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:3.1.27.5 (RNase)
17,967 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

Proteins bound to SV 40 DNA in sarkosyl-treated nuclei have been studied. The major component is topoisomerase I, a 60-70 kDa protein which possesses a strong DNA-nicking activity in the presence of sarkosyl and camptothecin. An SV 40 DNA fraction containing sarkosyl-resistant proteins constitutes 2 to 3% of the total nuclear SV 40 DNA and is enriched in transcriptionally active DNA (as monitored by distribution of RNase-resistant in vivo pulse-labeled RNA). An SV 40 DNA fraction, which is nicked due to covalent binding of topoisomerase I upon sarkosyl treatment is also enriched in transcriptionally active DNA. Topoisomerase I cleavage sites on SV 40 DNA which arise following sarkosyl treatment of nuclei or camptothecin treatment of infected cells have been mapped. The strongest site is located at nucleotide 381 on the non-coding strand and is framed by nuclease hypersensitive sites.
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PMID:Topoisomerase I is associated with the regulatory region of transcriptionally active SV 40 minichromosomes. 169 56

Proteins bound to SV40 DNA in sarkosyl-treated nuclei have been studied. The major component is topoisomerase I, a 60-70 kDa protein, which possesses a strong DNA-nicking activity in the presence of detergents. An SV40 fraction containing tightly bound proteins constitutes 2-3% of the total nuclear SV40 DNA and is enriched in transcriptionally active DNA as monitored by distribution of RNase-resistant in vivo pulse labelled RNA. A small SV40 DNA fraction which is relaxed due to covalent binding of topoisomerase I upon sarkosyl treatment of isolated nuclei is also enriched in transcriptionally active DNA. In vivo topoisomerase I cleavage sites on SV40 DNA have been located by indirect end-labelling. Two preferential binding sites have been detected, both in the SV40 regulatory region.
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PMID:[Topoisomerase I is connected with the regulatory zone of transcripted active mini-chromosomes of the SV40 virus]. 254 94

DNA topoisomerases, nuclear enzymes that regulate DNA topology, are recognized as the primary targets of effective anti-tumor drugs. These enzymes may also have a role in the repair of DNA damage induced by alkylating agents and platinum compounds; therefore, their expression may be a determinant of tumor response to chemotherapy. Our study was undertaken in an attempt to establish a correlation between the enzyme expression and response of ovarian cancer to cisplatin-based chemotherapy. The expression of topoisomerase I, II alpha and II beta genes was assessed by RNase protection assay in tumor specimens obtained from 37 untreated patients with advanced epithelial ovarian cancer at initial surgery and from 13 pre-treated patients at subsequent laparotomy. The expression levels were compared with those found in 5 specimens from benign ovarian tissue and 5 specimens from normal ovarian tissue. The expression levels in untreated patients were used to establish a correlation with response to high-dose cisplatin therapy. A significant intertumor variability of mRNA expression was noted for all the genes examined. However, a comparison of median values indicated a remarkable increase of expression in malignant tumors over benign or normal tissues only for topoisomerase II alpha. This change is not related to alterations or amplification of topoisomerase II alpha gene. Interestingly, a correlation was found between tumor response to chemotherapy and the expression level of the isoform alpha (but not of topoisomerase II beta and topoisomerase I). The observed correlation suggests a contribution of the enzyme in determining tumor sensitivity. Alternatively, increased expression levels of the alpha isoenzyme gene in responsive tumors might reflect higher fractions of proliferating tumor cells that may be more drug-sensitive than resting cells.
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PMID:Gene expression of DNA topoisomerases I, II alpha and II beta and response to cisplatin-based chemotherapy in advanced ovarian carcinoma. 875 4

Transcription through tandemly arranged nucleosomes was studied to determine the frequency at which the nucleosomes would disrupt and cause displacement of the associated histones to a competitor DNA. In order to more effectively preserve topological effects, the template that was used in the in vitro transcription system was a large covalently, closed circular plasmid (8.9 kb). The plasmid contained two promoters for T7 RNA polymerase, each separated by 4.4 kb, and transcription was done in the presence of topoisomerase I at physiological ionic strength. Nucleosome disruption was observed at an approximate frequency of 1 in 4 nucleosomes such that after several rounds of transcription on the plasmid 80% of the nucleosomes were disrupted. Unexpectedly, all four histones were found associated with the RNA rather than the competitor DNA. The histones bound the competitor DNA only after removal of the RNA by RNase A treatment. By analyzing the topological state of the competitor DNA, it was observed that the majority of the histones that were displaced from the RNA were able to re-form nucleosomes. Additional experiments were done to determine the reasons for the preferential binding of histones to the newly synthesized RNA. It was found that the large molecular weight RNA binds histones with an approximate 100-fold greater affinity relative to DNA when at physiological ionic strength. Within the cell, this high-affinity binding would be expected to require cellular mechanisms to regulate the interaction of RNA with histones. The relatively high frequency of displacement of all four histones during transcription is higher than what is observed in vivo and suggests that additional factors are needed to regulate this displacement. These observations are discussed and compared with previous studies that have examined the process of transcription through nucleosomes.
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PMID:Measurement of the frequency of histone displacement during the in vitro transcription of nucleosomes: RNA is a competitor for these histones. 931 78

Type I topoisomerases alter DNA topology by cleaving and rejoining one strand of duplex DNA through a covalent protein-DNA intermediate. Here we show that vaccinia topoisomerase, a eukaryotic type IB enzyme, catalyzes site-specific endoribonucleolytic cleavage of an RNA-containing strand. The RNase reaction occurs via transesterification at the scissile ribonucleotide to form a covalent RNA-3'-phosphoryl-enzyme intermediate, which is then attacked by the vicinal 2' OH of the ribose sugar to yield a free 2', 3' cyclic phosphate product. Introduction of a single ribonucleoside at the scissile phosphate of an otherwise all-DNA substrate suffices to convert the topoisomerase into an endonuclease. Human topoisomerase I also has endoribonuclease activity. These findings suggest potential roles for topoisomerases in RNA processing.
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PMID:Site-specific ribonuclease activity of eukaryotic DNA topoisomerase I. 965 6

Introduction of a single ribonucleoside immediately 5' of the scissile phosphate of a duplex DNA substrate converts eukaryotic topoisomerase I into an endoribonuclease. Here, I demonstrate that the RNase reaction is reversible. Vaccinia topoisomerase can ligate 2', 3'-cyclic phosphate and 5'-hydroxyl termini annealed to a bridging template strand. Remarkably, the ligase activity of topoisomerase does not require the active site tyrosine, implying that strand joining can occur via direct attack of the 5' hydroxyl on the cyclic phosphate without a covalent intermediate. Ligation does require other catalytic side chains on the enzyme. These findings underscore how a common ancestral mechanism of phosphoryl and nucleotidyl transfer can be harnessed to perform seemingly diverse tasks through subtle changes at the active site.
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PMID:Polynucleotide ligase activity of eukaryotic topoisomerase I. 966 Sep 57

Apoptosis of lymphocytes recognizing self-antigens is an essential mechanism to protect the organism against autoimmune diseases. Programmed cell death of susceptible B cells occurs in response to surface IgM cross-linking mediated by self-antigens. This effect can be mimicked in the Burkitt's lymphoma line BL60-2 by addition of anti-IgM antibodies. In order to identify genes with differential expression in response to the apoptotic stimulus, total RNA prepared from BL60-2 cells before and at different points in time after IgM cross-linking was used for Atlas arrays, high-density oligonucleotide microarrays (GeneChip arrays, Affymetrix) and in RNase protection assays (RPA). One of our major observations was the downregulation of six genes involved in the ligation of DNA strand breaks, like DNA ligases and DNA-PK, indicating a shutdown of DNA repair mechanisms in apoptotic cells. In addition, we found changes on mRNA level for several transcription regulators, including early growth response genes 1 and 2, TAFII30 and topoisomerase I. Furthermore, we show accumulation of mRNA for the phosphatases CD45 and DUSP5 in anti-IgM stimulated BL60-2 cells. Our data provide a basis for further analysis of the differentially expressed genes and their roles in IgM-induced B cell death as well as in apoptosis in other cellular systems.
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PMID:Downregulation of genes involved in DNA repair and differential expression of transcription regulators and phosphatases precede IgM-induced apoptosis in the Burkitt's lymphoma cell line BL60-2. 1473 93

Transcription in the absence of topoisomerase I, but in the presence of DNA gyrase, can result in the formation of hypernegatively supercoiled DNA and associated R-loops. In this paper, we have used several strategies to study the effects of elongation/termination properties of RNA polymerase on such transcription-induced supercoiling. Effects on R-loop formation were exacerbated when cells were exposed to translation inhibitors, a condition that stimulated the accumulation of R-loop-dependent hypernegative supercoiling. Translation inhibitors were not acting by decreasing (p)ppGpp levels as the absence of (p)ppGpp in spoT relA mutant strains had little effect on hypernegative supercoiling. However, an rpoB mutation leading to the accumulation of truncated RNAs considerably reduced R-loop-dependent hypernegative supercoiling. Transcription of an rrnB fragment preceded by a mutated and inactive boxA sequence to abolish the rrnB antitermination system also considerably reduced R-loop-dependent supercoiling. Taken together, our results indicate that RNA polymerase elongation/termination properties can have a major impact on R-loop-dependent supercoiling. We discuss different possibilities by which RNA polymerase directly or indirectly participates in R-loop formation in Escherichia coli. Finally, our results also indicate that what determines the steady-state level of hypernegatively supercoiled DNA in topA null mutants is likely to be complex and involves a multitude of factors, including the status of RNA polymerase, transcription-translation coupling, the cellular level of RNase HI, the status of DNA gyrase and the rate of relaxation of supercoiled DNA.
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PMID:Effects of RNA polymerase modifications on transcription-induced negative supercoiling and associated R-loop formation. 1518 24

A eukaryotic cambialistic superoxide dismutase (SOD) has been purified to homogeneity from mature seeds of the disease- and insect-resistant camphor tree (Cinnamomum camphora). Besides the known role of this SOD in protecting cells against oxidative stress, it can induce the cleavage of supercoiled double-stranded DNA into nicked and linear DNA. It can not cleave linear DNA or RNA, demonstrating there is no DNase or RNase in the purified cambialistic SOD. Furthermore, the SOD can linearize circular pGEM-4Z DNA that is relaxed by topoisomerase I. This result indicates that the DNA-cleaving activity requires substrates being topologically constrained. The supercoiled DNA-cleaving activity of the cambialistic SOD can be inhibited by either SOD inhibitor (azide) or catalase and hydroxyl radical scavengers (ethanol and mannitol). The chelator of iron, diethylenetriaminepentaacetic acid (DTPA), also inhibits the supercoiled DNA-cleaving activity. These results show that the dismutation activity is crucial for the supercoiled DNA cleavage. The modification of tryptophan residue of the cambialistic SOD with N-bromosuccinimide (NBS) shows that these two activities are structurally correlative. The reaction mechanism is proposed that the hydroxyl radical formed in a transition-metal-catalyzing Fenton-type reaction contributes to the DNA-cleaving activity. In addition, the cleavage sites in supercoiled pGEM-4Z DNA are random.
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PMID:Cleavage of supercoiled circular double-stranded DNA induced by a eukaryotic cambialistic superoxide dismutase from Cinnamomum camphora. 1534 98

It has long been known that Escherichia coli cells deprived of topoisomerase I (topA null mutants) do not grow. Because mutations reducing DNA gyrase activity and, as a consequence, negative supercoiling, occur to compensate for the loss of topA function, it has been assumed that excessive negative supercoiling is somehow involved in the growth inhibition of topA null mutants. However, how excess negative supercoiling inhibits growth is still unknown. We have previously shown that the overproduction of RNase HI, an enzyme that degrades the RNA portion of an R-loop, can partially compensate for the growth defects because of the absence of topoisomerase I. In this article, we have studied the effects of gyrase reactivation on the physiology of actively growing topA null cells. We found that growth immediately and almost completely ceases upon gyrase reactivation, unless RNase HI is overproduced. Northern blot analysis shows that the cells have a significantly reduced ability to accumulate full-length mRNAs when RNase HI is not overproduced. Interestingly, similar phenotypes, although less severe, are also seen when bacterial cells lacking RNase HI activity are grown and treated in the same way. All together, our results suggest that excess negative supercoiling promotes the formation of R-loops, which, in turn, inhibit RNA synthesis.
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PMID:RNase HI overproduction is required for efficient full-length RNA synthesis in the absence of topoisomerase I in Escherichia coli. 1545 16


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