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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)

The NlpD/LppB homolog of the human pathogen, Bartonella bacilliformis, is an immunogenic 43-kDa protein that is encoded by a 1206-bp open reading frame (ORF-401). The regions flanking the nlpD/lppB gene of B. bacilliformis were sequenced to determine if it is located within the rpoS operon, as it is in most bacteria. We report that the B. bacilliformis nlpD/lppB gene is located immediately downstream of pcm, a gene encoding a 25-kDa protein, L-isoaspartyl protein carboxyl methyltransferase, that is a component of the rpoS operon in other bacteria. However, the genomic organization downstream of the B. bacilliformis nlpD/lppB gene appears to be distinct. In other bacteria, the third gene in the operon is rpoS, a gene that codes for an alternative sigma factor of RNA polymerase. In B. bacilliformis, an open reading frame encoding a protein homologous to the immunodominant YajC protein is located directly downstream of the nlpD/lppB gene. We show that Bartonella henselae, a close relative of B. bacilliformis, also shares this unusual organizational feature. Thus, the genomic organization of the nlpD/lppB genes of B. bacilliformis, and B. henselae appears to be unique among all bacteria for which the sequence of this region has been reported.
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PMID:Molecular cloning and analysis of a region of the Bartonella bacilliformis genome encoding NlpD, L-isoaspartyl methyltransferase and YajC homologs. 1294 Nov 62

Twenty-three chlorovirus genes expressed in host cells as early as 5-10 min postinfection (p.i.), or immediate early, were isolated and characterized. Some showed significant homology with those for transcriptional factors and mRNA-processing proteins including TFIIB, helicases, mRNA capping enzyme, nucleolin, and bean transcription factor. Others code for (i) factors influencing translation such as aminoacyl tRNA synthetases and ribosomal protein, and (ii) unknown proteins. Enzymes involved in polysaccharide synthesis were also found. All transcripts of these genes had a poly(A) tail, which decreased in size after 20 min p.i., possibly caused by the shortening by an exonuclease. Often, due to readthrough either from an upstream ORF or into a downstream ORF, a few extra transcripts for each gene appeared after 40 min p.i., suggesting a change in promoter selection and termination accuracy at this point. A typical TATA-box and a common element 5'-ATGACAA were in the promoter region of almost all of the immediate early genes, which may be recognized by host RNA polymerase and transcription factors.
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PMID:Immediate early genes expressed in chlorovirus infections. 1497 49

The Saccharomyces cerevisiase protein phosphatase Fcp1 has been implicated in the regulation of transcription by RNA polymerase II, and is encoded by the essential gene FCP1. A screen was carried out for multicopy suppressors of the temperature-sensitive phenotype of two phosphatase mutants, fcp1-2 and fcp1-4. Only the wild-type FCP1 was found to suppress (complement) the fcp1-4 mutation. For fcp1-2 three second-site suppressors were identified. One contained the ORF for ZDS1. The remaining two suppressors mapped to the centromere regions of chromosomes I and V. Suppression due to centromere DNA was found to be more dependent on the CDEIII region than on other regions of the centromere. The presence of a suppressor centromere affected the level of Fcp1 protein and the overall phosphorylation state of RNA polymerase II (RNAPII) in fcp1-2 cells, but not wild-type cells, grown at both permissive and non-permissive temperatures. In addition, genetic interactions were identified between this FCP1 mutant and the genes SKP1, CEP3 and CBF1, which code for centromere binding proteins. The mechanism of suppression and regulation of Fcp1-2 protein activity by centromeric DNA is discussed.
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PMID:Genetic interactions between an RNA polymerase II phosphatase and centromeric elements in Saccharomyces cerevisiae. 1513 55

The torI gene has been identified by using a genetic multicopy approach as a negative regulator of the torCAD operon that encodes the trimethylamine N-oxide reductase respiratory system in Escherichia coli. The negative effect was due to a previously unidentified small ORF (66 aa) of phage origin that we called torI for Tor inhibition. Overexpression of torI led to an 8-fold decrease of the torCAD operon transcription. This operon is positively regulated, in the presence of trimethylamine N-oxide, by a four-step phosphorelay involving the TorS sensor and the TorR response regulator. Epistatic experiments showed that TorI acts downstream of TorS and needs the presence of TorR. In vitro experiments showed that it is neither a TorR phosphatase nor a histidine kinase inhibitor and that it binds to the effector domain of TorR. Unexpectedly, TorI did not impede TorR DNA binding, and we propose that it may prevent RNA polymerase recruitment to the torC promoter. This study thus reveals a previously uncharacterized class of response regulator inhibitors.
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PMID:TorI, a response regulator inhibitor of phage origin in Escherichia coli. 1519 50

The plastid accD gene encoding the carboxyltransferase b subunit of acetyl-coenzyme A carboxylase (ACCase) was cloned from potato. Potato accD (saccD) is 2487 bp in length with a 614 bp 5 cent upstream promoter region and an ORF of 1524 bp, corresponding to a polypeptide of 507 amino acids. The N-terminal region lacks recognizable motifs, while the C-terminal regions contains five motifs. Among these is motif II, PLIIVCASGGARMQE, the sole motif present in all available accD sequences of plants and animals, and of E. coli, suggesting that this motif may correspond to the catalytic site. saccD has the typical prokaryotic promoter signatures, TTGACA and TATCAA, which are -35 and -10-like sequences for plastid-encoded RNA polymerase (PEP), at positions -184 and -160, respectively. However, it seems to be transcribed by the nucleus-encoded RNA polymerase because it is expressed in tuber and root, and in the dark (under crippled PEP conditions) and its transcription initiation sites do not correspond to those of PEP. saccD is expressed in all potato tissues, i.e., leaf, stem, root, and tuber, and its transcript is produced at a similar rate in the light and dark, at different developmental stages, and during growth in the presence of different sugars and carbon sources. Taken together, our results suggest that potato accD is a housekeeping gene constitutively expressed in both chloroplast and amyloplast.
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PMID:Characterization of the plastid-encoded carboxyltransferase subunit (accD) gene of potato. 1523 16

The Haloferax mediterranei nar operon has been sequenced and its regulation has been characterized at transcriptional level. The nar operon encodes seven open reading frames(ORFs) (ORF1 narB, narC, ORF4, narG, narH, ORF7 and narJ). ORF1, ORF4 and ORF7 are open reading frames with no assigned function, however the rest of them encoded different proteins. narB codes for a 219-amino-acid-residue iron Rieske protein. narC encodes a protein of 486 amino acid residues identified by databases searches as cytochrome-b (narC). The narG gene encodes a protein with 983 amino acid residues and is identified as a respiratory nitrate reductase catalytic subunit (narG). NarH protein has been identified as an electron transfer respiratory nitrate reductase subunit (narH). The last ORF encodes a chaperonin-like protein (narJ) of 242 amino acid residues. The respiratory nitrate reductase was purified 21-fold from H. mediterranei membranes. Based on SDS-PAGE and gel-filtration chromatography under native conditions, the enzyme complex consists of two subunits of 112 and 61 kDa. The optimum temperature for activity was 70 degrees C at 3.4 M NaCl and the stability did not show a direct dependence on salt concentration. Respiratory nitrate reductase showed maximum activity at pH 7.9 and pH 8.2 when assays were carried out at 40 and 60 degrees C, respectively. The absorption spectrum indicated that Nar contains Fe-S clusters. Reverse transcriptase (RT-PCR) shows that regulation of nar genes occurs at transcriptional level induced by oxygen-limiting conditions and the presence of nitrate.
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PMID:Respiratory nitrate reductase from haloarchaeon Haloferax mediterranei: biochemical and genetic analysis. 1534 13

This study, based on the genetic engineering approach, concerns the regulation of the insect gene expression, but it has also a strong significance for plant protection, which is associated with the future possibility to control insect development more effectively, especially in those species that are pests of cultivated plants. The I-18 C gene of Chironomus tentans is activated by heat-shock and the steroid hormone--ecdysone. This gene produces different transcripts (at least four) by alternative splicing. Two different open reading frames, i.e. ORFs I and II of the two main transcripts of this gene, i.e. the 1.8 and 4.6 kb RNA, had been isolated, at the DNA level, as the ORFs reflecting DNA fragments, using the polymerase chain reaction, then were cloned into the bluescript vector and finally were cloned into the pET-3a vector to be translated in the T7 RNA polymerase/promoter system of E. coli. As the preliminary outcome of these experiments it was possible to obtain ORF I overexpressed as the polypeptide, whereas ORF II was expressed as the polypeptide that was strongly visible on SDS-polyacrylamide gel. This could facilitate further studies regarding the mechanisms of expression of this gene, including the level of expression of this gene during the C. tentans development.
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PMID:Isolation, cloning and expression of DNA fragments reflecting open reading frames of 1.8 and 4.6 kb RNAs of the I-18 C gene of Chironomus tentans. 1574 67

Fragaria chiloensis latent virus (FClLV), a member of the genus Ilarvirus was first identified in the early 1990s. Double-stranded RNA was extracted from FClLV infected plants and cloned. The complete nucleotide sequence of the virus has been elucidated. RNA 1 encodes a protein with methyltransferase and helicase enzymatic motifs while RNA 2 encodes the viral RNA dependent RNA polymerase and an ORF, that shares no homology with other Ilarvirus genes. RNA 3 codes for movement and coat proteins and an additional ORF, making FClLV possibly the first Ilarvirus encoding a third protein in RNA 3. Phylogenetic analysis reveals that FClLV is most closely related to Prune dwarf virus, the type member of subgroup 4 of the Ilarvirus genus. FClLV is also closely related to Alfalfa mosaic virus (AlMV), a virus that shares many properties with Ilarviruses . We propose the reclassification of AlMV as a member of the Ilarvirus genus instead of being a member of a distinct genus.
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PMID:New features in the genus Ilarvirus revealed by the nucleotide sequence of Fragaria chiloensis latent virus. 1587 14

Noroviruses are important etiologic agents of acute gastroenteritis and show great genetic diversity. To characterize more fully previously detected strains that could not be assigned unequivocally to one particular genotype based on the RNA polymerase, we have sequenced a region in the capsid gene and, in some cases, in the junction between open reading frame 1 (ORF 1) and ORF 2. The results allowed us to identify several recombinant noroviruses: GGIIb viruses were detected for the first time in France in August 2000 and then spread through France and to Europe during the following winter. Here we present the characterization of three other probable GII recombinants which showed different phylogenetic positions depending on their ORF 1 and ORF 2 sequences. Analysis of the region located between ORF 1 and ORF 2 by a nucleotide identity window search showed a sudden shift in similarities. Moreover, recombination breakpoints were identified upstream and downstream of the beginning of ORF 2 by using a statistical test, thus confirming the involvement of this region in recombination. Unlike GGIIb, the three recombinants described here do not seem to have diffused widely in the community: one was found in a waterborne outbreak, and the other two were found in sporadic cases. Recombination is important for the evolution of RNA viruses and has already been described for noroviruses. Our results suggest that recombination is not a rare phenomenon among noroviruses, but not all these presumed recombinants that formed during RNA replication are able to spread widely.
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PMID:Characterization of new recombinant noroviruses. 1620 81

Seven organophosphorus pesticide-degrading bacteria harboring the methyl parathion degrading (mpd) gene were isolated from a methyl parathion contaminated site. In this study, the 4.7 kb mpd gene cluster, conserved in all seven bacteria capable of degrading methyl parathion, was cloned and further analysis revealed that this cluster contained five ORFs and the mpd gene was associated with a mobile element, IS6100. In addition to mpd gene ORF and tnpA ORF, three other ORFs showed high homology to the permease component of ABC-type transport system, the general secretion pathway protein B, and the RNA polymerase sigma 70 factor, respectively. The mpd genes of these 7 strains were subcloned and expressed in E. coli, SDS-PAGE and zymogram analysis showed that two expression products of mpd genes in E. coli were found, but the one without signal peptide showed the hydrolytic activities. Our evidences collectively suggest that mpd gene cluster may be disseminated through horizontal gene transfer based on phylogenetic analysis of the cluster and their host bacterial strains, and comparisons of GC content of the cluster and respective host's chromosome.
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PMID:Cloning of the organophosphorus pesticide hydrolase gene clusters of seven degradative bacteria isolated from a methyl parathion contaminated site and evidence of their horizontal gene transfer. 1647 56


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