Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “RNA Aggregation”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 127 records · Page 7Linked to original sources
PubMed1980

Infectivity and reconstitution of TMV RNA modified with N-acetoxy-2-acetylaminofluorene or benzol [a] pyrene 7,8-dihydrodiol 9,10 oxide.

TMV RNA was modified by two bulky carcinogens, N-acetoxy-2-acetylamino-fluorene (AAAF) and (+/-)-7beta, 8alpha- dihydroxy-9alpha, 10alpha-epoxy-7,8,9,10-tetrahydrobenzo[alpha]pyrene (BPDE), and the effects of such substituents on biological and physical properties was studied. For both types of modification, the loss of infectivity was directly proportional to the number of chemical modifications indicating that all modifications are lethal. Neither AAAF nor BPDE produced measurable mutations. Reconstitution of modified RNA with TMV protein was partially inhibited, but such inhibition occurred to similar extents with either carcinogen and a varying levels of modification. The data suggest that both types of substitution of TMV RNA generally permit the TMV coat protein to aggregate normally around the RNA, but that AAAF and BPDE may induce some conformational change in the initiation region that inhibits the initiation step.

2-Acetylaminofluorene↗
PubMed1981

The RNA of the human syncytium-forming (foamy) virus.

Human syncytium-forming (foamy) virus was labeled with 3H-uridine and banded isopycnically in sucrose gradients (buoyant density = 1.16 to 1.18 g/cm3). Viral RNA extracted from the banded virus was analyzed either by rate zonal separation in sucrose gradients or by polyacrylamide-agarose gel electrophoresis. The results indicated that purified HSFV contains a 60S RNA component plus several smaller molecular weight RNA components. On dissociation with heat, smaller RNA structures were released from the 60S component. These results indicate that the genome of HSFV, like the other members of the Retroviridae family, is composed of an aggregate of several RNA species.

Centrifugation, Isopycnic↗
PubMed1986

Molecular assembly of tobacco mosaic virus in vitro.

TMV assembly starts with a specific interaction between the assembly origin on the RNA and a disk aggregate of coat protein. The assembly origin is located in the 30K protein cistron for common and tomato strains of TMV and in the coat protein cistron for cowpea strain of TMV and for CGMMV. All the assembly origins have three essential structures: a long base-paired hairpin loop structure; a target sequence, GAPuGUUG, at the top of the hairpin loop structure; and a tract where every third base is a purine. The protein aggregate responsible for the initiation of TMV assembly is a 20S disk, a two-layered aggregate of 34 protein subunits. The two layers of a disk open apart onto the central hole and this structure may be critical for the disk to interact with the assembly origin on the RNA. The target sequence may bind specifically to this structure. Although only a low concentration of 20S disks exists in the usual assembly condition, one disk is enough to initiate TMV assembly. TMV elongation proceeds in two directions. Elongation to the 5'-end proceeds rapidly by preferential incorporation of protein subunits (or A protein) and in 5-7 min gives rise to 260 nm intermediate particles whose 5'-end is coated. A model of elongation toward the 5'-end is shown in Fig. 15. Protected RNAs from nuclease digestion during the assembly reaction produce a banding pattern on gels by electrophoresis. The banding pattern reflects features of the RNA rather than protein that are used in the assembly reaction, since the pattern was the same for assembly between TMV-RNA and CGMMV protein subunits as for assembly between TMV-RNA and TMV protein containing 20S aggregates. The 20S aggregate in the assembly solution has a helical structure with 39 protein subunits rather than the disk structure. Rapid addition of 20S helical aggregates to the top of the growing rod seems to be impossible because of its topological complexity. Elongation toward the 3'-end does not start for at least the first 4 min after initiation. It probably cannot begin until the 5'-end RNA tail disappears into the intermediate rod. Elongation toward the 3'-end favors 20S aggregates as the protein source and gives rise to the full-length rods in about 30 min after the initiation. There are no topological difficulties in adding 20S helical aggregates to the protruding RNA tail.(ABSTRACT TRUNCATED AT 400 WORDS)

Genes, Viral↗
PubMed1978

Effect of estrogen on gene expression in the chick oviduct. In vitro transcription of the ovalbumin gene.

Problems involved in using the Hg-nucleotide technique for in vitro chromatin transcription are 2-fold. First, Escherichia coli RNA polymerase can utilize endogenous RNA as template and synthesize complementary sequences which remain base-paired to the template, thereby allowing it to bind to the SH-Sepharose column and copurify with the newly synthesized Hg-RNA. Second, non-mercurated endogenous RNA can bind to the SH-Sepharose through aggregation with Hg-RNA and thus be retained in the final RNA preparation. These two problems associated with the Hg-nucleotide technique can be minimized by modifying the conditions for RNA synthesis and SH-Sepharose chromatography. Using the modified procedure the Hg-nucleotide and SH-Sepharose technique can remove more than 90% of endogenous RNA contaminants. In order to directly demonstrate that the mRNAov sequences detected in vitro result from de novo transcription of oviduct chromatin, experiments were carried out which show that the hybridizable RNA sequences contain the Hg element and that the synthesis of these RNA sequences is sensitive to low concentrations of actinomycin D. These combined results strongly suggest that the majority of mRNAov sequences detected by hybridization to cDNAov is indeed due to DNA-dependent RNA synthesis by E. coli RNA polymerase and not due to an artifact of endogenous RNA contamination. This observation was further supported by data obtained using a filter hybridization method which measures directly the mRNAov sequences present in [3H]RNA synthesized from chromatin. The 3H-labeled ovalbumin messenger RNA was assayed by hybridization to cloned pOV230 DNA containing the ovalbumin structural gene sequence. With this modified Hg-nucleotide-SH-Sepharose technique and filter hybridization technique, we have restudied the in vitro transcription of the ovalbumin gene from chromatins isolated at different stages of hormone-induced oviduct development. The results are in agreement with our previous findings which suggest that the primary regulation of ovalbumin synthesis by steroid hormones occurs at the transcriptional level.

Animals↗
PubMed1990

The E. coli dnaK gene product, the hsp70 homolog, can reactivate heat-inactivated RNA polymerase in an ATP hydrolysis-dependent manner.

Pelham previously proposed that the hsp70 family of heat shock proteins could prevent the formation and/or allow the dissolution of protein aggregates created during stress conditions. We confirmed this hypothesis by showing that the E. coli hsp70 homolog, the dnaK gene product, protects the host RNA polymerase enzyme from heat inactivation in an ATP-independent reaction. In addition, we show that heat-inactivated and aggregated RNA polymerase is both disaggregated and reactivated following simultaneous incubation with DnaK protein and hydrolyzable ATP. The DnaK756 mutant protein has lost the ability to disaggregate the inactivated RNA polymerase enzyme. Our results demonstrate that the DnaK protein contributes to E. coli's growth not only by protecting some enzymes from denaturation but also by reactivating some once they are misfolded or aggregated.

Adenosine Triphosphate↗
PubMed1971

Association of 4S ribonucleic acid with oncornavirus ribonucleic acids.

Oncornavirus 60 to 70S ribonucleic acids (RNA), such as those from avian myeloblastosis virus, Schmidt-Ruppin virus, or mouse sarcoma-mouse leukemia viruses, isolated by conventional techniques, contain 4S transferlike RNA molecules that are released upon dissociation of the 60 to 70S RNA with heat. The 4S RNA represents 2.5 to 3.0% of the RNA in the 65S aggregate or 4 to 5 molecules per molecule of 35S RNA formed.

Autoradiography↗
PubMed1984

Quercetin inhibits the action of 12-O-tetradecanoylphorbol-13-acetate, a tumor promoter.

Quercetin, a mutagenic but noncarcinogenic flavonoid, inhibited the increased incorporation of inorganic phosphate into phospholipids of human embryo fibroblasts induced by 12-O-tetradecanoylphorbol-13-acetate (TPA), a potent tumor promoter. Quercetin also inhibited TPA-induced increases of sugar transport and RNA synthesis in chick embryo fibroblasts, and TPA-induced aggregation of human platelets. These results suggest that quercetin may have antitumor promoter activity, which provides a possible reason why quercetin does not develop malignant tumors despite its mutagenicity.

Animals↗
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↗
PubMed1997

Formation of plant RNA virus replication complexes on membranes: role of an endoplasmic reticulum-targeted viral protein.

The mechanisms that direct positive-stranded RNA virus replication complexes to plant and animal cellular membranes are poorly understood. We describe a specific interaction between a replication protein of an RNA plant virus and membranes in vitro and in live cells. The tobacco etch virus (TEV) 6 kDa protein associated with membranes as an integral protein via a central 19 amino acid hydrophobic domain. In the presence or absence of other viral proteins, fluorescent fusion proteins containing the 6 kDa protein associated with large vesicular compartments derived from the endoplasmic reticulum (ER). Infection by TEV was associated with a collapse of the ER network into a series of discrete aggregated structures. Viral RNA replication complexes from infected cells were also associated with ER-like membranes. Targeting of TEV RNA replication complexes to membranous sites of replication is proposed to involve post-translational interactions between the 6 kDa protein and the ER.

Amino Acid Sequence↗
PubMed1988

Expression of a murine homeobox gene precedes the induction of c-fos during mesodermal differentiation of P19 teratocarcinoma cells.

The controlled expression of regulatory genes is the basis of normal mouse embryo development. Recent studies in our laboratory have revealed temporally and spatially restricted expression of homeobox-containing genes and the cellular protooncogene c-fos in developing mouse embryos. In order to gain insight into cellular control mechanisms responsible for differential expression of these potential regulatory genes during developmental processes, we set out to analyze their expression in teratocarcinoma cells as an in vitro model system for cellular differentiation. We demonstrated that the homeobox-containing gene Hox 1.3 and the c-fos protooncogene are expressed in P19 teratocarcinoma cells prior to their terminal myogenic differentiation, which is indicated by the expression of muscle-specific myosin. Using a combination of the transcriptional run-on assay and Northern analysis, we defined some of the cellular control mechanisms that are responsible for the changes in transcription pattern during P19 differentiation. The development-dependent activation of c-fos and muscle-specific myosin mRNA was found to result from an increased transcription rate. In contrast, the primary induction of Hox 1.1 (m6)-specific mRNA was controlled on the posttranscriptional level by changes in the half-life of the transcript. In addition, in situ hybridization studies revealed a characteristic spatially restricted expression of Hox 1.1 RNA in P19 aggregates, which may point to an important role of cell-cell interactions for Hox 1.1 expression in the mesodermal muscle differentiation pathway.

Animals↗
PubMed2005

Inhibition of sequestosome 1/p62 up-regulation prevents aggregation of ubiquitinated proteins induced by prostaglandin J2 without reducing its neurotoxicity.

The mechanisms implicated in the aggregation of ubiquitinated proteins detected in neurodegenerative disorders remain elusive. We report that prostaglandin J2 (PGJ2), an endogenous product of inflammation, up-regulates sequestosome 1/p62 in a time- and dose-dependent manner in human neuroblastoma SK-N-SH cells. We previously demonstrated that prostaglandins of the J2 series inhibit ubiquitin hydrolases, such as UCH-L1. Herein, we show that sequestosome 1/p62 is co-localized with ubiquitinated proteins and the ubiquitin hydrolase UCH-L1 in cytoplasmic aggregates induced by PGJ2. Preventing sequestosome 1/p62 up-regulation by RNA interference abolishes the aggregation but not the accumulation of ubiquitinated proteins or PGJ2 cytotoxicity. Sequestosome 1/p62 is known to bind poly-ubiquitinated proteins through its ubiquitin-associated domain. Our data support the notion that sequestosome 1/p62 up-regulation under stress conditions contributes to the "sequestration" of poly-ubiquitinated proteins into aggregates. However, the overwhelming accumulation of ubiquitinated proteins, rather than their aggregation, is likely to be an important contributor to PGJ2 cytotoxicity.

Adaptor Proteins, Signal Transducing↗
PubMedDate not supplied

2-propanol dependent RNA absorbance.

RNA absorbances Ad were determined by bichromatic spectrophotometry at 240, 260 and 280 nm, versus 350 nm values, on paper disks containing different 2-propanol concentrations and NaCl amounts. No significant differences in terms of the NaCl content could be observed at alcohol concentrations higher than 70%; the maximum Ad value was found to correspond to about 50% 2-propanol. The possible phenomena implied in the absorbance changes are discussed taking into account the peculiar action of 2-propanol on the water structure and content in the bulk phase within the paper capillaries and inside the macromolecular and aggregation structures of RNA and cellulose.

1-Propanol↗
PubMed1993

Replication of the A7(74) strain of Semliki Forest virus is restricted in neurons.

In neonatal mice the A7(74) and L10 strains of Semliki Forest virus (SFV) are virulent. In 3- to 4-week-old mice the L10 strain is virulent, the A7(74) strain is avirulent. Following intraperitoneal inoculation of 3- to 4-week-old mice both strains produce a transient plasma viremia. This is cleared by IgM antibodies. IgG antibodies of all subclasses are produced. The distribution of viral RNA in the brain as determined by autoradiographic analysis of in situ hybridizations shows that in all cases virus is first apparent as small foci of infected cells around cerebral capillaries. In both neonatal and 3- to 4-week-old mice infected with L10 or neonatal mice infected with A7(74), infection spreads rapidly from the original foci to infect large areas throughout the brain. Both neurons and glial cells are infected resulting in pycnosis and death of the animals. In the brains of 3- to 4-week-old mice infected with A7(74) virus there is little spread from the original perivascular foci. Again neurons and oligodendrocytes are infected but cellular destruction is minimal. The same pattern of A7(74) infection is observed in 3- to 4-week-old athymic nu/nu mice and mice with severe combined immunodeficiency, indicating that failure to spread is not related to specific immune responses. Furthermore, in nu/nu and SCID mice the small restricted foci of A7(74) infection persist. Comparison of the replication of these two viruses by electronmicroscopy shows that although A7(74) virus replicates completely in the neurons of neonatal mice, the virus is unable to bud from the neurons of 3- to 4-week-old mice and aggregates of viral RNA and capsid accumulate. We conclude that there is an age-related restriction of A7(74) replication in mouse neurons and that this restriction is not associated with the maturity of virus-specific immune responses but probably reflects age-related changes in neurons.

Animals↗
PubMed1986

Regulation by calcium of parathyroid hormone mRNA in cultured parathyroid tissue.

We have examined the effect of changes in the concentration of extracellular calcium on parathyroid hormone mRNA in both short-term (hours) and long-term (days) cultures of bovine parathyroid tissue. Using a 32P-labeled PreProPTH cDNA probe, PTH mRNA was measured by gel blot hybridization of total RNA from tissue slices incubated for 4 h in low (0.5 mM) or high (5 mM) calcium concentrations and also by dot blot hybridization of cytoplasmic RNA extracted from aggregates of partially dispersed cells cultured up to 72 h in low (0.4 mM), normal (1 mM), or high (3 mM) calcium concentrations. PTH mRNA was unchanged over 4 h while high calcium had suppressed PTH secretion. However PTH mRNA did respond during long-term culture. By 24 h in high calcium there was a 50% suppression which was maintained for a further 48 h. PTH mRNA in normal calcium remained unchanged over 72 h while in low calcium it had increased slightly by 48 h. In contrast to the effect seen in cultured bovine parathyroid cells, PTH mRNA in human parathyroid adenoma cells cultured for 48 h in high calcium was decreased by only 10%.

Adenoma↗
PubMed2005

RASA1: variable phenotype with capillary and arteriovenous malformations.

Capillary malformation-arteriovenous malformation (CM-AVM) is a newly discovered hereditary disorder. Its defining features are atypical cutaneous multifocal capillary malformations often in association with high-flow lesions: cutaneous, subcutaneous, intramuscular, intraosseous and cerebral arteriovenous malformations and arteriovenous fistulas. Some patients have Parkes Weber syndrome - a large congenital cutaneous vascular stain in an extremity, with bony and soft tissue hypertrophy and microscopic arteriovenous shunting. In the past, arteriovenous malformations and arteriovenous fistulas had been considered non-hereditary. A classical genetic approach was used to identify the locus. Candidate gene screening pinpointed mutations in RASA1 (p120-RASGAP) - a RasGTPase. RASA1 reverts active GTP-bound Ras into inactive GDP-bound form. Murine Rasa1 knockout and tetraploid-aggregated embryos with RNA interference exhibited abnormal vascular development. Lack of RASA1 activity caused inhibition of cell motility, possibly through p190-RhoGAP. Thus, RASA1 defects probably cause abnormal angiogenic remodeling of the primary capillary plexus that cannot be compensated for by other RasGAPs: RASA2, RASAL and NF1. Signaling pathways involving RASA1 might offer novel targets for treatment of high-flow vascular anomalies.

Animals↗
PubMed1973

The nature of polydisperse ribonucleic acid in plants.

The aggregation of ribosomal RNA species during chromatography on methylated albumin on kieselguhr was decreased from 50 to 15% by the lower salt concentrations made possible by the use of higher pH values. The polydisperse RNA was resolved into two fractions. About 50% was eluted with the rRNA whereas the remainder was bound to the column, and was recovered only by solubilization of the methylated albumin. Both fractions of polydisperse RNA were similar in size range, but the bound fraction was considerably richer in AMP. No D-RNA (DNA-like RNA) peak was resolved under these conditions of column fractionation. However, the properties of the bound RNA were consistent with it containing both D-RNA and TB-RNA (tenaciously bound RNA). The relationship between these two fractions of AMP-rich RNA was considered. The bound RNA and ribosomal RNA responded differently to various treatments. The salt concentration required to elute ribosomal RNA was halved by increasing the pH of the fractionation, but the amount of bound RNA was in fact increased. Denaturation by hot urea decreased the binding of ribosomal RNA to the methylated albumin, but did not facilitate elution of bound RNA. The high affinity between the AMP-rich polydisperse RNA and the methylated albumin does not therefore appear to arise for the secondary structure conferred by the high AMP content.

Adenosine Monophosphate↗
PubMed1976

Assembly of a spherical plant virus.

The conditions previously reported as necessary for the reassembly of spherical viruses have been distinctly unphysiological and such reassembly cannot be related directly to the in vivo reaction. Mild conditions for the in vitro reassembly of cowpea chlorotic mottle virus (CCMV) from its isolated components have now been described (Adolph & Butler 1975) and the reassembled virus characterized. This reassembly involved the co-aggregation of the RNA and protein around neutrality and at ionic strength 0.2, giving yields of 70% encapsidation at pH 6.0. The reaction was independent of temperature over the range 5-25 degrees C and did not require the presence of Mg2+ ions. The reassembled virus shows a stability similar to that of native CCMV, with the same change in sedimentation coefficient around pH 6.5. The molecular mass and buoyant density in CsCl are also the same as those of native CCMV, while the electron microscope reveals a surface morphology on the reassembled particles like that on native CCMV. Analysis of the number-average, mass-average, and Z-average molecular masses of the purified protein at both pH 6.0 and pH 7.5 suggests that the active unit for reassembly is a dimer of the protein subunit.

Capsid↗