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:3.1.26.9 (ribonuclease)
6,589 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

Transcription was determined in liver chromatin from rats fed for 6 days, an optimal (20%) or suboptimal (3%) amount of high-quality protein. Transcription by Escherichia coli RNA polymerase (EC 2.7.7.6) was lower after prolonged incubation with chromatin from rats fed 3% as compared with 20% protein. Differences were detected in the transcripts of the two types of chromatin after analysis by sucrose density gradient centrifugation. But no measurable differences were found in the melting profiles at low ionic strength of the two chromatin preparations. Transcription per milligram chromatin DNA was 25-fold higher using E. coli RNA polymerase instead of rat liver RNA polymerase II. The use of UTP as radioactive precursor in the absence of ATP, GTP and CTP resulted in a low labelling of RNA. One [lambda32P]UTP nucleotide was incorporated/8 UMP nucleotides. The product obtained was sensitive to ribonuclease treatment. In the presence of ATP, GTP and CTP [lambda-32P]UTP nucleotide incorporation was reduced and that of UMP nucleotide was increased giving a ratio of 1:188.
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PMID:Transcription of rat liver chromatin by Escherichia coli RNA polymerase: template properties after protein restriction. 36 67

Atypical eukaryotic RNA polymerase activity was demonstrated in nuclei of Crypthecodinium cohnii, a eukaryote devoid of histones. Nuclei were isolated from growing cultures of this dinoflagellate and assayed for endogenous RNA polymerase (EC 2.7.7.6) activity. There was a biphasic response to Mg2+ with optima at approximately 0.01 and 0.02 M MgCl2, but in contrast to other eukaryotic RNA polymerases, this enzyme activity was inhibited by low MnCl2 concentrations. In the presence of 0.01 M MgCL2 the optimum (NH4)2SO4 concentration was 0.025 M, a concentration at which the nuclei were lysed. Incorporation of [3H]UMP into RNA was inhibited by actinomycin D and dependent on the presence of undergraded DNA, and the reaction product was sensitive to ribonuclease and KOH digestion. Omission of one or more ribonucleoside triphosphates greatly reduced the incorporation. Only a slight enhancement of RNA polymerase activity resulted from the addition of various amounts of native and denatured calf thymus DNA. Spermine caused a marked inhibition while spermidine had little effect on RNA synthesis in the nuclei. Under the optimum conditions described in the present paper the nuclei incorporated approximately 3 pmoles of [3H]UMP/microgram DNA at 25 C for 15 min, and approximately 80% of this activity was inhibited by the eukaryotic RNA polymerase II inhibitor, alpha-amanitin (20 micrograms/ml). A unique situation therefore exists in C. cohnii nuclei, in which absence of histones (a prokaryotic trait) is combined with alpha-amanitin-sensitive RNA polymerase activity (a eukaryotic trait).
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PMID:RNA synthesis in isolated nuclei of the dinoflagellate Crypthecodinium cohnii. 57 93

Evidence is presented from three experimental systems to support the allosteric model of Walker et al. (1975) (Biochem. J. 147, 425-433) which explains the substrate-concentration-dependent transition observed in the RNAase (ribonuclease)-catalysed hydrolysis of 2':3'-cyclic CMP (cytidine 2':3'-cyclic monophosphate). 1. Kinetic studies of the initial rate of hydrolysis of 2':3'-cyclic CMP show that the midpoint of the transition shifts to lower concentrations of 2':3'-cyclic CMP in the presence of the substrate analogues 3'-CMP, 5'-CMP, 3'-AMP, 3'-UMP and Pi; 2'-CMP and 2'-UMP do not cause such a shift. 2. Trypsin-digestion studies show that a conformational change in RNAase to a form less susceptible to tryptic inactivation is induced in the presence of the substrate analogues 3'-CMP, 5'-CMP, 3'-AMP, and 3'-UMP. 2'-CMP, 2'-AMP and 2'-UMP do not induce this conformational change. 3. Equilibrium-dialysis experiments demonstrate the multiple binding of molecules of 3'-CMP, 3'-AMP and 5'-AMP to a molecule of RNAase. 2'-CMP binds the ratio 1:1 over the analogue concentration range studied.
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PMID:Further evidence for an allosteric model for ribonuclease. 127 91

We have isolated Escherichia coli transcription complexes, paused in the presence and absence of Nus A, which contain RNA substituted at every UMP residue with a photocrosslinking nucleotide analog. The pause site is immediately downstream from an RNA stem-loop structure, and although pausing occurs in the absence of Nus A, it is substantially enhanced in the presence of Nus A. We have analyzed the secondary structure of this RNA and show that the analog does not interfere with the formation of the normal stem-loop structures. Additionally, the analog substrate does not alter transcriptional pausing, in the presence or absence of Nus A, indicating that Nus A recognition of the transcription complex is not affected by the presence of the crosslinking groups in the RNA. Ribonuclease digestion of the RNA in paused complexes identifies two accessible regions, two nucleotides in the loop and one near the base of the upstream side of the stem-loop. Cleavage at one loop nucleotide is enhanced by Nus A, while the nucleotide near the base of the stem-loop is partially protected. Upon irradiation of the transcription complex, Nus A is not photoaffinity labeled by the RNA, even at a high molar ration to RNA polymerase (250:1). Both the beta and beta' subunits are labeled, however, indicating that the putative stem-loop binding domain on the core polymerase involves both subunits. Because the nucleotide protected from ribonuclease by Nus A is very near two analogs, yet Nus A is not crosslinked to the RNA, it is unlikely that Nus A could be protecting this position through direct contact. Furthermore, analog is substituted at positions in both the loop and at several positions in the stem, and again, no crosslinking to Nus A is observed. We conclude that enhancement of pausing by Nus A probably does not require direct interaction with the bases in the RNA stem-loop.
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PMID:RNA-protein interactions in a Nus A-containing Escherichia coli transcription complex paused at an RNA hairpin. 170 33

1. Isolated rat-liver nuclei incorporated [(14)C]UMP into RNA when incubated in the presence of Mg(2+) and all four ribonucleoside triphosphates. The addition of bentonite to the system diminished the breakdown of the newly synthesized RNA. 2. AMP and CMP were incorporated in the absence of the other added triphosphates, and in the presence of deoxyribonuclease. 3. RNA synthesized in the presence of Mg(2+) contained a high proportion of CMP and GMP, and sedimented in the regions of ribosomal RNA and of heavier molecules. About 1% of this RNA hybridized with homologous DNA, and hybrid formation was more effectively inhibited by nuclear RNA than by ribosomal RNA. 4. RNA synthesized in the presence of Mn(2+) plus ammonium sulphate had a composition intermediate between that of ribosomal RNA and of DNA, and about 4% of this RNA formed hybrids with DNA. 5. Less than 2% of the newly synthesized RNA was capable of forming ribonuclease- and deoxyribonuclease-resistant complexes. 6. It was concluded that the newly synthesized RNA arose as a result of an asymmetric process and included both ribosomal and DNA-like species.
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PMID:Characterization of the ribonucleic acid synthesized by isolated rat-liver nuclei. 603 Feb 79

A base-specific ribonuclease (RNase) Ru (EC 3.1.27.5) was isolated and purified from Rhizopus niveus in a yield of 17% by the procedures of acetone precipitation, column chromatography on Duolite A-2, DEAE-cellulose, CM-cellulose, and 2'(3')-aminohexyl-5'-UMP-agarose. The enzyme was shown to be homogeneous by polyacrylamide disc electrophoresis. The amino- and carboxyl-terminal amino acids of the enzyme were determined to be an arginine and an aspartic acid, respectively. The enzyme has a base specificity: it released only 3'-UMP from yeast RNA or poly(U) and, in addition, small amounts of 3'-CMP from poly(C).
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PMID:Purification of a base-specific ribonuclease Ru from Rhizopus niveus. 616 47

A soluble RNA-dependent RNA polymerase was purified from the cytoplasm of poliovirus-infected HeLa cells. A single virus-specific protein designated as p63 (or NCVP4) copurified with this activity. The purified polymerase was free of ribonuclease activity and was shown to copy poliovirion RNA when oligo(U) was added to the in vitro reaction mixture. Characterization of the product RNA by electrophoresis in methylmercury (II) hydroxide-agarose gels showed that genome-sized copies of poliovirion RNA were synthesized in vitro by the purified polymerase. The product RNA was shown to be heteropolymeric, complementary to virion RNA, and covalently linked to oligo(U). The product RNA contained the expected distribution of UMP and GMP containing dinucleotide pairs which included a very low frequency of CpG pairs. The amount, size distribution, and rate of synthesis of product RNA was very dependent on the in vitro reaction conditions. Full sized product RNA was synthesized in about 6 min when reaction conditions were used that yielded maximum elongation rates (pH 8.0, 7 mM Mg2+, 37 degrees C). Under these conditions, most of the product RNA recovered from a 1-h reaction was full sized. Thus, the polymerase was found to specifically initiate synthesis at the 3'-end of the template using an oligo(U) primer and to carry out an elongation reaction at about 1250 nucleotides/min that resulted in the synthesis of full sized product RNA.
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PMID:Genome-length copies of poliovirion RNA are synthesized in vitro by the poliovirus RNA-dependent RNA polymerase. 627 40

In experiments to determine the mechanism of glucocorticoid induced decreases in thymic transcription, adrenalectomized rats were injected with hydrocortisone (50 mg/kg) or vehicle. Thymic nuclei were used to prepare chromatins and soluble nuclear extracts containing RNA polymerase II for cross-over experiments. With calf thymus DNA or rat thymic chromatins as templates limiting RNA polymerase II from rats treated with hydrocortisone 3 h previously had 130% of the [3H]UMP incorporating activity of RNA polymerase II from control vehicle treated rats. In contrast, limiting RNA polymerase II from rats treated with hydrocortisone 12 h previously had 40-50% of the [3H]UMP incorporating activity of RNA polymerase II from controls. When limiting calf thymus DNA or rat thymic chromatins were used in 12 h cross-over experiments. Individual RNA polymerases II produced equal [3H]UMP incorporations, but RNA polymerase II activity from hydrocortisone treated rats was again only 50% of control values. Thus with template saturation, RNA polymerase II from hydrocortisone treated rats could not transcribe rat thymic chromatin templates to the level achieved by RNA polymerase II from control rats. This suggests that the activity, rather than the amount, of RNA polymerase II from hydrocortisone treated rats is reduced. Double reciprocal plots of [3H]UMP incorporation on rat chromatins with increasing concentrations of RNA polymerases II were made at 12 h. The apparent Km for RNA polymerase II from animals treated with hydrocortisone was identical to that of RNA polymerase II from controls, but the Vmax of RNA polymerase II from hydrocortisone treated animals was reduced. These data suggest the presence of an inhibitor of transcription or an RNA polymerase II defective in its capacity to initiate and/or elongate RNA transcripts. Further experiments demonstrated that these effects were not due to steroid induced changes in ribonuclease or protease activities.
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PMID:Studies on the mechanism of glucocorticoid hormone induced alterations in rat thymic transcription--I. Evidence from reconstituted cross-over transcription assays that sequential increases and decreases in transcription are due to changes in the activity of RNA polymerase II rather than in the activity of chromatin template. 667 54

Viral replication complexes (RCs) were gradient-purified from cowpea mesophyll protoplasts 21 h after inoculation with alfalfa mosaic virus. These membranous structures incorporate [32P]UMP into double- and single-stranded RNAs in the absence of added template. When coat protein is added prior to the reaction the incorporation in both RNA fractions is stimulated several times. Part of the single-stranded product RNAs are released from the RCs. The stimulation of incorporation in high molecular mass RNAs by coat protein can be mimicked only to a certain extent by addition of a ribonuclease inhibitor or of an excess of viral RNA prior to the reaction. This shows that the coat protein is not only protecting the product of the RCs against degradation by ribonuclease, but that it is stimulating the synthesis and release of viral RNAs from RCs as well. This leads to the hypothesis that with alfalfa mosaic virus some coat protein is necessary for the release of messenger RNA from the RC. The hypothesis explains why the viral genome RNAs, although they are of messenger polarity, cannot start a replication cycle in the absence of coat protein: RCs containing the parental RNAs could be formed but no amplification of them could take place since no messenger RNAs needed for the production of viral polymerase proteins would be released into the cytoplasm.
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PMID:Coat protein stimulates replication complexes of alfalfa mosaic virus to produce virion RNAs in vitro. 826 61

Different modes of binding of pyrimidine monophosphates 2'-UMP, 3'-UMP, 2'-CMP and 3'-CMP to ribonuclease (RNase) A are studied by energy minimization in torsion angle and subsequently in Cartesian coordinate space. The results are analysed in the light of primary binding sites. The hydrogen bonding pattern brings out roles for amino acids such as Asn44 and Ser123 apart from the well known active site residues viz., His12,Lys41,Thr45 and His119. Amino acid segments 43-45 and 119-121 seem to be guiding the ligand binding by forming a pocket. Many of the active site charged residues display considerable movement upon nucleotide binding.
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PMID:Computer modelling studies of ribonuclease A-pyrimidine nucleotide complexes. 828 64


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