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At least 127 records · Page 7Linked to original sources
PubMed2005

A convenient and sensitive fluorescence resonance energy transfer assay for RNase L and 2',5' oligoadenylates.

Interferon action against viruses is mediated in part through a ribonucleic acid (RNA) decay pathway known as the 2-5A system. Unusual 5'-triphosphorylated, 2',5'-linked oligoadenylates (2-5A) are produced in mammalian cells by interferon-inducible 2-5A synthetases (OAS) in response to viral double-stranded RNA. 2-5A activates a uniquely regulated endoribonuclease, RNase L, resulting in the cleavage of single-stranded viral and cellular RNAs, thus suppressing viral replication. In addition, RNase L was recently identified as a strong candidate for the hereditary prostate cancer 1 susceptibility allele. RNase L is ubiquitously expressed at basal levels in a wide range of mammalian cell types. Conventional RNase L assays, which can be inconvenient and cumbersome, typically involve cleavage of radioactively labeled RNA species or of endogenous ribosomal RNA. Here we describe a convenient, rapid, nonradioactive, and relatively inexpensive fluorescence resonance energy transfer (FRET) that may be used to accurately measure levels of either 2-5A or RNase L activity with a high degree of specificity and sensitivity. The RNA probe used in the FRET assay was designed based on a region of respiratory syncytial genomic RNA. We demonstrate the utility of our FRET assay with several novel biostable analogs of 2-5A.

2',5'-Oligoadenylate Synthetase↗
PubMed1996

A mammalian 2-5A system functions as an antiviral pathway in transgenic plants.

Resistance to virus infections in higher vertebrates is mediated in part through catalysis of RNA decay by the, interferon-regulated 2-5A system. A functional 2-5A system requires two enzymes, a 2-5A synthetase that produces 5'-phosphorylated, 2',5'-linked oligoadenylates (2-5A) in response to double-stranded RNA, and the 2-5A-dependent RNase L. We have coexpressed these human enzymes in transgenic tobacco plants by using a single plasmid containing the cDNAs for both human RNase L and a low molecular weight form of human 2-5A synthetase under control of different, constitutive promoters. Expression of the human cDNAs in the transgenic plants was demonstrated from Northern blots, by specific enzyme assays, and by immunodetection (for RNase L). Infection of leaves, detached or in planta, of the coexpressing transgenic plants by tobacco mosaic virus, alfalfa [correction of alfafa] mosaic virus, or tobacco etch virus resulted in necrotic lesions. In contrast, leaves expressing 2-5A synthetase or RNase L alone and leaves containing the plasmid vector alone produced typical systemic infections. While alfalfa mosaic virus produced lesions only in the inoculated leaves regardless of the concentration of virus in the inoculum, high, but not low, levels of tobacco etch virus inoculum resulted in escape of virus to uninoculated leaves. Nevertheless, there was a substantial reduction of tobacco etch virus yield as measured by ELISA assay in the coexpressing transgenic plants. These results indicate that expression of a mammalian 2-5A system in plants provides resistance to virus infections.

Adenine Nucleotides↗
PubMed2005

Exoribonuclease R interacts with endoribonuclease E and an RNA helicase in the psychrotrophic bacterium Pseudomonas syringae Lz4W.

Endoribonuclease E, a key enzyme involved in RNA decay and processing in bacteria, organizes a protein complex called degradosome. In Escherichia coli, Rhodobacter capsulatus, and Streptomyces coelicolor, RNase E interacts with the phosphate-dependent exoribonuclease polynucleotide phosphorylase, DEAD-box helicase(s), and additional factors in an RNA-degrading complex. To characterize the degradosome of the psychrotrophic bacterium Pseudomonas syringae Lz4W, RNase E was enriched by cation exchange chromatography and fractionation in a glycerol density gradient. Most surprisingly, the hydrolytic exoribonuclease RNase R was found to co-purify with RNase E. Co-immunoprecipitation and Ni(2+)-affinity pull-down experiments confirmed the specific interaction between RNase R and RNase E. Additionally, the DEAD-box helicase RhlE was identified as part of this protein complex. Fractions comprising the three proteins showed RNase E and RNase R activity and efficiently degraded a synthetic stem-loop containing RNA in the presence of ATP. The unexpected association of RNase R with RNase E and RhlE in an RNA-degrading complex indicates that the cold-adapted P. syringae has a degradosome of novel structure. The identification of RNase R instead of polynucleotide phosphorylase in this complex underlines the importance of the interaction between endo- and exoribonucleases for the bacterial RNA metabolism. The physical association of RNase E with an exoribonuclease and an RNA helicase apparently is a common theme in the composition of bacterial RNA-degrading complexes.

Adenosine Triphosphate↗
PubMed1990

Mechanism of post-segregational killing by the hok/sok system of plasmid R1: sok antisense RNA regulates formation of a hok mRNA species correlated with killing of plasmid-free cells.

The hok/sok system of plasmid R1, which mediates plasmid stabilization via killing of plasmid-free segregants, encodes two genes: hok and sok. The hok gene product is a potent cell-killing protein. The expression of hok is regulated post-transcriptionally by the sok gene-encoded repressor, an antisense RNA complementary to the hok mRNA leader region. We show here that the hok mRNA is very stable, while the sok RNA decays rapidly. We also observe a new hok mRNA species which is 70 nucleotides shorter in the 3'-end than the full-length hok transcript. The appearance of the truncated hok mRNA was found to be regulated by the sok antisense RNA. Furthermore, the presence of the truncated hok mRNA was found to be correlated with efficient expression of the Hok protein. On the basis of these findings, we propose an extended model in order to explain the killing of plasmid-free segregants by the hok/sok system.

Base Sequence↗
PubMed2001

AU binding proteins recruit the exosome to degrade ARE-containing mRNAs.

Inherently unstable mammalian mRNAs contain AU-rich elements (AREs) within their 3' untranslated regions. Although found 15 years ago, the mechanism by which AREs dictate rapid mRNA decay is not clear. In yeast, 3'-to-5' mRNA degradation is mediated by the exosome, a multisubunit particle. We have purified and characterized the human exosome by mass spectrometry and found its composition to be similar to its yeast counterpart. Using a cell-free RNA decay system, we demonstrate that the mammalian exosome is required for rapid degradation of ARE-containing RNAs but not for poly(A) shortening. The mammalian exosome does not recognize ARE-containing RNAs on its own. ARE recognition requires certain ARE binding proteins that can interact with the exosome and recruit it to unstable RNAs, thereby promoting their rapid degradation.

3' Untranslated Regions↗
PubMed1995

Catalytic cleavage of an RNA target by 2-5A antisense and RNase L.

2-5A antisense (2-5A-AS) molecules are chimeric oligonucleotides that cause 2-5A-dependent RNase (RNase L) to catalyze the selective cleavage of RNA in human cells. These composite nucleic acids consist of a 5'-monophosphorylated, 2',5'-linked oligoadenylate known as 2-5A (an activator of RNase L) covalently attached to antisense 3',5'-oligodeoxyribonucleotides. Here, we characterize the targeted cleavage of the double-stranded RNA-dependent protein kinase (PKR) mRNA by purified, recombinant human RNase L. A 2-5A-AS chimera, which contains complementary sequence to PKR mRNA, and unmodified 2-5A, which causes general RNA decay, were about 20- and 40-fold more active, respectively, than 2-5A-AS chimeras in which the DNA domains are not complementary to sequences in PKR mRNA. Directed cleavage was efficient because each 2-5A-AS chimera targeted many RNA molecules. Moreover, RNase L caused the catalytic cleavage of the RNA target (kcat of approximately 7 s-1). The precise sites of PKR mRNA cleavage caused by 2-5A-AS were mapped, using a primer extension assay, to phosphodiester bonds adjacent to the 3' terminus of the chimera binding site (5' on the RNA target) as well as within the chimera's oligonucleotide binding site itself. The selectivity of this approach is shown to be provided by the antisense arm of the chimera, which places the RNA target in close proximity to the RNase.

Base Sequence↗
PubMed1994

ard-1: a human gene that reverses the effects of temperature-sensitive and deletion mutations in the Escherichia coli rne gene and encodes an activity producing RNase E-like cleavages.

The Escherichia coli rne gene affects a variety of bacterial functions, including the activity of RNase E. We report the existence of a human gene (ard-1, for activator of RNA decay) that complements temperature-sensitive and deletion mutations of rne in E. coli, allowing growth of rne-defective cells, correcting abnormal cell shape, activating chemical decay of bulk mRNA, and producing site-specific cleavages characteristic of RNase E in vivo and in vitro. ard-1 encodes a highly basic 13.3-kDa proline-rich peptide that has features in common with Rne and also with eukaryotic proteins implicated in RNA binding and macromolecular transport.

Amino Acid Sequence↗
PubMed2003

Pathways of post-transcriptional gene regulation in mammalian germ cell development.

Male germ cell development is orchestrated by complex and disparate patterns of gene expression operating in different cell types. The mechanisms of gene expression underlying these have been dissected in the mouse because of its readily available genetics. These analyses have shown that as well as the traditional transcriptional mechanisms, post-transcriptional regulatory pathways of gene expression are essential for mouse spermatogenesis. Proteins essential for germ cell development have been identified which operate at different points throughout the life cycle of RNA from pre-mRNA splicing to translation and RNA decay in the cytoplasm. Recent data suggests that these post-transcriptional pathways respond to environmental cues via signalling pathways.

Animals↗
PubMed2005

The 2',5'-oligoadenylate synthetase 1b is a potent inhibitor of West Nile virus replication inside infected cells.

The 2',5'-oligoadenylate synthetase (OAS) proteins associated with endoribonuclease RNase L are components of the interferon-regulated OAS/RNase L system, which is an RNA decay pathway known to play an important role in the innate antiviral immunity. A large body of evidence suggests a critical role for the 1b isoform of the mouse Oas gene (Oas1b) in resistance to West Nile virus (WNV) infection in vivo. WNV is a positive, single-stranded RNA virus responsible for severe encephalitis in a large range of animal species and humans. To investigate the molecular basis for the sensitivity of WNV to the Oas1b antiviral pathway, we established a stable mouse fibroblastic cell clone that up-regulates Oas1b protein expression under the control of the Tet-Off expression system. We showed that murine cells respond to Oas1b expression by efficiently inhibiting WNV replication. The antiviral action of Oas1b was essentially restricted to the early stages in virus life cycle. We found that the inability of WNV to productively infect the Oas1b-expressing cells was attributable to a dramatic reduction in positive-stranded viral RNA level. Thus, Oas1b represents an antiviral pathway that exerts its inhibitory effect on WNV replication by preventing viral RNA accumulation inside infected cells.

2',5'-Oligoadenylate Synthetase↗
PubMed2004

Global analysis of Escherichia coli RNA degradosome function using DNA microarrays.

RNase E, an essential endoribonuclease of Escherichia coli, interacts through its C-terminal region with multiple other proteins to form a complex termed the RNA degradosome. To investigate the degradosome's proposed role as an RNA decay machine, we used DNA microarrays to globally assess alterations in the steady-state abundance and decay of 4,289 E. coli mRNAs at single-gene resolution in bacteria carrying mutations in the degradosome constituents RNase E, polynucleotide phosphorylase, RhlB helicase, and enolase. Our results show that the functions of all four of these proteins are necessary for normal mRNA turnover. We identified specific transcripts and functionally distinguishable transcript classes whose half-life and abundance were affected congruently by multiple degradosome proteins, affected differentially by mutations in degradosome constituents, or not detectably altered by degradosome mutations. Our results, which argue that decay of some E. coli mRNAs in vivo depends on the action of assembled degradosomes, whereas others are acted on by degradosome proteins functioning independently of the complex, imply the existence of structural features or biochemical factors that target specific classes of mRNAs for decay by degradosomes.

Bacterial Proteins↗
PubMed1964

IONIZING RADIATION: EFFECT ON GENETIC TRANSCRIPTION.

Cells of Escherichia coli grown on maltose can be induced by the addition of thiomethyl galactoside to produce beta-galactosidase. If cells are irradiated shortly after induction, the transcription of the DNA ceases, and the enzyme produced by the messenger RNA is observed to reach a maximum. From these data the calculated half-life of unstable messenger RNA is given over a temperature range from 8.1 minutes at 10 degrees C to 0.7 minute at 45 degrees C. The kinetics of cessation of transcription give information on both meassenger RNA decay and rate of transcription. Arrhenius graphs for both these rates are given, and the activation energies mtieasured are 11,000 calories per mole for decay and 22,000 calories per mole for transcription. This relation to temperature is characteristic of enzymatic behavior.

DNA↗
PubMed1996

Nonsense mutations inhibit RNA splicing in a cell-free system: recognition of mutant codon is independent of protein synthesis.

Mutations resulting in premature termination codons reduce the corresponding mRNA levels. We describe a cell-free system in which depletion of the mutant immunoglobulin kappa mRNA pool correlates with inefficient splicing and not with RNA decay. Splicing deficiency does not depend on the sequence surrounding the in-frame nonsense codon and can be partially corrected by mutating the methionine initiation codon. Despite the apparent link between translation and low mutant mRNA levels, inefficient splicing is not dependent on protein synthesis. Abnormal splicing of mutant immunoglobulin RNA is observed with B-cell but not with HeLa or T-cell extracts. A nonsense mutant beta-globin RNA is normally spliced by B-cell extract. We propose that the phenomenon exhibits tissue and gene specificity.

Animals↗
PubMed1994

Number and location of AUUUA motifs: role in regulating transiently expressed RNAs.

Many RNAs coding for either cytokines or oncogenes are unstable and have a short half-life (t1/2). The AUUUA motif is a highly conserved sequence and is repeated three or more times in the 3' untranslated region (3'UTR) of RNAs encoding many of these short-lived cytokines and oncogenes. These sequences can confer instability. In this study, we investigated the role of number and location of AUUUA motifs in stabilization of RNA. We introduced 1xATTTA, 2xATTTA, ATTTTTTTA (second adenosine of 2xATTTA was substituted with a thymidine), 3xATTTA, 5xATTTA, 7xATTTA [AT-rich sequence from granulocyte-macrophage colony-stimulating factor [GM-CSF] gene (AT-62)], and GC-62 (GC sequences were substituted for ATTTA sequences in the 7xATTTA) into the 3'UTR of rabbit beta-globin (R beta G) gene. This construct also contained the neomycin-resistance gene. These expression vectors were transfected into human lung fibroblasts (W138), which constitutively expressed low levels of GM-CSF mRNA. Stable transfectants were selected by growth in G418. Northern blot analysis of actinomycin D-treated, stably transfected cells demonstrated that the number of AUUUA sequences correlated with rapidity of turnover of the chimeric R beta G mRNA. The rank order of stability was GC-62 = 1xATTTA = 2xATTTA (no RNA decay at 4 hours) > 3xATTTA = 5xATTTA (t1/2, 4 hours) > 7xATTTA (t1/2, 2 hours). Stability of mRNA of R beta G also was reduced (t1/2, 2 to 4 hours) when AT-62 was introduced into the second exon of R beta G gene. In these same cells, the t1/2 of GM-CSF RNA was approximately 10 to 15 minutes, suggesting that the AUUUA motifs cannot alone account for the rapid degradation of this cytokine mRNA. Phorbol diesters, including 12-0-tetradecanoyl phorbol 13-acetate (TPA), stabilize a variety of transiently expressed RNAs, including GM-CSF RNA. We found that TPA markedly increased (> 30-fold) the accumulation of GM-CSF RNA. In contrast, TPA was unable to stimulate the levels of the chimeric R beta G when either 1x, 2x, 3x, or 5xATTTA motifs were fused to 3'UTR, or when either AT-62 or GC-62 control sequences were fused to the second exon. The chimeric beta-globin construct with either AT-62 or ATTTTTTTA in the 3'UTR had only an approximately twofold to threefold increase in accumulation.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed2006

The exosome: a macromolecular cage for controlled RNA degradation.

The exosome, a large multisubunit complex with exoribonucleic activity, emerges as the central 3' RNA degradation and processing factor in eukaryotes and archaea. But how are the many RNA substrates of the exosome degraded in a processive, yet controlled manner? Recent functional and structural progress shows that the exosome is a macromolecular cage, where the nuclease active sites are situated in a central processing chamber. A narrow entry pore controls access to the active sites in the processing chamber and prevents uncontrolled RNA decay. The emerging mechanism of exosome function suggests a strikingly parallel architectural concept to protein degradation by proteasomes.

Archaea↗
PubMedDate not supplied

[The effect of exogenous RNA and their fragments on yeast beta-galactosidase activity].

It is shown that a degradation level of exogenic high-polymeric RNA does not change their stimulating effect on beta-galactosidase synthesis in yeast protoplasts. Nucleoside monophosphates are a product of RNA degradation which promotes an increase in the beta-galactosidase activity. The exogenic RNA is established to act at the transcription level. RNA and its degradation products stimulate the beta-galactosidase synthesis without any effect on the intensity of the total RNA and protein synthesis in the yeast protoplasts. All mentioned permitted a conclusion that products of RNA decay participate in the regulation of the beta-galactosidase synthesis of yeast. A possible mechanism of their action is under discussion.

Galactosidases↗
PubMed2006

The early HCV RNA dynamics in patients with acute hepatitis C treated with pegylated interferon-alpha2b.

Interferon and pegylated interferon (peg-IFN) are highly effective in patients with acute hepatitis caused by hepatitis C virus (acute hepatitis C, AHC), but the optimal timing of treatment is still under debate. In this open-labelled, uncontrolled trial, 19 patients with AHC, including 12 intravenous drug users (IVDUs), were treated early in the course of the infection with peg-IFN-alpha2b for 12 weeks. Diagnosis was made according to standardized criteria. The HCV RNA decay was analysed during the first 4 weeks of treatment by quantitative branched-DNA and by qualitative RT-PCR. Of the patients, 11 (58%) had genotype 1. Sustained virological response (SVR) was achieved in 14 out of 19 patients (74%) and the mean time to achieve a negative RT-PCR for HCV RNA was 2.5 weeks. The SVR was associated by univariate analysis with peg-IFN dosage < or = 1.33 microg/kg/week (P = 0.026) and HCV RNA level at onset of therapy (P = 0.017). Using a logistic regression model, only peg-IFN dosage > or = 1.33 microg/kg/weekly was significantly associated with SVR (P = 0.0379, OR: 14.7; 95% CI: 1.16-185.2). The SVR was 100% and 83.3%, respectively, in genotype 1 and non-1 infected patients treated with a dosage equal to or higher than 1.33 microg/kg, compared with 40% and 50%, respectively, in those who received a lower dosage. Efforts should be made to propose a 12-week treatment with peg-IFN-alpha2b for AHC, and to maximize peg-IFN dosage. Early treatment is associated with early disappearance of HCV RNA.

Acute Disease↗
PubMed1994

HIV-1 TAR RNA has an intrinsic ability to activate interferon-inducible enzymes.

The TAR sequence at the 5'-termini of all HIV-1 mRNA species forms a stable structure that is responsible for both transcriptional and translational regulation of HIV-1. Previously we and others reported that purified TAR RNA synthesized by in vitro transcription could activate two interferon-induced enzymes, the protein kinase (PKR) and 2-5A-synthetase. Because the PKR- and 2-5A-systems block protein synthesis initiation and induce RNA decay, respectively, these findings suggested mechanisms for the control of HIV-1 replication by the interferon system. To determine if contaminating dsRNA from in vitro transcription reactions was responsible for this effect, as suggested by Gunnery et al. 1990, (Proc., Natl. Acad. Sci. USA 87, 8687), we have reexamined these findings using chemically synthesized TAR (nucleotides +1 to +57). TAR RNA is shown here to have an intrinsic ability to activate PKR and 2-5A-synthetase. In contrast, a mutant form of TAR designed to have a disrupted secondary structure did not stimulate either enzyme. Chemically synthesized TAR mimicked other dsRNA species in its ability to activate and inhibit PKR at low and high RNA concentrations, respectively. HIV-1 TAT protein inhibited activation of PKR by HIV-1 TAR RNA suggesting an escape mechanism for the virus.

2',5'-Oligoadenylate Synthetase↗
PubMed2003

Selective labeling and detection of specific mRNA in a total-RNA sample.

We report a unique approach to selectively label and detect specific RNA using its internal sequence, without separation, reverse transcription, and/or polymerase chain reaction. This approach is especially useful for individual mRNA labeling and detection. To expose mRNA internal sequence for selective labeling and detection, RNase H digestion is used to remove the 3(')-common sequences. We have designed a DNA-2(')-O-Me-RNA hybrid as the template for both RNase H digestion and Klenow extension and have found buffer conditions for both enzymes. Sharing the same template and buffer by these two enzymes largely simplifies experimental procedures. Using this approach, lacZ mRNA was selectively labeled and detected in the presence of thousands of mRNAs. We have successfully demonstrated for the first time the direct labeling and detection of an individual mRNA in a total-RNA sample. The detection sensitivity can reach up to attomole level (5 x 10(-18)mole). This method has great potential in RNA decay and metabolic regulation studies via individual mRNA labeling and in methodology of mRNA direct detection on microchip and direct gene expression profiling, without reverse transcription and polymerase chain reactions.

Biochemistry↗