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)

Gene activation by a DNA-binding regulatory protein in yeast requires the protein to have two components: one to recognize a specific DNA sequence and a second, the 'activating region', to interact with a general transcription factor or perhaps with RNA polymerase. The activating regions that have been characterized are acidic, and mutational analysis of one indicates that this acidity is important for activity. Here we report the design of an artificial protein bearing a novel 15-amino acid peptide linked to a DNA binding fragment of the yeast regulatory protein GAL4). The synthetic peptide is acidic and should it form an alpha-helix, that helix would be amphipathic, having one hydrophilic face bearing the acidic residues, and one hydrophobic face. When expressed in yeast, the artificial protein bearing this peptide efficiently activates the GAL1 gene which is ordinarily activated by GAL4. An otherwise identical protein with the novel 15 amino acids in a scrambled order, and which is thus unable to form an amphipathic structure, does not activate GAL1 transcription.
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PMID:Transcription in yeast activated by a putative amphipathic alpha helix linked to a DNA binding unit. 331 67

Salmonella typhimurium periodically confronts acid environments during its life. These situations arise in chemically compromised ponds, soil, degradative cellular organelles, host digestive systems, and may even result from byproducts of their own metabolism. The levels of acid that are encountered range from mild to extreme. As a neutralophile, S. typhimurium prefers to grown in pH environments above pH 5.5. They can survive down to pH 4 for extended periods of time. However, the limits of endurance can be stretched if the organisms are first adapted to a moderate acid pH before exposing them to acidity below pH 4.0. This adaptation, called the acid-tolerance response (ATR), includes several log phase and stationary phase systems. Some of these systems are dependent on an alternate sigma factor for RNA polymerase called sigma s, whereas other systems are sigma s-independent. A key to the ATR is the synthesis of a series of acid shock inducible proteins (ASPs), 51 for log phase ATR and 15 for stationary phase ATR. Some of these ASPs require sigma s for their synthesis; others require the participation of the ferric uptake regulator protein Fur. Effective acid tolerance involves RecA-independent DNA repair systems, iron, and facets of fatty acid metabolism. Aspects of medium composition and carbon metabolism are also known to influence the nature of acid tolerance in this organism. In addition to aiding survival in the natural non-host environment, aspects of acid tolerance are also tied to virulence, as evidenced by the involvement of the mouse virulence locus mviA and the fact that acid-sensitive strains of S. typhimurium exhibit reduced virulence. This review summarizes these aspects of acid adaptation and includes a discussion of acid-regulated gene expression.
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PMID:Low pH adaptation and the acid tolerance response of Salmonella typhimurium. 868 53

The gene coding for the largest subunit (RPA1) of RNA polymerase I (A) of Drosophila melanogaster (DmRPA1) was cloned and sequenced. The gene is interrupted by seven small introns and the cDNA reveals an open reading frame of 4932 nucleotides. The deduced polypeptide consists of 1644 amino acids with a calculated molecular weight of 185 kDa. Although the protein sequence exhibits the specific pattern of conserved regions found in all RNA polymerase largest subunits characterized so far, the overall sequence similarity among the RPA1 subunits of different species is much lower than seen with the corresponding subunits of RNA polymerases II and III. Two highly divergent hydrophilic domains characteristic for RPA1 separate the conserved blocks a and b in the N-terminal region and blocks g and h in the C-terminal section, respectively. In both cases the distance between the homologous blocks is enlarged by about 70 amino acids relative to the largest subunits of RNA polymerases II and III, and the corresponding subunit of the archaebacterial enzyme. Compared with RPA1 sequences of lower eukaryotes, the C-terminal hydrophilic domain in DmRPA1 is similar in length and acidity whereas the N-terminal domain is slightly shorter but retains the same basicity. The sequence insertions do not feature common motifs, suggesting a role for them in the interaction of RNA polymerase I with proteins required for the species-specific transcription of rDNA. The RPA1 subunits of Drosophila melanogaster and lower eukaryotes share an additional Zn-binding motif at the N-terminus with archaebacterial and RPC1 subunits, testifying to the complex evolutionary relationships among the RNA polymerases.
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PMID:Identification of the gene coding for the largest subunit of RNA polymerase I (A) of Drosophila melanogaster. 906 85

Escherichia coli responds to external acidification (pH 4.0 to 5.0) by synthesizing a newly identified, approximately 450-nucleotide RNA component. At maximal levels of induction it is one of the most abundant small RNAs in the cell and is relatively stable bacterial RNA. The acid-inducible RNA was purified, and the gene encoding it, designated asr (for acid shock RNA), mapped at 35.98 min on the E. coli chromosome. Analysis of the asr DNA sequence revealed an open reading frame coding for a 111-amino-acid polypeptide with a deduced molecular mass of approximately 11.6 kDa. According to computer-assisted analysis, the predicted polypeptide contains a typical signal sequence of 30 amino acids and might represent either a periplasmic or an outer membrane protein. The asr gene cloned downstream from a T7 promoter was translated in vivo after transcription using a T7 RNA polymerase transcription system. Expression of a plasmid-encoded asr::lacZ fusion under a native asr promoter was reduced approximately 15-fold in a complex medium, such as Luria-Bertani medium, versus the minimal medium. Transcription of the chromosomal asr was abolished in the presence of a phoB-phoR (a two-component regulatory system, controlling the pho regulon inducible by phosphate starvation) deletion mutant. Acid-mediated induction of the asr gene in the Delta(phoB-phoR) mutant strain was restored by introduction of the plasmid with cloned phoB-phoR genes. Primer extension analysis of the asr transcript revealed a region similar to the Pho box (the consensus sequence found in promoters transcriptionally activated by the PhoB protein) upstream from the determined transcription start. The asr promoter DNA region was demonstrated to bind PhoB protein in vitro. We discuss our results in terms of how bacteria might employ the phoB-phoR regulatory system to sense an external acidity and regulate transcription of the asr gene.
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PMID:The acid-inducible asr gene in Escherichia coli: transcriptional control by the phoBR operon. 1009 85

The nature of the equatorial ligands spanning the dirhodium core was shown to affect the ability and mechanism of various lantern-type complexes to inhibit transcription in vitro. The inhibition of transcription by Rh(2)(mu-O(2)CCF(3))(4), Rh(2)(mu-HNCOCF(3))(4), and [Rh(2)(mu-O(2)CCH(3))(2)(CH(3)CN)(6)](2+) appears to proceed predominantly via binding of the complexes to T7-RNA polymerase (T7-RNAP) and is dependent on the concentration of enzyme and Mg(2+) ions in solution. The concentrations of the aforementioned complexes required to inhibit 50% of the transcription, C(inh)(50), are similar to that measured for activated cisplatin, whereas a significantly higher concentration of Rh(2)(mu-HNCOCH(3))(4) is required to effect similar inhibition; the inhibition induced by Rh(2)(mu-HNCOCH(3))(4) does not involve binding to T7-RNAP. The spectral changes observed for each complex upon addition of enzyme are consistent with Rh(2)(mu-O(2)CCF(3))(4), Rh(2)(mu-HNCOCF(3))(4), and [Rh(2)(mu-O(2)CCH(3))(2)(CH(3)CN)(6)](2+) binding to the enzyme and may involve partial displacement of the equatorial (eq) groups by the Lewis basic sites of T7-RNAP. In contrast, addition of enzyme to solutions of Rh(2)(mu-HNCOCH(3))(4) does not result in significant spectral changes, a finding consistent with lack of enzyme dependence in the transcription inhibition. These differences in reactivity and transcription inhibition mechanism among complexes with different bridging ligands are explained by variations of the Lewis acidity of the axial (ax) sites in the series of complexes Rh(2)(mu-O(2)CCF(3))(4), Rh(2)(mu-HNCOCF(3))(4), and Rh(2)(mu-HNCOCH(3))(4). The Lewis acidity of the ax sites is expected to affect the initial interaction of the complexes with the biomolecules, followed by their rearrangement to eq positions if the bridging ligands are labile.
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PMID:Effect of equatorial ligands of dirhodium(II,II) complexes on the efficiency and mechanism of transcription inhibition in vitro. 1475 42

Stringent control mediated by the bacterial alarmone guanosine 5'-diphosphate 3'-diphosphate (ppGpp) is a key regulatory process governing bacterial gene expression. By devising a system to measure ppGpp in plants, we have been able to identify ppGpp in the chloroplasts of plant cells. Levels of ppGpp increased markedly when plants were subjected to such biotic and abiotic stresses as wounding, heat shock, high salinity, acidity, heavy metal, drought, and UV irradiation. Abrupt changes from light to dark also caused a substantial elevation in ppGpp levels. In vitro, chloroplast RNA polymerase activity was inhibited in the presence of ppGpp, demonstrating the existence of a bacteria-type stringent response in plants. Elevation of ppGpp levels was elicited also by treatment with plant hormones jasmonic acid, abscisic acid, and ethylene, but these effects were blocked completely by another plant hormone, indole-3-acetic acid. On the basis of these findings, we propose that ppGpp plays a critical role in systemic plant signaling in response to environmental stresses, contributing to the adaptation of plants to environmental changes.
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PMID:Identification of the bacterial alarmone guanosine 5'-diphosphate 3'-diphosphate (ppGpp) in plants. 1501 May 37

The dinucleotide d(pGpG) is an often employed DNA model to study various kinds of interactions between DNA and metal ions, but its acid-base properties were not yet described in detail. In this study the six deprotonation reactions of H4[d(pGpG)]+ are quantified. The acidity constants for the release of the first proton from the terminal P(O)(OH)2 group (pKa = 0.65) and for one of the (N7)H+ sites (pKa = 2.4) are estimated. The acidity constants of the remaining four deprotonation reactions were measured by potentiometric pH titrations in aqueous solution (25 degrees C; I = 0.1 M, NaNO3): The pKa values for the deprotonations of the second (N7)H+, the P(O)2(OH)-, and the two (N1)H sites are 2.98, 6.56, 9.54 and 10.11, respectively. Based on these results we show how to estimate acidity constants for related systems that have not been studied, e.g. pGpG, which is involved in the initiation step of a rotavirus RNA polymerase. The relevance of our results for nucleic acids in general is briefly indicated.
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PMID:Acid-base properties of the nucleic-acid model 2'-deoxyguanylyl(5'-->3')-2'-deoxy-5'-guanylate, d(pGpG)3-, and of related guanine derivatives. 1652 52

Zn(II)-curcumin, a mononuclear (1:1) zinc complex of curcumin was synthesized and examined for its antiulcer activities against pylorus-ligature-induced gastric ulcer in rats. The structure of Zn(II)-curcumin was identified by elemental analysis, NMR and TG-DTA analysis. It was found that a zinc atom was coordinated through the keto-enol group of curcumin along with one acetate group and one water molecule. Zn(II)-curcumin (12, 24 and 48 mg/kg) dose-dependently blocked gastric lesions, significantly reduced gastric volume, free acidity, total acidity and pepsin, compared with control group (P<0.001) and curcumin alone (24 mg/kg, P<0.05). Reverse transcriptase polymerase chain reaction (RT-PCR) analysis showed that Zn(II)-curcumin markedly inhibited the induction of nuclear factor-kappa B (NF-kappaB), transforming growth factor beta(1) (TGF-beta(1)) and interleukin-8 (IL-8), compared with control group (P<0.05). These findings suggested that Zn(II)-curcumin prevented pylorus-ligation-induced lesions in rat by inhibiting NF-kappaB activation and the subsequent production of proinflammatory cytokines, indicating a synergistic effect between curcumin and zinc. An acute toxicity study showed that mice treated with SDs of Zn(II)-curcumin (2 g/kg) manifested no abnormal signs.
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PMID:Gastroprotective effects of a new zinc(II)-curcumin complex against pylorus-ligature-induced gastric ulcer in rats. 1958 37