalaxyl in plant, soil, water, and animals. Major metabolic routes include hydrolysis of the methyl ester and methyl ether oxidation of the ring-methyl groups. The latter are precursors of conjugates in plants and animals. In soils the most relevant metabolite is the metalaxyl acid, which is formed predominantly by soil microorganisms. Plant uptake, microbial degradation, photodecomposition, and leaching are the major route of metalaxyl dissipation. It has a tendency to migrate to deeper soil horizons with a potential to contaminate groundwater, particularly in soils with low organic matter and clay content. Therefore, precautions should be taken for the continuous application of metalaxyl to crops. If use of metalaxyl is greately increased, the risk of occurrence in groundwater must be reassessed, as by monitoring studies in the most vulnerable areas in main use regions. The R-isomer of metalaxyl (mefenoxam) has recently been registered as the only active compound. Therefore, quantitative studies on the fate of this specific isomer are needed, including appropriate analytical methods. As the use rates of mefenoxam are approximately one-half those recommended for metalaxyl and mefenoxam dissipates more rapidly, concerns for mefenoxam reaching groundwater are even less justified.
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PMID:Metalaxyl: persistence, degradation, metabolism, and analytical methods. 1258 32

The Colletotrichum graminicola tagged mutant T30 has conidia that burst and hyphal tips that swell in media with low osmotic pressure. The disrupted gene in T30 was identified as a class V chitin synthase (CSV) "chsA," which has an open reading frame of 1783 amino acids and two introns that are 52 and 54 bp. C. graminicola has one copy of chsA and no other highly homologous class V CHSs. Reverse transcriptase PCR indicated that the T30 mutant does not express the chsA transcript fragment in the conserved region in CSVs. Complementation of the mutant with chsA indicates that the encoded protein is responsible for approximately 29% of the chitin in conidial walls, is essential for conidial wall strength in media with high water potential and contributes to strength of hyphal tips. Analysis of the aligned deduced amino acid sequences of the 10 fully sequenced CSVs suggests that they are in two subgroups.
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PMID:A class V chitin synthase gene, chsA is essential for conidial and hyphal wall strength in the fungus Colletotrichum graminicola (Glomerella graminicola). 1268 17

The transcription elongation factor TFIIS induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II. We have diffused TFIIS into Pol II crystals and derived a model of the Pol II-TFIIS complex from X-ray diffraction data to 3.8 A resolution. TFIIS extends from the polymerase surface via a pore to the internal active site, spanning a distance of 100 A. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active center. Our results support the idea that Pol II contains a single tunable active site for RNA polymerization and cleavage, in contrast to DNA polymerases with two separate active sites for DNA polymerization and cleavage.
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PMID:Architecture of the RNA polymerase II-TFIIS complex and implications for mRNA cleavage. 1291 90

Lipoatrophy (LA)/lipodystrophy and nucleoside reverse-transcriptase inhibitor (NRTI)-associated syndrome are of central importance in human immunodeficiency virus (HIV)/acquired immune deficiency syndrome (AIDS) care. Neither of these conditions has had a clear pathogenesis or biomarker defined for early detection, prevention research, or patient management. I describe the recent development of kinetic biomarkers for LA and mitochondrial toxicity that involve the measurement of biosynthetic fluxes rather than static concentrations of molecules. The turnover of adipose-tissue components (lipids and cells) and tissue mitochondrial DNA is measured by the incorporation of deuterium from heavy water, using mass spectrometry. Preliminary results in animal models and humans, including the effects of NRTIs on mitochondrial DNA synthesis in rats and adipose-tissue lipid kinetics in HIV-associated LA, are reviewed. The results suggest that the kinetics of adipose-tissue components and mitochondrial DNA are measurable in vivo and that these measurements may prove useful as clinical biomarkers in patients with HIV/AIDS.
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PMID:Turnover of adipose components and mitochondrial DNA in humans: kinetic biomarkers for human immunodeficiency virus-associated lipodystrophy and mitochondrial toxicity? 1294 75

RNA polymerase II-dependent transcription requires the assembly of a multi-protein, preinitiation complex on core promoter elements. Transcription factor IID (TFIID) comprising the TATA box-binding protein (TBP) and TBP-associated factors (TAFs) is responsible for promoter recognition in this complex. Subsequent association of TFIIA and TFIIB provides enhanced complex stability. TFIIA is required for transcriptional stimulation by certain viral and cellular activators, and favors formation of the preinitiation complex in the presence of repressor NC2. The X-ray structures of human and yeast TBP/TFIIA/DNA complexes at 2.1A and 1.9A resolution, respectively, are presented here and seen to resemble each other closely. The interactions made by human TFIIA with TBP and DNA within and upstream of the TATA box, including those involving water molecules, are described and compared to the yeast structure. Of particular interest is a previously unobserved region of TFIIA that extends the binding interface with TBP in the yeast, but not in the human complex, and that further elucidates biochemical and genetic results.
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PMID:Novel interactions between the components of human and yeast TFIIA/TBP/DNA complexes. 1297 51

The choroid plexus epithelium of the brain ventricular system produces the majority of the cerebrospinal fluid and thereby defines the ionic composition of the interstitial fluid in the brain. The transepithelial movement of Na+ and water in the choroid plexus depend on a yet-unidentified basolateral stilbene-sensitive Na+-HCO3- uptake protein. Reverse transcriptase-polymerase chain reaction (RT-PCR) analysis revealed the expression in the choroid plexus of SLC4A10 mRNA, which encodes a stilbene-sensitive Na+-HCO3- transporter. Anti-COOH-terminal antibodies were developed to determine the specific expression and localization of this Na+-HCO3- transport protein. Immunoblotting demonstrated antibody binding to a 180-kDa protein band from mouse and rat brain preparations enriched with choroid plexus. The immunoreactive band migrated as a 140-kDa protein after N-deglycosylation, consistent with the predicted molecular size of the SLC4A10 gene product. Bright-field immunohistochemistry and immunoelectron microscopy demonstrated strong labeling confined to the basolateral plasma membrane domain of the choroid plexus epithelium. Furthermore, the stilbene-insensitive Na+-HCO3- cotransporter, NBCn1, was also localized to the basolateral plasma membrane domain of the choroid plexus epithelium. Hence, we propose that the SLC4A10 gene product and NBCn1 both function as basolateral HCO3- entry pathways and that the SLC4A10 gene product may be responsible for the stilbene-sensitive Na+-HCO3- uptake that is essential for cerebrospinal fluid production.
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PMID:A SCL4A10 gene product maps selectively to the basolateral plasma membrane of choroid plexus epithelial cells. 1459 10

Prokaryotic transcription elongation factors GreA and GreB stimulate intrinsic nucleolytic activity of RNA polymerase (RNAP). The proposed biological role of Gre-induced RNA hydrolysis includes transcription proofreading, suppression of transcriptional pausing and arrest, and facilitation of RNAP transition from transcription initiation to transcription elongation. Using an array of biochemical and molecular genetic methods, we mapped the interaction interface between Gre and RNAP and identified the key residues in Gre responsible for induction of nucleolytic activity in RNAP. We propose a structural model in which the C-terminal globular domain of Gre binds near the opening of the RNAP secondary channel, the N-terminal coiled-coil domain (NTD) protrudes inside the RNAP channel, and the tip of the NTD is brought to the immediate vicinity of RNAP catalytic center. Two conserved acidic residues D41 and E44 located at the tip of the NTD assist RNAP by coordinating the Mg2+ ion and water molecule required for catalysis of RNA hydrolysis. If so, Gre would be the first transcription factor known to directly participate in the catalytic act of RNAP.
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PMID:Transcript cleavage factors GreA and GreB act as transient catalytic components of RNA polymerase. 1463 91

We found a novel inhibitor specific to eukaryotic DNA polymerase epsilon(pol epsilon) from plant cultured cells, Nicotina tabacum L. The compound (compound 1) was a dipeptide alcohol, L-homoserylaminoethanol. The 50% inhibition of pol epsilon activity by the compound was 43.6 microg/mL, and it had almost no effect on the activities of the other eukaryotic DNA polymerases such as alpha, beta, gamma and delta, prokaryotic DNA polymerases, nor DNA metabolic enzymes such as human telomerase, human immunodeficiency virus type 1 reverse transcriptase, T7 RNA polymerase, human DNA topoisomerase I and II, T4 polynucleotide kinase and bovine deoxyribonuclease I. Kinetic studies showed that inhibition of pol epsilon by the compound was non-competitive with respect to both template-primer DNA and nucleotide substrate. We succeeded in chemically synthesizing the stereoisomers, L-homoserylaminoethanol and D-homoserylaminoethanol, and found both were effective to the same extent. The IC(50) values of L- and D-homoserylaminoethanols for pol epsilon were 42.0 and 41.5 microg/mL, respectively. This represents the second discovery of a pol epsilon-specific inhibitor, and the first report on a water-soluble peptide-like compound as the inhibitor, which is required in biochemical studies of pol epsilon.
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PMID:L-Homoserylaminoethanol, a novel dipeptide alcohol inhibitor of eukaryotic DNA polymerase from a plant cultured cells, Nicotina tabacum L. 1498 Jun 8

Recent studies have demonstrated the widespread contamination of river and seawater with noroviruses (NV), often with more than one strain. The heteroduplex mobility assay (HMA) in which amplicons from study samples are hybridised (by denaturing and reannealing) to amplicons from reference strains and resolved by electrophoresis, has the potential to provide a simple and rapid means to identify samples containing multiple NV strains and to establish the diversity of strains within that sample. PCR amplicons from environmental samples that were tested directly in the HMA assay were shown to contain more than one strain. In order to evaluate HMA for investigations of NV diversity in environmental samples, amplicons from three representative samples were cloned and, for each, 20 amplicons derived from individual clones were analysed by HMA. Between two and six different HMA profiles were demonstrated among clones from a single sample indicating the extent of NV diversity in the sample. Sequence analysis confirmed the relationship of HMA profile and NV 'genotype'. Far greater diversity was seen among Genogroup (G) II (Ni/E3) amplicons than Genogroup (G) I (Ando/E3) amplicons (generated from the RNA dependent RNA polymerase region of the ORF1 of noroviruses), which often contained only a single strain, which is reflective of the greater prevalence of GII NVs over GI NVs. Overall, four GII and four GI strains were identified in these environmental water/sewage samples.
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PMID:Application of the heteroduplex mobility assay (HMA) for the investigation of the genomic diversity among noroviruses in environmental samples. 1523 10


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