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)

Proper 3' end formation is critical for the production of functional mRNAs. Termination by RNA polymerase II is linked to mRNA cleavage and polyadenylation, but it is less clear whether earlier stages of mRNA production also contribute to transcription termination. We performed a genetic screen to identify mutations that decreased transcriptional readthrough of a defective GAL10 poly(A) terminator. A partial deletion of the GAL10 downstream region leads to transcription through the downstream GAL7 promoter, resulting in the inability of cells to grow on galactose. Mutations in elongation factors Spt4 and Spt6 suppress the readthrough phenotype, presumably by decreasing the amount of polymerase transcribing through the downstream GAL7 promoter. Interestingly, mutations in the mRNA-binding protein Npl3 improve transcription termination. Both in vivo and in vitro experiments suggest that Npl3 can antagonize 3' end formation by competing for RNA binding with polyadenylation/termination factors. These results suggest that elongation rate and mRNA packaging can influence polyadenylation and termination.
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PMID:Npl3 is an antagonist of mRNA 3' end formation by RNA polymerase II. 1590 70

CHANGES in transcriptional activity at defined loci are often correlated with significant local structural changes in the genome(1), and in polytene chromosomes, such changes are thought to be associated with compositional or conformational changes in the protein complement at these particular bands(2,3). Thus, various studies on Balfoiani rings and specific 'puffs' in such chromosomes are useful for elucidating the role of defined chromosomal components in both chromosome structure and gene activity. Such studies require specific probes which will allow in situ localisation of a chromosomal component during the various stages of puffing. Antibodies specific to purified histone fractions(4-7), HMG proteins(8), RNA polymerase(9) and non-histone protein subfractions(10) have been used in studies on chromatin and chromosome structure. We reported previously that concanavalin A (Con A) specifically binds to three types of non-histone proteins present in chromatin purified from rat liver nuclei and suggested that derivatives of Con A might serve as specific probes to study the in situ organisation of these non-histone proteins(11). We have now reacted fluorescein-labelled Con A with polytene chromosomes isolated from different developmental stages of Chironomus thummi and visualised the location of the bound Con A by fluorescence microscopy. We observed that the fluorescent lectin, which has an affinity for glucose- and mannose-containing molecules, specifically bound to the transcriptionally active regions of chromosome IV. The extent of binding of Con A to the Balbiani rings present in regions b and c of chromosome IV is proportional to the size of the respective ring. Our results indicate that glucose- or mannose-containing molecules are present in these Balbiani rings and that the availability of these sugars to interact with Con A can be correlated with the developmental stage of a puff. We suggest that lectins can be useful cytological tools with which to study the in situ organisation of defined chromosomal components during various functional states of the genome.
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PMID:Concanavalin A binds to puffs in polytene chromosomes. 1606 91

Polyphasic analysis of four new Vibrio isolates originating from the haemolymph of diseased cultured oysters is described. The new isolates were closely related to Vibrio splendidus, having 98 % 16S rRNA gene sequence similarity. Phylogenetic analysis based on DNA gyrase subunit B (gyrB), RNA polymerase sigma70 factor (rpoD), replication origin-binding protein (rctB) and transmembrane regulatory protein (toxR) genes, fluorescent amplified fragment length polymorphism and DNA-DNA hybridization experiments clearly showed that the new isolates form a tight genomic group that is different from the currently known Vibrio species. It is proposed that these new isolates should be accommodated in a novel species, Vibrio gigantis sp. nov. Phenotypic features that differentiate V. gigantis from other known Vibrio species include arginine dihydrolase, gelatinase and beta-galactosidase activities, NO(2) production, growth at 35 degrees C, and utilization of sucrose, melibiose, amygdalin, glycerol, galactose, starch and glycogen. The type strain is LGP 13T (=LMG 22741T=CIP 108656T).
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PMID:Vibrio gigantis sp. nov., isolated from the haemolymph of cultured oysters (Crassostrea gigas). 1628 Apr 78

Arom gene, encoding a single polypeptide that catalyses steps two to six of the aromatic amino acid (phenylalanine, tyrosine and tryptophan) biosynthetic pathway, has been amplified from Scleortinia sclerotiorum genomic DNA by PCR and sequenced. In order to identify the fragment encoding AROM protein experimentally and search a method of obtaining the enzyme in a large amount, the open reading frame of arom gene of S. sclerotiorum was amplified by Pyrobest DNA Polymerase and inserted between Kpn I and Not I sites of the vector pYES2 to construct the expression vector pYES2-arom. The construct was transformed into Saccharomyces cerevisiae H158 by the method of LiAc/ SSDNA/PEG. The rate of transformation was 2 x 10(2)/microg DNA, which was enough for the selection of the positive transformants. PCR using the extracted plasmids as the templates and restriction enzyme analysis of the plasmids extracted from E. coli cells transformed by the above plasmids were performed respectively to screen the positive S. cerevisiae transformants since the copy number of the plasmid in S. cerevisiae was low. Subsequently, the transformant activated by the SC-U medium containing 2% raffinose was inoculated into the SC-U medium containing 2% galactose and the SC-U medium containing 2% glucose respectively to induce and depress the expression of the foreign arom gene. The results of RT-PCR analysis showed: there was not any DNA band in the negative control without the anti-transcriptase, which indicated there was no DNA contamination in the extracted total RNA; there was an expected DNA band in the positive control using the expression vector pYES2-arom as the template, which indicated the used amplification condition was proper; there was not any DNA band in the negative control using total RNA from the depressed transformant as the template, which indicated the DNA bands amplified from total RNA of the induced transformant were not false; there were the expected DNA bands in the samples using total RNA of the transformant induced for 48h, 60h, 72h or 84h as the templates, which indicated the heterogeneous arom gene was transcribed in S. cerevisiae H158 cells. The result of Northern hybridization was consistent with that of RT-PCR, and showed that arom gene of S. sclerotiorum had been transcribed in S. cerevisiae H158 cells when the cells were induced for 48h in the SC-U medium containing 2% galactose at 30 degrees C at 180r/min. 5-enolpyruvylshikimate-3-phosphate synthase activity of the transformant, which was one of AROM protein activities, was measured by estimating the rate of Pi release to check the expressed AROM protein was active or not. The results of enzyme assay in the different culture period indicated that the transformant had 5-enolpyruvylshikimate-3-phosphate synthase activity and the activity reached the peak when the transformant was induced for 72h in SC-U medium at 30 degrees C at 180r/min. The molecular weight of AROM protein is high, it exists in cytoplasm as a dimmer and its expression is controlled by the amounts of amino acids. Therefore, it is very difficult to purify the enzyme. A great lot protein can be obtained by heterogeneous expression. S. cerevisiae expression system has the merits of safe status, authentic posttranslational modification, fast cultivation etc. and usually is the first choice eukaryotic expression system. S. cerevisiae expression system of AROM protein from S. sclerotiorum was successfully constructed for the first time, which provided the basis for the research on the catalysis mechanism of the enzyme and an economical means of simultaneously synthesizing five aromatic amino acid biosynthetic pathway enzymes.
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PMID:[Cloning and expression of arom gene of Sclerotinia sclerotiorum]. 1657 63

Previous biochemical studies have demonstrated that Lys-123 ubiquitination of histone H2B is globally required for up-regulation of mono-, di, and trimethylation of Lys-4 of histone H3. However, recent studies have implicated H2B-Lys-123 ubiquitination in the regulation of di- and trimethylation, but not monomethylation, of H3-Lys-4 in vivo. Using a formaldehyde-based cross-linking and chromatin immunoprecipitation assay, we show that H3-Lys-4 trimethylation, but not dimethylation, is up-regulated by H2B-Lys-123 ubiquitination in vivo at the coding sequences of a set of transcriptionally active genes such as ADH1, PHO84, and PYK1. Both the ubiquitination of H2B-Lys-123 and the methylation of H3-Lys-4 are dispensable for recruitment of RNA polymerase II to the coding sequences of these genes, and hence, their transcription is not altered in the absence of these covalent modifications. However, recruitment of RNA polymerase II to the coding sequence of a galactose-inducible gene, GAL1, is significantly reduced in the absence of H2B-Lys-123 ubiquitination but not H3-Lys-4 methylation. Consistently, transcription of GAL1 is altered in the H2B-K123R point mutant strain. Finally, we show that H3-Lys-4 methylation does not regulate H3-Lys-9/14 acetylation. Collectively, our data reveal a "trans-tail" regulation of H3-Lys-4 tri- but not dimethylation by H2B-Lys-123 ubiquitination, and these modifications are dispensable for transcription of a certain set of genes in vivo.
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PMID:Functional analysis of H2B-Lys-123 ubiquitination in regulation of H3-Lys-4 methylation and recruitment of RNA polymerase II at the coding sequences of several active genes in vivo. 1667 45

We investigated the effect of transforming growthfactor beta (TGFbeta1) short hairpin RNA (shRNA) mediated by pcDU6 plasmid on TGFbeta1 expression in human peritoneal mesothelial cells (HPMCs) and compared that effect with the effect of antisense TGFbeta1 RNA. We designed two pairs of oligonucleotides for two selectedfragments of coding sequence containing a 21-nucleotide (nt) TGFbeta1 sequence starting with GGCC. After annealing, double-stranded DNA was formed and separately ligated to plasmid pcDU6 [pcDNA3.1(-) with U6 promoter). The inverted motif contained six spacers and four Ts, which made it possible to form shRNA (TGFbgeta1 shRNA1 and TGFbeta1 shRNA2). We generated recombinant human TGFbeta1 antisense mammalian expression vector, and we isolated HPMCs from human greater omentum by pancreatin disaggregation to establish a stable cell-culture model. We used Lipofectamine 2000 to transfect third-passage HPMCs with plasmid pcDU6 mediating the expression of TGFbeta1 and plasmid pcDNA3.1(-) mediating the expression of antisense TGFbeta1 messenger RNA (mRNA). The resulting transfected cells were then stimulated with 4.25% D-glucose and 10 microg/mL lipopolysaccharide (GS+LPS). We used semi-quantitative reverse-transcriptase polymerase chain reaction to detect the expression of TGFbeta1, fibronectin (FN), collagen 1, and plasminogen activator inhibitor type 1 (PAI-1) mRNA by the stimulated cells. The TGFbeta1, FN, and PAI-1 protein levels in the culture supernatant were measured with a sandwich enzyme-linked immunosorbent assay. Expression of TGFbeta1 was significantly upregulated in HPMCs stimulated with GS+LPS (p < 0.01). As compared with control HPMCs in serum-free F12 medium, HPMCs transfected with TGFbeta1 antisense RNA showed inhibited expression of FN, collagen 1, and PAI-1 mRNA (17%, 26%, and 9.6% respectively after 24 hours). Forty-eight hours after transfection, the FN and PAI-I proteins were inhibited by 54.55% and 61.13% respectively (p < 0.05). In the pcDU6 plasmid vector-mediated TGFbeta1 shRNA groups, TGFbeta1 expression was obviously downregulated as compared with the GS+LPS group and the pcDU6 void vector group (p < 0.01). No significant difference was observed between the pcDU6 plasmid vector-mediated TGFbeta1 shRNA groups (p > 0.05). No significant difference was observed between the pcDNA3.1(-) vector-mediated antisense RNA group and the pcDU6 void vector group (p > 0.05). The expression of TGFbeta1 in pcDU6 plasmid vector-mediated TGFbeta1 shRNA groups was obviously downregulated as compared with the pcDNA3.1(-) plasmid vector-mediated antisense RNA group (p < 0.01). In HPMCs stimulated with GS+LPS, pcDU6 plasmid vector-mediated shRNA can significantly inhibit the induced expression of TGFbeta1. These results suggest the possible application of pcDU6 plasmid vector-mediated shRNA in preventing peritoneal fibrosis in patients receiving peritoneal dialysis.
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PMID:Inhibition of transforming growth factor beta (TGFbeta1) expression and extracellular matrix secretion in human peritoneal mesothelial cells by pcDU6 vector-mediated TGFbeta1 shRNA and by pcDNA3.1(-)-mediated antisense TGFbeta1 RNA. 1668 83

Fifty isolates of Lactobacillus sanfranciscensis from Italian sourdoughs were identified and typed by a polyphasic approach which included genotypic and phenotypic criteria. Genotypic diversity was characterized by Ribosomal Intergenic Spacer Analysis (RISA) of PCR amplified 16S-23S rDNA spacer region, denaturing gradient gel electrophoresis (DGGE) of PCR amplified rpoB (beta subunit of RNA polymerase) gene, and rep-PCR (PCR amplification of repetitive bacterial DNA elements) analyses. The RISA analysis produced a unique electrophoretical profile of four bands (ranging from 300 to 600 bp) for all L. sanfranciscensis isolates. The DGGE analysis of rpoB gene allowed the subdivision of isolates in four clusters. The resolution found by using rep-PCR with primers BOXA1R and REP1R-I/REP2-I allowed the widening of the level of isolates heterogeneity. Phenotypic diversity was evaluated by Biolog System and characterization of several technological traits (e.g., acidification kinetics, proteinase and peptidase activities). L. sanfranciscensis isolates used a large varieties of carbon sources such as dextrin, D-fructose, L-fucose, alpha-D-glucose, maltose, palatinose, L-rhanmose, L- and D,L-lactic acids and L-methionine. The acidification activity and related quotient of fermentation, and the peptidase (PepN, PepV, PepT, PepI, PepX, PepQ and PepR) activities markedly varied among strains. The same was found concerning the capacity to liberate amino acids during sourdough fermentation. This study could be considered as an example of a computerized analysis of the genotypic and phenotypic traits to reliably and rapidly differentiate sourdough isolates. Although some L. sanfranciscensis isolates combined several technological traits, the association of more selected strains seemed to be a requisite to get optimal sourdough characteristics.
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PMID:Molecular and functional characterization of Lactobacillus sanfranciscensis strains isolated from sourdoughs. 1722 14

Glycosylations are well-established steps in numerous biosynthetic pathways, and the attached sugar moieties often influence the specificity or pharmacology of the modified compounds. The sorangicins belong to the polyketide family of natural products, and exhibit antibiotic activity through inhibition of bacterial RNA polymerase. We have identified the sorangicin biosynthetic gene cluster in the producing myxobacterium Sorangium cellulosum So ce12. Within the cluster, sorF encodes a putative glycosyltransferase. To determine its function in sorangicin biosynthesis, SorF was heterologously expressed as a fusion protein in Escherichia coli. After purification by affinity chromatography, SorF was found to glucosylate sorangicin A in vitro, utilizing UDP-alpha-D-glucose as the natural donor substrate. Additionally, SorF showed high flexibility towards further UDP- and dTDP-sugars and was able to transfer several other sugar moieties-alpha-D-galactose, alpha-D-xylose, beta-L-rhamnose, and 6-deoxy-4-keto-alpha-D-glucose-onto the aglycon. SorF is therefore one of the rare glycosyltransferases able to transfer both D- and L-sugars, and could thus be used to generate novel sorangiosides.
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PMID:SorF: a glycosyltransferase with promiscuous donor substrate specificity in vitro. 1740 27

The distribution pattern of a 70 kDa cytokinin-binding protein (CBP70) was studied in 4-d-old etiolated maize seedlings (Zea mays L., cv. Elbrus). CBP70 was detected in crude protein extracts of all root zones and shoot parts by western blotting and by the sandwich ELISA (enzyme-linked immunosorbent assay) technique, using a pair of monoclonal anti-CBP70 antibodies cross-reacting with non-overlapping protein epitopes. The highest amount of CBP70 was found in the root meristem, which corresponds to the concentration in the meristem of zeatin, its riboside, nucleotide, and 9N-glucoside. CBP70 accumulation was also detected in other zones of cell division: in the root cap, shoot apex, and vascular tissues, suggesting involvement of the protein in the processes related to cell proliferation. This suggestion was also supported by CBP70 distribution in the root meristem: mitotically inactive cells of the quiescent centre did not contain a detectable amount of the protein. Stem cells adjoining the quiescent centre contained less CBP70 than their daughter cells. Using monoclonal antibodies against CBP70 for immunocytochemistry, the presence of the protein in the cytoplasm and its accumulation in nuclei and especially in nucleoli was demonstrated; such a pattern was observed in all cell types of seedlings. The subcellular distribution pattern of CBP70 was analysed by immunogold electron microscopy of the meristem and leaf cells; CBP70 was localized in the cytoplasm and nucleoplasm, and its highest concentration was detected in nucleoli. CBP70 was not detected in the vacuole and cell wall. In the RNA polymerase I model system, purified CBP70 mediated a trans-zeatin-dependent activation of transcription in vitro, and anti-CBP70 monoclonal antibodies blocked this activation. Other natural and synthetic physiologically active cytokinins also activated transcript elongation in the model system in the presence of CBP70. Adenine and inactive analogues of cytokinins had no such effects. These data suggest that CBP70 is a transcript elongation factor or a modulator of elongation factor activity specifically mediating a cytokinin-dependent regulation of transcription.
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PMID:Cytokinin-binding protein (70 kDa): localization in tissues and cells of etiolated maize seedlings and its putative function. 1758 53

RNA polymerase is a central macromolecular machine controlling the flow of information from genotype to phenotype, and insights into global transcriptional regulation can be gained by studying mutational perturbations in the enzyme. Mutations in the RNA polymerase beta subunit gene rpoB causing resistance to rifampin (Rif(r)) in Bacillus subtilis were previously shown to lead to alterations in the expression of a number of global phenotypes known to be under transcriptional control, such as growth, competence for transformation, sporulation, and germination (H. Maughan, B. Galeano, and W. L. Nicholson, J. Bacteriol. 186:2481-2486, 2004). To better understand the global effects of rpoB mutations on metabolism, wild-type and 11 distinct congenic Rif(r) mutant strains of B. subtilis were tested for utilization of 95 substrates by use of Biolog GP2 MicroPlates. A number of alterations of substrate utilization patterns were observed in the Rif(r) mutants, including the utilization of novel substrates previously unknown in B. subtilis, such as gentiobiose, beta-methyl-D-glucoside, and D-psicose. The results indicate that combining global metabolic profiling with mutations in RNA polymerase provides a system-wide approach for uncovering previously unknown metabolic capabilities and further understanding global transcriptional control circuitry in B. subtilis.
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PMID:Uncovering new metabolic capabilities of Bacillus subtilis using phenotype profiling of rifampin-resistant rpoB mutants. 1764 85


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