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)

Helicobacter pylori is an important risk factor of gastric cancer (GC). Although many H. pylori virulence factors have been reported, the pathogenic mechanism by which H. pylori infection causes GC remains unclear. The aims of this study were to identify GC-related antigens from H. pylori and characterize their roles in the development of GC. As GC and duodenal ulcer (DU) are considered clinically divergent, we compared two-dimensional immunoblots of an acid-glycine extract of H. pylori probed with serum samples from 15 patients with GC and 15 with DU to find GC-related antigens, which were subsequently identified by mass spectrometry. Many protein spots were recognized by more than one serum, and 24 of these were better recognized by GC sera. The proteins showing higher frequency of recognition in GC group are threonine synthase, rod shape-determining protein, S-adenosylmethionine synthetase, peptide chain release factor 1, DNA-directed RNA polymerase alpha subunit, co-chaperonin GroES (monomeric and dimeric forms), response regulator OmpR, and membrane fusion protein. Of these proteins, GroES was identified as a dominant GC-related antigen with a much higher seropositivity of GC samples (64.2%, n = 95) compared with 30.9% for gastritis (n = 94) and 35.5% for DU (n = 124). GroES seropositivity was more commonly associated with antral GC than with non-antral GC (odds ratio = 2.7; 95% confidence interval, 1.1-6.7). In peripheral blood mononuclear cells, GroES stimulated production of interleukin (IL)-8, IL-6, granulocyte macrophage colony-stimulating factor, IL-1beta, tumor necrosis factor-alpha, cyclooxygenase-2, and prostaglandin E(2). Moreover when incubated with gastric epithelial cells, GroES induced expression of IL-8, cell proliferation, and up-regulation of c-jun, c-fos, and cyclin D1 but caused down-regulation of p27(Kip1). We conclude that GroES of H. pylori is a novel GC-associated virulence factor and may contribute to gastric carcinogenesis via induction of inflammation and promotion of cell proliferation.
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PMID:Comparative immunoproteomics of identification and characterization of virulence factors from Helicobacter pylori related to gastric cancer. 1676 9

To examine the proteomes of 2 important causative agents of fish streptococcosis, Streptococcus iniae ATCC29178 and Lactococcus garvieae KG9408, we used 2-dimensional gel electrophoresis (2-DE) followed by mass spectrometry to generate 2-DE maps of these type strains. Silver-stained 2-DE gels of S. iniae ATCC29178 and L. garvieae KG9408 revealed approximately 320 and 300 spots, respectively, and immobilized pH gradient strips (13 cm, pH 4 to 7) revealed that the majority of the detected spots were concentrated in the pH range of 4.5 to 5.5. The spots were randomly selected from the 2-DE profiles and identified by peptide mass fingerprinting using matrix-assisted laser desorption/ionization time of flight mass spectrometry. The majority of the identified proteins were functionally related to energy and carbohydrate metabolism (e.g. enolase ATPase, glyceraldehyde-3-phosphate dehydrogenase) or translation and translocation (e.g. elongation factor G, elongation factor Tu, DNA-directed RNA polymerase alpha chain). These data, along with our partial 2-DE maps of S. iniae ATCC29178 and L. garvieae KG9408, may help suggest antigenic proteins for the development of effective diagnostic tools and vaccines against S. iniae and L. garvieae.
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PMID:Partial two-dimensional gel electrophoresis (2-DE) maps of Streptococcus iniae ATCC29178 and Lactococcus garvieae KG9408. 1687 93

Recent advances in functional genomics have helped generate large-scale high-throughput protein interaction data. Such networks, though extremely valuable towards molecular level understanding of cells, do not provide any direct information about the regions (domains) in the proteins that mediate the interaction. Here, we performed co-evolutionary analysis of domains in interacting proteins in order to understand the degree of co-evolution of interacting and non-interacting domains. Using a combination of sequence and structural analysis, we analyzed protein-protein interactions in F1-ATPase, Sec23p/Sec24p, DNA-directed RNA polymerase and nuclear pore complexes, and found that interacting domain pair(s) for a given interaction exhibits higher level of co-evolution than the non-interacting domain pairs. Motivated by this finding, we developed a computational method to test the generality of the observed trend, and to predict large-scale domain-domain interactions. Given a protein-protein interaction, the proposed method predicts the domain pair(s) that is most likely to mediate the protein interaction. We applied this method on the yeast interactome to predict domain-domain interactions, and used known domain-domain interactions found in PDB crystal structures to validate our predictions. Our results show that the prediction accuracy of the proposed method is statistically significant. Comparison of our prediction results with those from two other methods reveals that only a fraction of predictions are shared by all the three methods, indicating that the proposed method can detect known interactions missed by other methods. We believe that the proposed method can be used with other methods to help identify previously unrecognized domain-domain interactions on a genome scale, and could potentially help reduce the search space for identifying interaction sites.
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PMID:Co-evolutionary analysis of domains in interacting proteins reveals insights into domain-domain interactions mediating protein-protein interactions. 1694 97

Leishmania mutants have contributed greatly to extend our knowledge of this parasite's biology. Here we report the use of the mariner in vitro transposition system as a source of reagents for shuttle mutagenesis and targeted disruption of Leishmania genes. The locus-specific integration was achieved by the disruption of the subtelomeric gene encoding a DNA-directed RNA polymerase III subunit (RPC2). Further inactivation of RPC2 alleles required the complementation of the intact gene, which was transfected in an episomal context. However, attempts to generate a RPC2 chromosomal null mutant resulted in genomic rearrangements that maintained copies of the intact locus in the genome. The maintenance of the RPC2 chromosomal locus in complemented mutants was not mediated by an increase in the number of copies and did not involve chromosomal translocations, which are the typical characteristics of the genomic plasticity of this parasite. Unlike the endogenous locus, the selectable marker used to disrupt RPC2 did not display a tendency to remain in its chromosomal location but was targeted into supernumerary episomal molecules.
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PMID:Shuttle mutagenesis and targeted disruption of a telomere-located essential gene of Leishmania. 1716 65

Eukaryotic nuclei contain three classes of multisubunit DNA-directed RNA polymerase. At the core of each complex is a set of 12 highly conserved subunits of which five--RPB5, RPB6, RPB8, RPB10, and RPB12--are thought to be common to all three polymerase classes. Here, we show that four distantly related eukaryotic lineages (the higher plant and three protistan) have independently expanded their repertoire of RPB5 and RPB6 subunits. Using the protozoan parasite Trypanosoma brucei as a model organism, we demonstrate that these distinct RPB5 and RPB6 subunits localize to discrete subnuclear compartments and form part of different polymerase complexes. We further show that RNA interference-mediated depletion of these discrete subunits abolishes class-specific transcription and hence demonstrates complex specialization and diversification of function by conventionally shared subunit groups.
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PMID:Diversification of function by different isoforms of conventionally shared RNA polymerase subunits. 1726 88

Baculoviruses have adapted novel tactics to transcribe their genes during the late stages of replication. These include a DNA-directed RNA polymerase which is evolutionarily divergent from cellular polymerases. The viral RNA polymerase is a multisubunit and multifunctional RNA polymerase that has the ability to recognize late promoters, transcribe the linked genes, and process the transcripts at both 5' and 3' ends. The viral RNA polymerase binds to late viral gene promoter elements that are compact and differ from early viral gene and cellular promoters. Baculoviruses also encode a number of proteins devoted to the synthesis of late transcripts. Many of these are highly conserved among all the baculovirus genomes sequenced to date, suggesting common transcription mechanisms. Although viral late mRNAs resemble host mRNAs, the transcribing/processing machinery is distinct. Characterization of the late gene transcription apparatus will elucidate new viral mechanisms for transcription.
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PMID:Baculovirus late and very late gene regulation. 1797 70

Using T-type maize cytoplasmic male sterile line (T-CMS) and maintainer line as experimental materials, we separated mitochondrial proteins from leaves at seedling, shooting, booting stages, mesocotyl, root and anther at meiosis of pollen mother cell, single-double nucleus stage of pollen grain by two-dimensional electrophoresis with immobilized pH3-10 gradients. About 150 mitochondrial protein spots in seedling leaves, 150 spots in mesocotyls, 150 spots in roots and 100 spots in meiosis anther were observed respectively in this investigation. 6 difference protein spots were identified by MALDI-TOF-MS analysis and NCBI database searching. r40c1 protein was present in mesocotyl of T-CMS and absent in maintainer line. Mature anther-specific protein, DNA-directed RNA polymerase 23kDa subunit, hexokinase II were present and glutathione S-transferase, putative polyprotein were absent in pollen aborted anther of T-CMS. Developmental changes in mitochondrial proteins were found in leaves but no differences were observed in T-CMS and its maintainer line. Obvious differences of mitochondrial proteins were found at single-double nucleus stage anther in T-CMS and maintainer line. These different proteins were considered to be associated to pollen aborted in T-CMS.
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PMID:[Different proteins in mitochondrial proteome of T-type maize cytoplasmic male-sterile line and its maintainer line]. 1819 83

The emerging field of global mass-based metabolomics provides a platform for discovering unknown metabolites and their specific biochemical pathways. We report the identification of a new endogenous metabolite, N(4)-(N-acetylaminopropyl)spermidine and the use of a novel proteomics based method for the investigation of its protein interaction using metabolite immobilization on agarose beads. The metabolite was isolated from the organism Pyrococcus furiosus, and structurally characterized through an iterative process of synthesizing candidate molecules and comparative analysis using accurate mass LC-MS/MS. An approach developed for the selective preparation of N(1)-acetylthermospermine, one of the possible structures of the unknown metabolite, provides a convenient route to new polyamine derivatives through methylation on the N(8) and N(4) of the thermospermine scaffold. The biochemical role of the novel metabolite as well as that of two other polyamines: spermidine and agmatine is investigated through metabolite immobilization and incubation with native proteins. The identification of eleven proteins that uniquely bind with N(4)-(N-acetylaminopropyl)spermidine, provides information on the role of this novel metabolite in the native organism. Identified proteins included hypothetical ones such as PF0607 and PF1199, and those involved in translation, DNA synthesis and the urea cycle like translation initiation factor IF-2, 50S ribosomal protein L14e, DNA-directed RNA polymerase, and ornithine carbamoyltransferase. The immobilization approach demonstrated here has the potential for application to other newly discovered endogenous metabolites found through untargeted metabolomics, as a preliminary screen for generating a list of proteins that could be further investigated for specific activity.
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PMID:Identification of a new endogenous metabolite and the characterization of its protein interactions through an immobilization approach. 1905 53

Systematic studies of the Bacillus group have been biased towards terrestrial and pathogenic isolates, and relatively few studies have examined Bacillus species from marine environments. Here we took twenty Bacillus strains from diverse marine environments and sequenced their 16S rRNA. Using molecular comparisons, we separated the strains into thirteen Bacillus genotypes and identified 9 species: B. aquaemaris. B. badius, B. cereus group, B. firmus, B. halmapalus, B. hwajinpoensis, B. litoralis, B. sporothermodurans, B. vietnamensis, and three indistinguishable Bacilli. In addition, we sequenced the DNA-directed RNA polymerase beta subunit (rpoB) gene and assessed its discriminative power in identifying Bacilli. Phylogenetic trees of Bacillus rpoB genes separated each Bacillus according to their taxonomic positions and were supported statistically. The resolution of Bacillus on the rpoB phylogenetic tree was approximately 4.5 times greater than on the 16S rRNA phylogenetic tree. These results demonstrate that the polymorphism of the Bacillus rpoB gene can be used to identify Bacillus species, providing an improved identification scheme for Bacillus species.
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PMID:Discovery of marine Bacillus species by 16S rRNA and rpoB comparisons and their usefulness for species identification. 1916 82

Scrub typhus, caused by infection with Orientia tsutsugamushi, is probably the most common severe rickettsial disease. Early diagnosis followed by treatment with antibiotics such as doxycycline or chloramphenicol usually quickly decreases fever in patients, and they often recover well from other symptoms of the disease. However, poorly responsive cases have been reported from northern Thailand and southern India. In order to identify protein factors that may be partially responsible for differential drug sensitivity of isolates of Orientia, we compared the protein profiles of doxycycline sensitive (Karp) versus (vs.) insensitive (AFSC4 and AFSC7) isolates. Tryptic peptides from both total water-soluble proteins and from protein spots separated by 2D-PAGE were analyzed using LC-MS/MS. The identity of each protein was established using the published genomic sequence of Boryong strain O. tsutsugamushi. The profiles of protein released into water from these isolates were quite different. There were 10 proteins detected only in AFSC4, 3 only in Karp, and 1 only in AFSC7. Additionally, there were 2 proteins not detected only in AFSC4, 4 not found only in Karp, and 3 not found only in AFSC-7. A comparison of 2D-PAGE protein profiles of drug sensitive strain versus (vs.) insensitive isolates has led to the identification of 14 differentially expressed or localized proteins, including elongation factor Ts and Tu, DNA-directed RNA polymerase alpha-subunit, ATP synthase beta-subunit, and several hypothetical proteins. These data confirm the tremendous proteomic diversity of isolates of Orientia and suggest that drug insensitivity in this species may arise from multiple mechanisms.
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PMID:Comparative proteomic analysis of antibiotic-sensitive and insensitive isolates of Orientia tsutsugamushi. 1953 61


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