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)

The predicted amino acid sequence of OmpT, an Escherichia coli outer membrane protease, was found to be highly homologous to that predicted for the pgtE gene product of Salmonella typhimurium. In this paper, it is shown that pgtE codes for a protein functionally homologous to OmpT as judged by its ability to proteolyze T7 RNA polymerase and to localize in the outer membrane of E. coli.
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PMID:Comparison of Escherichia coli K-12 outer membrane protease OmpT and Salmonella typhimurium E protein. 265 22

Bacteriophage T7 RNA polymerase is stable in Escherichia coli but very susceptible to cleavage by at least one endoprotease after cell lysis. The major source of this endoprotease activity was found to be localized to the outer membrane of the cell. A rapid whole-cell assay was developed to screen different strains for the presence of this proteolytic activity. Using this assay, we identified some common laboratory strains that totally lack the protease. Genetic and Southern analyses of these null strains allowed us to conclude that the protease that cleaves T7 RNA polymerase is OmpT (formerly termed protein a), a known outer membrane endoprotease, and that the null phenotype results from deletion of the OmpT structural gene. A recombinant plasmid carrying the ompT gene enables these deletion strains to synthesize OmpT and converts them to a protease-positive phenotype. The plasmid led to overproduction of OmpT protein and protease activity in the E. coli K-12 and B strains we used, but only weak expression in the E. coli C strain, C1757. This strain-dependent difference in ompT expression was investigated with respect to the known influence of envZ on OmpT synthesis. A small deletion in the ompT region of the plasmid greatly diminishes the amount of OmpT protein and plasmid-encoded protease present in outer membranes. Use of ompT deletion strains for production of T7 RNA polymerase from the cloned gene has made purification of intact T7 RNA polymerase routine. Such strains may be useful for purification of other proteins expressed in E. coli.
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PMID:ompT encodes the Escherichia coli outer membrane protease that cleaves T7 RNA polymerase during purification. 327 50

Even though secretion offers numerous advantages for the production of proteins in Escherichia coli, the expression of many heterologous proteins is severely limited by degradation in the periplasmic space. We found that mutations in rpoH, the RNA polymerase sigma factor responsible for heat shock protein synthesis, affect the stability of heterologous secreted proteins. A particularly dramatic increase in expression was further observed in rpoH degP double mutants. To minimize proteolytic degradation, we constructed a family of 25 isogenic strains deficient in all known cell envelope proteases (DegP, Protease III, Tsp(Prc), and OmpT), as well as the rpoH15 mutant allele, and characterized their growth in both shake flasks and fermentors. The availability of this set of strains permits the selection of a suitable host based on the optimal combination between the optimum reduction in protease activity and acceptable growth properties.
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PMID:Construction and characterization of a set of E. coli strains deficient in all known loci affecting the proteolytic stability of secreted recombinant proteins. 776 53

A genetic response of Escherichia coli to nitric oxide or to superoxide-generating agents such as paraquat is controlled by the soxRS locus. The intracellular redox signals generated by these agents are sensed by the SoxR protein which, when activated, functions as a potent activator of soxS transcription. The resulting increased level of SoxS protein then activates approximately 10 genes that constitute the soxRS regulon. Although the SoxS protein is homologous to the COOH-terminal region of the AraC family of regulatory proteins, the mechanism by which SoxS protein activates the soxRS regulon promoters is unknown. We identified in extracts of cells expressing high levels of SoxS protein a DNA binding activity specific for fragments containing soxRS-regulated promoters. This binding activity was purified to physical homogeneity and proved to be the SoxS protein, as confirmed by NH2-terminal amino acid sequencing. The purified SoxS protein bound specifically to the promoters of the micF, zwf, nfo, and sodA genes. Multiple DNA-protein complexes were formed by SoxS in a concentration-dependent fashion with each of these promoters. This binding of SoxS protein also facilitated the subsequent binding of E. coli RNA polymerase to both the micF and the nfo promoters. The binding sites of SoxS in the zwf and micF promoters were identified by DNase I footprinting, which revealed an extended protected region immediately upstream of the respective -35 sites. These results indicate that the small SoxS protein (M(r) of only 12,900) is a direct transcriptional activator of the oxidative stress genes of the soxRS regulon, although the possible involvement of other proteins in transcription activation by SoxS has not been ruled out.
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PMID:SoxS, an activator of superoxide stress genes in Escherichia coli. Purification and interaction with DNA. 803 83

The Klebsiella aerogenes nac gene, whose product is necessary for nitrogen regulation of a number of operons, was identified and its DNA sequence determined. The nac sequence predicted a protein a 305 amino acids with a strong similarity to members of the LysR family of regulatory proteins, especially OxyR from Escherichia coli. Analysis of proteins expressed in minicells showed that nac is a single-gene operon whose product has an apparent molecular weight of about 32 kDa as measured in sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Immediately downstream from nac is a two-gene operon, the first gene of which encodes another member of the LysR family. Upstream from nac is a tRNAAsn gene transcribed divergently from nac. About 60 bp upstream from the nac open reading frame lies a sequence nearly identical to the consensus for sigma 54-dependent promoters, with the conserved GG and GC nucleotides at -26 and -14 relative to the start of transcription. About 130 bp farther upstream (at -153 relative to the start of transcription) is a sequence nearly identical to the transcriptional activator NTRC-responsive enhancer consensus. Another weaker NTRC-binding site is located adjacent to this site (at -133 relative to the start of transcription). Thus, we propose that nac is transcribed by RNA polymerase carrying sigma 54 in response to the nitrogen regulatory (NTR) system. A transposon located between the promoter and the nac ORF prevented NTR-mediated expression of nac, supporting this identification of the promoter sequence. The insertion of over 5 kb of transposon DNA between the enhancer and its target promoter had only a weak effect on enhancer-mediated regulation, suggesting that enhancers may be able to act at a considerable distance on the bacterial chromosome.
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PMID:The nac (nitrogen assimilation control) gene from Klebsiella aerogenes. 845 53

The expression of the gp100 antigen is generally thought to be confined to cells of the melanocytic lineage, which makes the protein a suitable melanoma-specific marker. Strikingly, after screening a panel of normal tissues, tumour samples and cell lines of non-melanocytic origin, we found transcripts encoding gp100 in virtually every tissue and cell line tested. In contrast, tyrosinase and MART-1/MelanA transcripts were detected only in cells of the melanocytic lineage. However, no gp100 protein could be detected by either Western blotting or cytotoxicity assays. Therefore, at the protein level, gp100 remains exclusive for cells of melanocytic origin despite its transcription in many cell types. The major implication of this finding is that screening of patient material for gp100 expression should preferrably be performed by antibody staining. Reverse transcriptase polymerase chain reaction (RT-PCR) can be employed, provided that it is performed in a tightly controlled, semiquantitative setting.
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PMID:Transcription of the gene encoding melanoma-associated antigen gp100 in tissues and cell lines other than those of the melanocytic lineage. 941 42

In pathogenic Vibrio cholerae, the transmembrane DNA-binding protein ToxR co-ordinates the expression of over 20 genes, including those encoding important virulence factors such as cholera toxin and the toxin-co-regulated pilus. The outer membrane protein OmpT is the only member of the ToxR regulon known to be repressed by ToxR. In this study, we examined the environmental conditions that regulate OmpT expression and demonstrated that ompT transcription is upregulated 14-fold when the bacteria enter late log phase from early log phase. Deletion of the crp gene completely abolishes OmpT expression. Comparison of ompT transcription levels in the isogenic crp-, toxR- and crp-toxR- mutants revealed that (i) in the absence of ToxR, constitutive high-level ompT transcription is dependent on cAMP receptor protein (CRP); (ii) ToxR not only interferes with CRP-dependent ompT activation, but also abolishes the CRP-independent, basal level ompT transcription; thus, the mechanism by which ToxR represses ompT transcription involves both antiactivation and direct repression; (iii) both CRP and ToxR are required for the regulation of OmpT expression by growth phase. To provide further insights into the molecular mecha-nism of CRP-dependent activation of ompT transcription, we demonstrated that CRP-dependent activation requires a CRP binding site centred at -310 of the ompT promoter, without which the interaction of CRP with other CRP binding site(s) more proximal to the promoter results in repression. Mutations in two regions on CRP (AR1 and AR2) that directly contact RNA polymerase (RNAP) abolish activation, suggesting direct interaction of CRP with RNAP from -310 of the ompT promoter via DNA looping.
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PMID:ToxR interferes with CRP-dependent transcriptional activation of ompT in Vibrio cholerae. 1195 6

Two strains of an unidentified perithecial ascomycete with a dactylaria-like anamorph and another morphologically similar strain of a dactylaria-like fungus were collected on decaying wood submerged in freshwater. To study their phylogenetic relationships we (i) combined sequence data from the nuclear small and large subunits ribosomal DNA (nc18S and nc28S) and the second largest subunit of RNA polymerase II (RPB2) for a multigene phylogenetic analysis and (ii) used sequences of the internal transcribed spacer region (ITS) of the rRNA operon for a species-level analysis. The new genus Pleurotheciella is described for two new species, Pla. rivularia and Pla. centenaria, with nonstromatic perithecia, unitunicate asci, persistent paraphyses and hyaline, septate ascospores and dactylaria-like anamorphs characterized by holoblastic, denticulate conidiogenesis, subhyaline conidiophores and hyaline, septate conidia. Based on morphological and molecular data, Pleurotheciella is closely related to the genera Pleurothecium and Sterigmatobotrys. A key to the three genera and the known species is provided. In the three-gene inferred phylogeny, these genera grouped as a sister clade to the Savoryellales within a robust clade of uncertain higher rank affiliation. Phylogenetic study of the 12 strains that represent Pleurothecium recurvatum revealed four that grouped apart from the core of the species. Two of these strains, which form a monophyletic well supported clade in both phylogenies and share similar morphological characteristics, are described as a new species, Pleurothecium semifecundum.
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PMID:Phylogenetic classification of Pleurothecium and Pleurotheciella gen. nov. and its dactylaria-like anamorph (Sordariomycetes) based on nuclear ribosomal and protein-coding genes. 2268 95

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