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Results for “RNA Stability”

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At least 19 recordsLinked to original sources
PubMed1975

Structure of B77 sarcoma virus RNA: stabilization of RNA after packaging.

Extracellular maturation of Bratislava 77(B77) sarcoma virus RNA involves a stabilization of linkage between 35S subunits since the Tm of 60 to 70S RNA in the presence of 0.5 M NaCl increases from 56 to 67.5 C as the age of the virus increases. This stabilization process is strongly temperature dependent; the rate at 45 C is increased fourfold over the rate at 37 C. As a result of the instability of the immature RNA, denaturation to subunits occurs at room temperature during phenol extraction. This dissociation can be prevented by increasing the NaCl concentration during the extraction. The data support a model which proposes that RNA subunits of oncornaviruses exist as assembled 60 to 70S RNA even in immature virions but that the linkages between subunits are stabilized as a function of time. These linkages appear to be maintained by nucleotide base pairing rather than by protein. However, isolated RNA does not undergo stabilization, suggesting that some other component of the virion is necessary for the process to occur.

Avian Sarcoma Viruses↗
PubMed1991

Protein overproduction in Escherichia coli: RNA stabilization, cell disruption and recovery with a cross-flow microfiltration membrane.

After optimizing overproduction of a heterologous gene product (chloramphenicol acetyltransferase, CAT) using an RNA stabilization vector * in Escherichia coli (Chan et al., 1988), a single step cell disruption and recovery method * for obtaining a product stream essentially free of cell debris was developed. The behavior of an RNA stabilization plasmid (pKTN-CAT) containing stabilizing intron RNA was investigated in two different media both in batch and chemostat modes. CAT production of pKTN-CAT was consistently higher (3- to 7-fold) than that of the control lacking the stabilization sequences (pK-CAT). Highest CAT production was observed for cells grown in minimal medium in batch mode and induced for CAT expression early in growth. CAT production of cells grown in the chemostat mode exhibited an optimal dilution rate of about 0.1 h-1. Enhancement of protein production by pKTN-CAT as compared to pK-CAT tended to be higher when grown in rich medium rather than in minimal medium. Presence of the RNA stabilization plasmid did not significantly alter the growth rate of the cell. Using a combination of chemical treatment (1 mM EDTA) and shear stress resulting from cross-flow in a stainless steel microfiltration membrane *, CAT was released into the medium through disruption of the E. coli cells. The permeate flux increased from 2000 to 9000 kg m-2 h-1 with increasing axial Reynolds number from 10,000 to 60,000 or increasing mean shear stress from 12 to 47 Pa. The turbidity of the permeate was approximately 4% that of the retentate over this range of axial flow rates, indicating excellent removal of cell debris. Also, the concentration of CAT in the permeate was equal to that in the retentate over this range of axial flow rates, indicating complete passage of protein through the membrane. Thus, using a combination of chemical treatment and fluid-induced shear stress in a cross-flow membrane module, we were able to disrupt and recover the heterologous protein in a stream low in debris.

Biotechnology↗
PubMed1992

Irradiation increases levels of GM-CSF through RNA stabilization which requires an AU-rich region in cancer cells.

Granulocyte/macrophage colony stimulating factor (GM-CSF) is a hematopoietic growth factor that stimulates a wide range of myeloid hematopoietic cells; RNAs coding for many oncogenes and cytokines including GM-CSF have a very short half-life. The motif of AUUUA is a highly conserved sequence in the 3'untranslated regions (3'UTR) of these transcripts and is repeated a number of times in these short-lived cytokines and oncogenes. These sequences play a major role in controlling stability of these transcripts. Human cancer cells were transfected with a chimeric rabbit beta-globin gene linked to either a 58 bp sequence of the AT-rich region from GM-CSF or a control sequence. We have found that irradiation stimulates accumulation of GM-CSF, interleukin-6 (IL-6), and IL-1 beta RNAs. In addition, this accumulation of GM-CSF was at least, in part, a result of increased stabilization of GM-CSF transcripts. Further experiments showed that irradiation increased levels of the chimeric beta-globin transcripts containing AUUUA sequences from GM-CSF, but not those containing the control sequences. Our results suggest that irradiation increases expression of GM-CSF RNA and that posttranscriptional stabilization requiring AUUUA sequences probably is in part one of the mechanisms producing the increased levels of GM-CSF RNA by irradiation.

Base Sequence↗
PubMed1979

Interference of nonsense mutations with eukaryotic messenger RNA stability.

The fine structure map of the yeast URA 3 gene was established by meiotic recombination, and amber nonsense mutations were located at different points on the map. The effect of the length of the labeling time on the specific radioactivity of ura 3 messenger RNA and on its repartition between poly(A)-RNA and RNA not containing poly(A) has been followed in nonsense mutants. Nonsense mutations reduce the messenger level without lowering its instantaneous rate of synthesis. The strength of the reduction depends on the position of the nonsense codon within the locus and concerns essentially the accumulation of polyadenylylated ura 3 mRNA.

Drug Stability↗
PubMedDate not supplied

[Effect of histones on cell permeability, protein and RNA synthesis and RNA stability in Aerobacter cloaceae].

The histones of calf thymus were found to change the permeability of the cells of Aerobacter cloaceae, without producing any noticeable effect on their viability. Concomitant depolymerization of the cellular RNA indicates destruction of the ribosomes. The increased synthesis of RNA in interpreted as a manifestation of reparatory processes. Protein synthesis, virtually unaffected in the resting cells, was inhibited to some extent in the growing culture treated with histones. Some considerations concerning the mode of action of histones at the intracellular level are presented.

Alanine↗
PubMed1976

[Escherichia coli K12 mutant with increased RNA content and messenger RNA stability].

A strain of Escherichia coli has been isolated from a E. coli HfrH after a treatment with nitrosoguanidine for a partial resistance to thymineless death. This strain shows, in addition, a global increase of the RNA content amounting to 50 per cent. The half-life of the unstable RNA as well as of the messenger RNA of the beta-galactosidase is increased to a considerable degree. The RNA polymerase of this strain is modified with respect to its resistance to rifampicin and its transcription efficiency in vitro of various DNA templates. Our working hypothesis is that the primary alteration of this strain lies at the RNA polymerase level with a consequent increase of the synthetic rate of the ribosomal RNA. The increase of the messenger RNA half-life may be an indirect consequence of this event via a saturation of the RNAase by the excess of ribosomal RNAs not associated to their proteins.

DNA-Directed RNA Polymerases↗
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↗
PubMed1977

Rates of formation and thermal stabilities of RNA:DNA and DNA:DNA duplexes at high concentrations of formamide.

The thermal stabilities of RNA:DNA hybrids are substantially greater than those of DNA:DNA duplexes in aqueous electrolyte solutions containing high concentrations of formamide. Association rates to form DNA:DNA duplexes and DNA:RNA hybrids have been measured in these solvents. There is a temperature range in which DNA:DNA rates are negligible and RNA:DNA rates close to optimal.

DNA, Neoplasm↗
PubMed1976

RNA viruses: stabilization of brome mosaic virus.

The relative importances of protein-protein and RNA-protein interactions in stabilizing the architecture of brome mosaic virus particles are discussed in the light of the following experimental evidence: (a) disassembly pathways of the virus particles, (b) reassembly of the virus and self-association capacity of the protein moiety, and (c) the role of divalent cations in virus stabilization, and their relevance to localization of the RNA in the virus particles. Evidence is given that the capsid of BMV is primarily stabilized by hydrophobic bonds at low pH, but not around and above neutrality where RNA-protein electrostatic interactions are essential to the integrity of the virus particles. A model is proposed for the structure of BMV in the different configurational states.

Capsid↗
PubMed1975

The half-life of polyadenylated polysomal RNA from normal and transformed cells in monolayer culture.

The small genotypic differences between normal and transformed cells are insufficient to account directly for all their wide phenotypic differences, which probably in some cases at least involve alterations in control of gene expression. To ascertain whether such alterations involved changes in mRNA stability, RNA half-lives were estimated in five monolayer cell lines, including two pairs of normal cells and their transformed counterparts. The results for the polyadenylated fractions in all cases fit with those expected from a model in which the whole fraction has a single half-life, of less than one generation time. From both the transformed/untransformed cell pairs, there is evidence that a relationship exists between cell generation time and the half-life of the polyadenylated polysomal RNA fraction, which persists even through the process of transformation. Considerable alteration in the pattern of RNA stability is therefore unlikely to be obligatory in in vitro transformation.

Cell Line↗
PubMed2025

Minimal Perturbation Analysis of mRNA Degradation Rates with Tet-Off and RT-qPCR.

Messenger RNA stability is an important variable in gene expression and its dynamics. High stability ensures a constant level of synthesized protein, whereas mRNA instability can be critical for regulatory processes in which protein production needs to be stopped, such as development, inflammation, or adaptation to stress. Accurate measurements of RNA degradation rates are important for understanding how RNA features and RNA binding proteins affect the posttranscriptional life of an mRNA. As an alternative to global transcriptional inhibition methods, the use of a Tet-off repressible promoter has the advantage that cells are minimally perturbed by the addition of doxycyclin during the assay. We illustrate the use of a reporter mRNA expressed from a plasmid in Saccharomyces cerevisiae cells, but similar methods can be applied to other regulated promoters, on plasmids or by genome editing, and in other organisms. RNA levels are measured by reverse transcription followed by quantitative PCR. An exponential decay law is then used to estimate how well the measurements follow this expected trend for the simplest possible mechanism of RNA degradation, where the decay is proportional to the amount of RNA present at any given time.

RNA Stability↗
PubMed1976

Stability of RNA synthesized by the mouse oocyte during its major growth phase.

The RNA of growing mouse oocytes and ovulated ova was labeled by injection of a solution containing tritiated uridine into the ovarian bursa. The time course of incorporation into RNA by oocytes was followed by analysis of alkali-labile acid insoluble radioactivity and by autoradiography. The results show that most of the incorporation into RNA by growing oocytes takes place within one day of bursal injection of the precursor, reflecting the rapid fall of label in the acid soluble precursor pool. The RNA of growing oocytes of all sizes is unusually stable, at least 80% of the labeled RNA present two days after bursal injection being retained until ovulation 10 to 20 days later. The fraction of heterogeneous RNA in labeled RNA of ova was estimated as 20% by sucrose gradient analysis. It is likely that egg RNA is synthesized primarily during the period of oocyte growth one to three weeks before ovulation.

Animals↗
PubMed1976

Altered synthesis and stability of RNA polymerase holoenzyme subunits in mutants of Escherichia coli with mutations in the beta or beta' subunit genes.

Bacteria with specific temperature sensitive lethal mutations in the gene for the beta' subunit of RNA polymerase synthesize both the beta and beta' subunits at a several fold higher rate at 42 degrees C than wild-type cells relative to total protein. Synthesis of the alpha and sigma subunits proceeds at essentially the wild-type rates under these conditions. In contrast, a mutant with a temperature sensitive lethal mutation in the beta subunit gene synthesizes beta and beta' at 42 degrees C at slightly lower rates than wild-type, while alpha and sigma synthesis is not significantly altered. In all of the mutants at 42 degrees C, newly synthesized alpha subunits are stable, while the beta, beta' and sigma subunits are rapidly degraded. The apparent uncoupling of betabeta' and alpha subunit synthesis seen in the beta' mutants at 42 degrees C might suggest that the synthesis of these subunits is at least in part controlled by different mechanisms.

Escherichia coli↗
PubMed1978

Biochemical and electron microscopic characterization of DNA-RNA complexes from HeLa cell mitochondria.

The previous electron microscopic investigations on the occurrence in HeLa cell mitochondria of transcription complexes of mitochondrial DNA [Aloni, Y., and Attardi, G. (1972a), J. Mol. Biol. 70, 363-373] have been extended with the aim of obtaining these complexes in a reasonably pure form for biochemical analysis. By using conditions designed to minimize losses of such structures and any possible contamination by nuclear DNA, it has been shown that a substantial fraction (40 to 50%) of mitochondrial DNA can be isolated from exponentially growing HeLa cells in the form of fastsedimenting complexes with RNA. These complexes have been characterized with respect to density and sedimentation properties, content in newly synthesized RNA, stability of the association of RNA with DNA, presence of different forms of mitochondrial DNA, and electron microscopic appearance. The properties of these complexes, as well as the results of reconstruction experiments, strongly suggest that the majority of such structures represent true transcriptional intermediates. The occurrence in this fraction of replicating or newly replicated mitochondrial DNA molecules has been observed. Although the presence of single-stranded DNA segments makes the replicative intermediates particularly susceptible to aggregation with free RNA, electron microscopic observations point to the possibility that these intermediates may be recruited for transcription.

DNA, Mitochondrial↗