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At least 163 records · Page 9Linked to original sources
PubMed2003

Non-Watson Crick base pairs might stabilize RNA structural motifs in ribozymes -- a comparative study of group-I intron structures.

In recent decades studies on RNA structure and function have gained significance due to discoveries on diversified functions of RNA. A common element for RNA secondary structure formed by series of non- Watson/Watson Crick base pairs, internal loops and pseudoknots have been the highlighting feature of recent structural determination of RNAs. The recent crystal structure of group-I introns has demonstrated that these might constitute RNA structural motifs in ribozymes, playing a crucial role in their enzymatic activity. To understand the functional significance of these non-canonical base pairs in catalytic RNA, we analysed the sequences of group-I introns from nuclear genes. The results suggest that they might form the building blocks of folded RNA motifs which are crucial to the catalytic activity of the ribozyme. The conservation of these, as observed from divergent organisms, argues for the presence of non-canonical base pairs as an important requisite for the structure and enzymatic property of ribozymes by enabling them to carry out functions such as replication, polymerase activity etc. in primordial conditions in the absence of proteins.

Animals↗
PubMed1991

Chloroplast RNA Stability in Chlamydomonas: Rapid Degradation of psbB and psbC Transcripts in Two Nuclear Mutants.

Toward understanding regulation of chloroplast transcript abundance, we have isolated and analyzed nuclear mutant strains of Chlamydomonas reinhardtii that lack chloroplast-encoded mRNAs for photosystem II proteins. Mutant 6.2z5 accumulates no transcripts of the psbC locus for the 43-kilodalton chlorophyll-binding protein. In mutant GE2.10, transcripts of psbB, encoding the 47-kilodalton chlorophyll-binding protein, cannot be detected [Jensen, K.H., Herrin, D.L., Plumley, F.G., and Schmidt, G.W. (1986). J. Cell Biol. 103, 1315-1325]. Also, GE2.10 does not accumulate several low molecular weight transcripts from a region of the chloroplast genome proximal to psbB. The levels of mRNAs from other chloroplast genes are not affected in either mutant. Chloroplast transcription was analyzed in permeabilized cells and by in vivo pulse labeling. Although 5[prime] ribonuclease was found as an artifactual activity of permeabilized cells, the results from both assays demonstrated that wild-type levels of psbC transcription occur in mutant 6.2z5 and that chloroplasts of GE2.10 transcribe psbB and adjacent genes. Thus, it appears that the nuclear genes that are mutated in 6.2z5 and GE2.10 encode products that, respectively, confer stability to transcripts from the psbC and the psbB regions of the chloroplast genome.

Journal Article↗
PubMed2002

Identification and characterization of nuclease-stabilized RNA molecules that bind human prostate cancer cells via the prostate-specific membrane antigen.

We have identified two synthetic oligonucleotides (aptamers) that bind to prostate cancer cells,with low nanomolar affinity, via the extracellular portion of the prostate-specificmembrane antigen (PSMA). These two specific aptamers were selected from an initial 40mer library of approximately 6 x 10(14) random-sequence RNA molecules for their ability to bind to a recombinant protein representing the extracellular 706 amino acids of PSMA, termed xPSM. Six rounds of in vitro selection were performed, enriching for xPSM binding as monitored by aptamer inhibition of xPSM N-acetyl-alpha-linked acid dipeptidase (NAALADase) enzymatic activity. By round six, 95% of the aptamer pool consisted of just two sequences. These two aptamers, termed xPSM-A9 and xPSM-A10, were cloned and found to be unique, sharing no consensus sequences. The affinity of each aptamer for PSMA was quantitated by its ability to inhibit NAALADase activity. Aptamer xPSM-A9 inhibits PSMA noncompetitively with an average K(i) of 2.1 nM, whereas aptamer xPSM-A10 inhibits competitively with an average K(i) of 11.9 nM. Distinct modes of inhibition suggest that each aptamer identifies a unique extracellular epitope of xPSM. One aptamer was truncated from 23.4 kDa to 18.5 kDa and specifically binds LNCaP human prostate cancer cells expressing PSMA but not PSMA-devoid PC-3 human prostate cancer cells. These are the first reported RNA aptamers selected to bind a tumor-associated membrane antigen and the first application of RNA aptamers to a prostate specific cell marker. These aptamers may be used clinically as NAALADase inhibitors or be modified to carry imaging agents and therapeutic agents directed to prostate cancer cells.

Antigens, Surface↗
PubMed2000

Biological stability of RNA isolated from RNAlater-treated brain tumor and neuroblastoma xenografts.

BACKGROUND: Advances in molecular biological research have led to identification of prognostic factors such as Trk mRNA expression in primitive neuroectodermal tumors of the CNS and neuroblastoma. To study prospectively the importance of these prognostic factors in large groups of homogeneously treated patients, tumor specimens of good quality must be acquired, preserved, and stored at multiple institutions. Immediate freezing of tumor biopsy samples in liquid nitrogen and storage at -70 degrees C are the most commonly used method of tissue preservation for future RNA analysis. PROCEDURE: To evaluate alternative methods of preserving tissue samples for subsequent RNA analysis, we tested a new RNA stabilization solution. Using tumor tissue of two CNS tumor and one neuroblastoma human xenografts, we compared total RNA isolated from tumor tissue stored for 7 days at room temperature in stabilization solution to that of snap-frozen tissue. The quality of the RNA was studied by spectrophotometry, gel electrophoresis, RT-PCR, and gene expression profiling. RESULTS: No major differences were observed in the quality of RNA isolated from tumor samples stored at room temperature in the RNA stabilization solution compared to snap-frozen tumor samples stored at -70 degrees C. CONCLUSIONS: High-quality RNA can be prepared from tumor tissue stored at room temperature. Whenever snap freezing is not feasible, pieces of tumor tissue can be treated with RNAlater for subsequent RNA analysis. Short-term storage and shipment of well-preserved tumor tissue are clearly feasible for all institutions, thereby facilitating large multiinstitutional studies of biological prognostic factors.

Animals↗
PubMed2003

Stability of RNA from the retina and retinal pigment epithelium in a porcine model simulating human eye bank conditions.

PURPOSE: To assess RNA stability after death in a porcine model to simulate current human eye bank techniques. METHODS: Eye bank time interval data were collected from 191 donor specimens: death to refrigeration, enucleation, and tissue processing. A control porcine eye was enucleated, retina and RPE isolated, and specimens frozen (-80 degrees C). Fourteen porcine eyes remained at room temperature for 2 hours and then cooled to 4 degrees C. Retina and RPE were isolated and frozen (-80 degrees C) at 5, 12, 24, 29, 36, 48, and 72 hours. Four globes remained in a moist chamber, five whole and five sectioned globes were immersed in RNAlater (Ambion, Austin, TX) at 5, 12, 24, or 48 hours. RNA was isolated. The 28S and 18S rRNA peaks were analyzed by electrophoresis. RT-PCR was performed on each sample. Messenger RNA for GAPDH, beta-actin, mouse rhodopsin from retina (mRHO), and RPE-65 (from RPE) were analyzed with gel electrophoresis. RESULTS: The average time from death to refrigeration was 4.2 hours, to enucleation 6.4 hours, and to tissue processing 10.7 hours. RT-PCR gel electrophoresis patterns from retinal tissue had bands of similar intensity at each interval from beta-actin, GAPDH, and RHO. Band patterns from RPE demonstrated decay of the RT-PCR gene products after 5 hours. This decay was delayed by at least 24 hours with the use of RNAlater. The 28S rRNA decay was similar for retina and RPE. CONCLUSIONS: Retinal tissue RNA can be analyzed within the time constraints of current eye bank tissue processing, whereas analysis of RPE necessitates either rapid processing or use of RNAlater. These results should aid in future studies in which eye bank tissue is used for RNA analysis.

Actins↗
PubMed2026

PTBP1 at the host-virus interface: mechanistic roles in viral RNA translation, replication, and immune modulation.

Viruses require the involvement of host RNA binding proteins for completion of important steps of their life cycle. Polypyrimidine tract binding protein 1 (PTBP1) is an RNA-binding protein found ubiquitously which performs important regulatory functions like alternative splicing, RNA stability, RNA localization, and translation by virtue of its four RRMs and shuttling between nucleus and cytoplasm. There is increasing evidence showing that many viruses make use of such regulatory roles of PTBP1 to facilitate their gene expression and replication. This review describes the existing mechanistic knowledge about the PTBP1 functions during viral infection, paying attention to the role of PTBP1 in viral RNA translation, viral RNA genome replication, and regulation of host antiviral response. Special attention is paid to the regulation by PTBP1 of IRES-dependent translation of enteroviruses and hepatitis C virus, as well as to the PTBP1 contribution to RNA stabilization, long-distance RNA interactions, and genome cyclization of flaviviruses such as dengue virus and Japanese encephalitis virus. Recent data on the PTBP1 function in coronavirus RNA metabolism are discussed as well. Furthermore, the role of PTBP1 in being both proviral and antiviral is reviewed in terms of innate immunity signalling pathways, stress granule biology, and virus-host interaction. Finally, we will explore the possibility of PTBP1 being used as a host-directed antiviral drug target despite the hurdles in doing so considering its multifunctionality as an essential cellular RNA-binding protein.

Polypyrimidine Tract-Binding Protein↗
PubMed2005

Assignment and NOE analysis of 2'-hydroxyl protons in RNA: implications for stabilization of RNA A-form duplexes.

The ribose 2'-OH hydroxyl group distinguishes RNA from DNA. The 2'-OH hydroxyl protons are responsible for differences in conformation, hydration, and thermodynamic stability of RNA and DNA oligonucleotides. Additionally, the 2'-OH group plays a central role in RNA catalysis. This important group lies in the shallow groove of RNA, where it is involved in a network of hydrogen bonds with water molecules stabilizing RNA A-form duplexes. Structural and dynamical information on 2'-OH hydroxyl protons is essential to understand their respective roles. Here we report the 2'-OH hydroxyl proton assignments for a 30mer RNA, the HIV-2 transactivation region, in water using solution NMR techniques. We provide structural information on 2'-OH hydroxyl groups in the form of orientational preferences contradicting the paradigm that the 2'-OH hydroxyl typically points away from the ribose H1' proton.

HIV Long Terminal Repeat↗
PubMed2000

Regulation of insulin-like growth factor binding protein-5 mRNA abundance in rat intestinal smooth muscle.

IGF-I increases abundance of IGFBP-5 mRNA in rat intestinal smooth muscle cells (RISM), and IGFBP-5 protein in RISM conditioned media. The translational blocker, cycloheximide, decreased the abundance of IGFBP-5 mRNA to undetectable levels, suggesting that IGFBP-5 mRNA integrity is linked to protein synthesis. We studied the mechanism of IGF-I's effect on IGFBP-5 mRNA, and the role of cytoplasmic proteins in modulating IGFBP-5 mRNA abundance. Anisomycin, emetine, and puromycin abolished IGFBP-5 mRNA as seen with cycloheximide. Cycloheximide had a dose- and time-dependent effect on IGFBP-5 mRNA. IGF-I increased IGFBP-5 nuclear transcripts by reverse transcription-polymerase chain reaction (RT-PCR), suggesting that IGF-I acts at least partially by increasing IGFBP-5 mRNA transcription. Protein synthesis inhibitors did not affect IGFBP-5 nuclear transcripts, therefore, they affect only mature mRNA. The IGFBP-5 mRNA 3' and 5' UTRs were cloned and their sequences searched for adenosine-uridine rich elements (AUREs), elements shown to regulate RNA stability. RNA mobility gel shift assay showed two protein activities that bind to nt 922 to 2076 of the 3' UTR, a region that contains an AURE. One protein activity (BA2) was decreased in cytoplasmic extracts from cycloheximide-treated RISM. These data demonstrate that IGFBP-5 mRNA integrity is dependent on protein synthesis. The 3' UTR of IGFBP-5 contains elements shown to bind proteins important for RNA stability regulation. This region binds RISM cytoplasmic proteins, and may mediate the dramatic effect of cycloheximide on IGFBP-5 abundance. RNA-protein interactions may be important to IGFBP-5 mRNA stability and ultimately, to IGFBP-5 actions.

3' Untranslated Regions↗
PubMed2005

Influence of RNA structural stability on the RNA chaperone activity of the Escherichia coli protein StpA.

Proteins with RNA chaperone activity are able to promote folding of RNA molecules by loosening their structure. This RNA unfolding activity is beneficial when resolving misfolded RNA conformations, but could be detrimental to RNAs with low thermodynamic stability. In order to test this idea, we constructed various RNAs with different structural stabilities derived from the thymidylate synthase (td) group I intron and measured the effect of StpA, an Escherichia coli protein with RNA chaperone activity, on their splicing activity in vivo and in vitro. While StpA promotes splicing of the wild-type td intron and of mutants with wild-type-like stability, splicing of mutants with a lower structural stability is reduced in the presence of StpA. In contrast, splicing of an intron mutant, which is not destabilized but which displays a reduced population of correctly folded RNAs, is promoted by StpA. The sensitivity of an RNA towards StpA correlates with its structural stability. By lowering the temperature to 25 degrees C, a temperature at which the structure of these mutants becomes more stable, StpA is again able to stimulate splicing. These observations clearly suggest that the structural stability of an RNA determines whether the RNA chaperone activity of StpA is beneficial to folding.

Base Sequence↗
PubMed1996

Post-transcriptional regulation of chloroplast gene expression in Chlamydomonas reinhardtii.

The biosynthesis of the photosynthetic apparatus depends on the concerted action of the nuclear and chloroplast genetic systems. Numerous nuclear and chloroplast mutants of Chlamydomonas deficient in photosynthetic activity have been isolated and characterized. While several of these mutations alter the genes of components of the photosynthetic complexes, a large number of the mutations affect the expression of chloroplast genes involved in photosynthesis. Most of these mutations are nuclear and only affect the expression of a single chloroplast gene. The mutations examined appear to act principally at post-transcriptional steps such as RNA stability, RNA processing, cis- and trans-splicing and translation. Directed chloroplast DNA surgery through biolistic transformation has provided a powerful tool for identifying important cis elements involved in chloroplast gene expression. Insertion of chimeric genes consisting of chloroplast regulatory regions fused to reporter genes into the chloroplast genome has led to the identification of target sites of the nuclear-encoded functions affected in some of the mutants. Biochemical studies have identified a set of RNA-binding proteins that interact with the 5'-untranslated regions of plastid mRNAs. The binding activity of some of these factors appears to be modulated by light and by the growth conditions.

Animals↗
PubMed2006

Therapeutic anti-tumor immunity triggered by injections of immunostimulating single-stranded RNA.

Stabilized synthetic RNA oligonucleotides (ORN) and protected messenger RNA (mRNA) were recently discovered to possess an immunostimulatory capacity through their recognition by TLR 7 and 8. We wanted to find out whether this danger signal is capable of triggering anti-tumor immunity when injected locally into an established tumor. Using the mouse glioma tumor cell line SMA-560 in syngenic VM/Dk mice, we were able to show that intra-tumor injections of protamine-stabilized mRNA do indeed induce tumor regression and long-term anti-tumor immunity. Residual RNA-injected tumors show CD8 infiltration. Distant injections of protamine-protected mRNA and intra-tumor injection of naked mRNA also result in anti-tumor immunity. Although they are strong danger signals, RNA are labile molecules with a short half-life: they do not trigger side effects such as long-term, uncontrolled immunostimulation evidenced by splenomegaly in CpG DNA-treated mice. In conclusion, RNA molecules are potent and safe danger signals that are relevant for active immunotherapy strategies aimed at the eradication of solid tumors.

Animals↗
PubMed2006

Error propagation across levels of organization: from chemical stability of ribosomal RNA to developmental stability.

My hypothesis integrates molecular and whole-organism levels of development. A physico-chemical property of nucleotides (their dipole moment), confers structural thermostability on double-stranded sequences, and decreases chemical stability of single-stranded sequences. According to this approach, low ribosomal RNA stability should decrease the precision of protein synthesis and whole-organism developmental stability. Indeed, substitution frequencies in pseudogenes are proportional to the subtraction of the dipole moment of the substituting nucleotide from that of the substituted one, and developmental instability, estimated by morphological fluctuating asymmetry (FA), correlates with mammal 12s rRNA base content of loop (but not stem) regions. In lizards, fit to the single-strand rationale of sequence chemical stability decreases with the level of poikilothermy of the investigated lizard family, suggesting interactions between changes in body temperature, ribosomal structure and developmental instability. Results confirm the hypothesis (less than for 12s rRNA) in: third codon positions of cytochrome B, probably because, unlike rRNAs, specific mRNAs affect only the protein they code; and 16s rRNA, apparently because its base composition is more affected by genome-wide mutational biases than that of 12s rRNA.

Animals↗
PubMed1995

Thermodynamics of RNA unfolding: stabilization of a ribosomal RNA tertiary structure by thiostrepton and ammonium ion.

RNAs with interesting secondary and tertiary structures tend to melt in several broad and overlapping transitions over a wide temperature range, and it has been consequently difficult to resolve the thermodynamics of individual unfolding steps. In the case that a ligand selectively binds a single folded state of the RNA, it is possible to obtain reliable thermodynamic parameters for both RNA unfolding and RNA-ligand binding simply from the hyperchromicity of RNA denaturation. The analysis procedure involves fitting a three-dimensional surface to absorbance data collected as a function of both temperature and ligand concentration. Analysis of the unfolding of a fragment of the large subunit ribosomal RNA (Escherichia coli sequence 1051 to 1109) is presented; both an antibiotic (thiostrepton) and ammonium ion specifically stabilize a tertiary structure within this RNA. A consistent set of thermodynamic parameters (delta H and tm) for the first two sequentially linked unfolding transitions is obtained from the experiments, and the binding constants obtained for the two ligands are consistent with other independent measurements. The approach is applicable to a variety of RNAs that specifically bind proteins, antibiotics, ions or other ligands.

Ammonia↗
PubMed1992

Inhibitors of RNA and protein synthesis stabilize messenger RNA for the RII beta subunit of protein kinase A in different cellular compartments.

Messenger RNA for RII beta is transiently induced (greater than 50-fold) by cAMP analogs in primary cultures of rat Sertoli cells. The induction is dependent on protein synthesis. We have previously shown that mRNA for RII beta is stabilized by cAMP, as well as inhibitors of transcription and translation. This indicated that rapid degradation of RII beta mRNA involved a protein with a rapid turnover and its corresponding mRNA. The two RNA synthesis inhibitors used in the present study stabilized both nuclear and cytoplasmic RII beta mRNA, whereas inhibition of protein synthesis stabilized RII beta mRNA in the cytoplasm only. These results indicate that only cytoplasmic degradation of RII beta mRNA is dependent on a protein with high turnover. In contrast, nuclear degradation appears to be dependent on an RNA with a short half-life, not involving protein synthesis.

Animals↗
PubMed1984

Plant Desiccation and Protein Synthesis. IV. RNA Synthesis, Stability, and Recruitment of RNA into Protein Synthesis during Desiccation and Rehydration of the Desiccation-Tolerant Moss, Tortula ruralis.

Upon rehydration of desiccated Tortula ruralis, RNA synthesis is immediately resumed; this resumption is quicker in moss recovering from slow drying than from rapid drying. Newly synthesized RNA enters the protein synthetic complex almost immediately upon rehydration, reaching control steady state levels within 2 hours after slow drying and 6 hours after rapid drying. RNA synthesized in the 1st hour following the readdition of water enters into polysomes much earlier after slow drying than after rapid drying. The RNA components of the protein synthetic complex are stable to desiccation at either slow or rapid speeds, although more so following the former drying regime. Immediately upon rehydration, these conserved RNA are readily utilized for protein synthesis, and continue to be so at least 4 hours thereafter. Hence, the speed of desiccation affects the rate at which RNA is synthesized upon subsequent rehydration, as well as the mode of utilization of that RNA.

Journal Article↗
PubMed1970

Ribonuclease V of Escherichia coli: susceptibility of heated ribosomal RNA and stability of R17 phage RNA.

Native ribosomal RNA anid inttact pliage R17 RNA are insensitive to attack by ribonuclease V, an exonucleolytic activity associated with ribosome movement on the substrate RNA. However, ribosomal RNA becomes a substrate when it is heated under conditions that make it a template for protein synthesis, and R17 RNA is attacked if it is either heated or fragmnented. Accessibility of the 5' terminus of an RNA molecule is probably inzcreased by heating or fragmnentation and may determine its susceptibility to ribonuclease V.

Coliphages↗
PubMed2003

The effect of storage at different temperatures on the stability of Hepatitis C virus RNA in plasma samples.

One important issue related to Hepatitis C virus (HCV) RNA nucleic acid amplification testing (NAT) is the storage conditions of plasma samples in order to obtain reliable results. Many authors have reported that the storage conditions could affect the RNA stability and, hence, HCV RNA detection. We have studied HCV RNA stability in plasma samples after storage at different temperatures (-70, -20, 5 and 25 degrees C). Samples containing different HCV titres were stored and analysed by qualitative or quantitative NAT techniques at defined time points. At -20 degrees C, samples containing high HCV RNA titres were followed-up during approximately 2.6-2.7 years, samples with intermediate concentrations during approximately 1 year and samples with 100 International Units/millilitre (IU/ml) during 2.5 years. Independently of the HCV RNA concentration, the results show absence of decay in HCV RNA detectability. Samples stored at 25 degrees C maintain their HCV RNA titre during 14 days and samples at 5 degrees C were stable for at least 3 months.

Hepacivirus↗