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)

To provide direct evidence for the mechanism leading to resistance to rifampicin, two Neisseria meningitidis strains from one clonal lineage (so-called sibling strains) were studied; one of these strains was resistant, the other sensitive to rifampicin. The polymerase chain reaction (PCR) was used to amplify fragments of the known rifampicin resistance region on the rpoB gene coding for the beta subunit of DNA-directed RNA polymerase and the amplimers were then sequenced. In addition to the DNA from the sibling strains, DNA from further strains was analysed, including two Spanish, rifampicin-resistant strains, eight further N. meningitidis strains, strains of four further Neisseria spp. and one reference strain. The results demonstrated how quickly and easily N. meningitidis can acquire resistance to rifampicin, and also suggest a clonal population structure within the collection of strains studied. This finding is discussed with respect to recent studies that indicate a more panmictic population structure within particular serogroups of N. meningitidis.
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PMID:Rifampicin resistance in Neisseria meningitidis: evidence from a study of sibling strains, description of new mutations and notes on population genetics. 922 44

The primary structure of human selenium-dependent phospholipid hydroperoxide glutathione peroxidase (GPX4) was determined by genomic cloning. The gene structure of GPX4 spans only 2.8 kb and consists of 7 exons. The coding sequence resides on all 7 exons, and the mitochondrial leader sequence is contained entirely within the first exon. The selenocysteine coding nucleotide resides on the third exon. The introns all commenced with the consensus nucleotide sequence GTR and ended with the consensus nucleotide sequence YAG. Analysis of the GPX4 gene sequence identified a potential alternative tissue-specific first exon. Chromosomal FISH studies placed the GPX4 gene at 19p13.3 location, and downstream of the 23 k-Da polypeptide DNA-directed RNA polymerase gene.
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PMID:Structural organization of the human selenium-dependent phospholipid hydroperoxide glutathione peroxidase gene (GPX4): chromosomal localization to 19p13.3. 970 30

A DNA-dependent RNA polymerase was purified to homogeneity, starting from insect cells infected with the baculovirus Autographa californica nuclear polyhedrosis virus (AcNPV). The purified polymerase supported accurate and specific transcription from late and very late promoters but was not active on viral early promoters. Thus, promoter recognition is an integral function of the purified enzyme. The purified RNA polymerase was composed of only four equimolar subunits, which makes it the simplest DNA-directed RNA polymerase from a eukaryotic source described so far. Amino-terminal protein sequencing, peptide fingerprinting, and immunochemical analyses were used to identify the four subunits, all of which are virus encoded. Overexpression of the four viral proteins (LEF-8, LEF-4, LEF-9, and p47) in baculovirus-infected cells resulted in a significant increase in the levels of RNA polymerase produced in the infected cells. Thus, the overexpression data are consistent with our identification of the RNA polymerase subunits.
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PMID:A virus-encoded RNA polymerase purified from baculovirus-infected cells. 973 37

A 16,226-bp fragment from the genome of Aquifex pyrophilus was sequenced, containing the genes for ribosomal proteins L1, L10, and L7/12 (rplAJL), DNA-directed RNA polymerase subunits beta and beta' (rpoBC), alanyl-tRNA synthetase (alaS), and subunit A of proteinase Clp (clpA). Enzymatic activity and extreme thermostability of purified A. pyrophilus RNA polymerase were verified. Transcription initiation on a DNA construct harboring the T7 A1 promoter was demonstrated by elongation of a 32P-labeled trinucleotide. Phylogenetic analyses of the two largest subunits of bacterial RNA polymerases (beta and beta') showed overall consistency with the 16S rRNA-based phylogeny, except for the positions of the hyperthermophiles A. pyrophilus and Thermotoga maritima and for the location of the root of the domain Bacteria. In the phylogenies for both RNA polymerase subunits beta and beta', A. pyrophilus was placed within the Gram-negative bacteria below the epsilon subdivision of the Proteobacteria. No support was found for the 16S rRNA-based hypothesis that A. pyrophilus might be the deepest branch of the Bacteria, but the cell wall-less mycoplasmas were found with a high confidence at the root of the Bacteria phylogenies. This raised doubts not only about whether the original Bacteria were indeed like the hyperthermophiles, but also concerning the value of single-gene phylogenies for hypotheses about the evolution of organisms.
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PMID:RNA polymerase of Aquifex pyrophilus: implications for the evolution of the bacterial rpoBC operon and extremely thermophilic bacteria. 1019 19

There is a need to investigate the mechanistic basis of the human skin irritation response if relevant in vitro test systems for the predictive identification of skin irritation hazards are to be developed. Recent progress in genomics technologies mean that tools for the identification and investigation of important biochemical events in the processes of skin irritation are now available. The aim of this work was to identify genes (for further mechanistic investigation) which may be regulated in response to skin irritation, following exposure of the EpiDerm skin model to the known skin irritant sodium lauryl sulphate (SLS). EpiDerm cultures were treated in triplicate with a non-cytotoxic dose of SLS (0.1 mg/ml, as determined by the MTT assay and histological examination) for 15 min, 30 min, 1 h, 2 h, 3 h, 4 h and 24 h. Total RNA was extracted from the pooled EpiDerm cultures and used to probe Atlas human arrays (Clontech) covering approximately 3600 genes. Preliminary data indicated an up-regulation at early time points (15-30 min) of a number of genes involved in transportation (e.g. the sodium and chloride dependent taurine transporter) and receptors (e.g. ZAP70 and protocadherin 42 precursor). The gene encoding the UV excision repair protein and other DNA repair genes (e.g. DNA-directed RNA polymerase II) were up-regulated after 1-3 h, along with TGF beta 3 and other tumour suppressors, which play a role in cellular development and wound healing. At the later time points of 4-24 h, genes involved in protein translation (e.g. Cathepsin D receptor) and metabolism (e.g. CYP27A) were up-regulated. In addition, a number of genes were down-regulated in response to treatment with SLS, although these followed less of a time dependent pattern. These results indicate the differential regulation of a number of genes in response to treatment with SLS, some of which may provide additional clues to the molecular events underpinning the irritation response to this particular surfactant and possibly to other chemical irritants.
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PMID:Gene expression analysis of EpiDerm following exposure to SLS using cDNA microarrays. 1156 69

The late expression factor-8 gene (lef-8) of Autographa californica M nucleopolyhedrovirus encodes the largest subunit of the virally encoded DNA-directed RNA polymerase specific for the transcription of late and very late viral genes. The sequence of lef-8 predicts a C-terminal motif of 13 amino acids that is conserved in other polymerases. Detailed mutagenesis throughout lef-8 was performed, including this C-terminal motif, to define sequences required for late promoter activation. It was found that the conserved C-terminal motif was critical for late gene expression. In addition, regions throughout the entire lef-8-encoding sequence were important for optimal function, suggesting complex protein-protein and protein-DNA interrelationships in the late gene-specific viral transcriptosome.
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PMID:Functional dissection of the baculovirus late expression factor-8 gene: sequence requirements for late gene promoter activation. 1281 Aug 76

In recent years, the planctomycetes have been recognized as a phylum of environmentally important bacteria with habitats ranging from soil and freshwater to marine ecosystems. The planctomycetes form an independent phylum within the bacterial domain, whose exact phylogenetic position remains controversial. With the completion of sequencing of the genome of 'Rhodopirellula baltica' SH 1, it is now possible to re-evaluate the phylogeny of the planctomycetes based on multiple genes and genome trees in addition to single genes like the 16S rRNA or the elongation factor Tu. Here, evidence is presented based on the concatenated amino acid sequences of ribosomal proteins and DNA-directed RNA polymerase subunits from 'Rhodopirellula baltica' SH 1 and more than 90 other publicly available genomes that support a relationship of the Planctomycetes and the Chlamydiae. Affiliation of 'Rhodopirellula baltica' SH 1 and the Chlamydiae was reasonably stable regarding site selection since, during stepwise filtering of less-conserved sites from the alignments, it was only broken when rigorous filtering was applied. In a few cases, 'Rhodopirellula baltica' SH 1 shifted to a deep branching position adjacent to the Thermotoga/Aquifex clade. These findings are in agreement with recent publications, but the deep branching position was dependent on site selection and treeing algorithm and thus not stable. A genome tree calculated from normalized BLASTP scores did not confirm a close relationship of 'Rhodopirellula baltica' SH 1 and the Chlamydiae, but also indicated that the Planctomycetes do not emerge at the very root of the Bacteria. Therefore, these analyses rather contradict a deep branching position of the Planctomycetes within the bacterial domain and reaffirm their earlier proposed relatedness to the Chlamydiae.
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PMID:Evaluation of the phylogenetic position of the planctomycete 'Rhodopirellula baltica' SH 1 by means of concatenated ribosomal protein sequences, DNA-directed RNA polymerase subunit sequences and whole genome trees. 1514 26

Methanococcus jannaschii is an autotrophic hyperthermophilic archaeon isolated from an oceanic hydrothermal vent. Its primary pathway for energy production is methanogenesis from H2 and CO2. High-throughput Multidimensional Protein Identification Technology based on microcapillary LC/LC/ MS/MS was used to investigate the proteome of M. jannaschii and the methanogenesis pathway in cells grown in complex medium with high H2 supply. A total of 963 proteins have been unambiguously identified. The identified proteins represent approximately 54% of the whole genome of M. jannaschii. About 44% of the identified proteins are either conserved hypothetical or hypothetical proteins. We identified 83-95% of the proteins predicted to be involved in amino acid biosynthesis, cellular processes, central intermediary metabolism, energy metabolism, protein synthesis, transcription, and purine, pyridine, nucleoside, and nucleotide synthesis. Over 40% of these proteins have better than 50% sequence coverage. Approximately 90% of the predicted methanogenesis proteins were detected. In contrast, only 27-37% of predicted hypothetical proteins, proteins involved in transport and binding, and proteins with regulatory functions were identified. High peptide number, spectrum count, and sequence coverage have been used as indicators of high expression levels and are in good agreement with codon bias analysis. Predicted intein peptides were detected in MJ1043 (DNA-directed RNA polymerase, subunit A"), MJ0542 (phosphoenolpyruvate synthase), MJ0782 (transcription initiation factor IIB), and MJ1422 (putative replication factor C subunit). New peptides created by protein splicing were detected in MJ0885 (DNA dependent DNA polymerase), MJ0542, and MJ0782. The methanogenesis pathway and the enzymes involved are also discussed.
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PMID:Shotgun proteomics of Methanococcus jannaschii and insights into methanogenesis. 1525 35

Mitochondrial RNA polymerases (mtRNAPs) are necessary for the biogenesis of mitochondria and for proper mitochondrial function since they transcribe genes on mtDNA for tRNAs, rRNAs, and mRNAs. The unique type of RNA editing identified in mitochondria of Physarum polycephalum is thought to be closely associated with transcription, and as such, RNA editing activity would be expected to be closely associated with the mtRNAP. In order to better characterize the role of mtRNAPs in mitochondrial biogenesis and to determine the role of the Physarum mtRNAP in RNA editing, the cDNA of the Physarum mtRNAP was identified using PCR and degenerate primers designed from conserved motifs in mtRNAPs. This amplification product was used to screen a cDNA library for the cDNA corresponding to the Physarum mtRNAP. A cDNA corresponding to a 3.2 kb transcript containing a 997 codon open reading frame was identified. The amino acid sequence inferred from the open reading frame contains motifs characteristic of mtRNAPs. To confirm that a cDNA for an RNA polymerase had been isolated, the cDNA was expressed in E. coli as an N-terminal maltose binding protein (MBP) fusion protein. The fusion protein was purified by affinity chromatography and shown to have DNA-directed RNA polymerase activity. This functional mtRNAP will be useful for in vitro studies of mitochondrial transcription and RNA editing.
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PMID:Identification of a putative mitochondrial RNA polymerase from Physarum polycephalum: characterization, expression, purification, and transcription in vitro. 1640 3

Three Gram-positive bacterial strains, 7-3, 255-15 and 190-11, previously isolated from Siberian permafrost, were characterized and taxonomically classified. These microorganisms are rod-shaped, facultative aerobic, motile with peritrichous flagella and their growth ranges are from -2.5 to 40 degrees C. The chemotaxonomic markers indicated that the three strains belong to the genus Exiguobacterium. Their peptidoglycan type was A3alpha L-Lys-Gly. The predominant menaquinone detected in all three strains was MK7. The polar lipids present were phosphatidyl-glycerol, diphosphatidyl-glycerol and phosphatidyl-ethanolamine. The major fatty acids were iso-C13:0, anteiso-C13:0, iso-C15:0, C16:0 and iso-C17:0. Phylogenetic analysis based on 16S rRNA and six diverse genes, gyrB (gyrase subunit B), rpoB (DNA-directed RNA polymerase beta subunit), recA (homologous recombination), csp (cold shock protein), hsp70 (ClassI-heat shock protein-chaperonin) and citC (isocitrate dehydrogenase), indicated that the strains were closely related to Exiguobacterium undae (DSM 14481(T)) and Exiguobacterium antarcticum (DSM 14480(T)). On the basis of the phenotypic characteristics, phylogenetic data and DNA-DNA reassociation data, strain 190-11 was classified as E. undae, while the other two isolates, 7-3 and 255-15, comprise a novel species, for which the name Exiguobacterium sibiricum sp. nov. is proposed.
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PMID:Characterization of Exiguobacterium isolates from the Siberian permafrost. Description of Exiguobacterium sibiricum sp. nov. 1648 12


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