Appearance of rapidly labeled, high molecular weight RNA in nuclear ribonucleoprotein. Release from chromatin and association with protein

Effects of RNA secondary structure on alternative splicing of pre-mRNA: is folding limited to a region behind the transcribing RNA polymerase?

The use in vivo of an alternative 5' splice site sequestered within a short stem of potential RNA secondary structure is determined by the length of the loop. Above a threshold length of loop, the alternative site is used despite the potential structure. In contrast, the alternative site is used very little or not at all during splicing in vitro with all lengths of loop that we have tested. A model is proposed which suggests that pre-mRNA is free to fold only within a limited period after transcription.

Turnover of the major polypeptides of 40-S monomer particles

The pulse-chase experiments with Friend erythroleukemia cells designed to reveal the metabolic properties of the protein complex of 40-S particles showed that the major polypeptides of this complex turn over with half-lives between 19 h and 206 h. the main conclusion from the experiments is that the complex does not degrade as a single unit. Since the individual polypeptides forming the complex live much longer than hnRNA, and in addition degrade at a different rate, we considered the following two modes of degradation as most likely. (1) The complex might not be subjected to a profound degradation at the end of the processing of associated pre-mRNA. In this case it should exist as a long-lived recyclable mosaic of metabolically differing polypeptides whose replacement takes place at a specific rate. (2) Alternatively, the protein complex might be completely degraded at the end of processing, but in a way that liberates free individual polypeptides available for recycling. The further experiments indicate that the 37 000-Mr, 34 000-Mr and 32 000-Mr core proteins in isolated 40-S particles and in particles associated with a nuclear fraction released from chromatin after micrococcal nuclease digestion degrade at different rates. These experiments suggest the existence of at least a metabolic heterogeneity among the population of nuclear particles carrying pre-mRNA.

Comparison of the nuclear ribonucleoproteins containing the transcripts of adenovirus-2 and HeLa cell dna

A method as devised allowing the preparation of hnRNA-containing ribonucleproteins (hnRNP) frm HeLa cells infected with adenovirus type 2 under conditions where the extraction of viral replication complexes as minimal. Approximately 60% of the RNA from such hnRNP hybridized with adenovirus DNA. The hnRNP from infected cells had the same general characteristics as those from uninfected cells. Their size was heterogeneous (30-260 S) and depended upon that of their RNA. Their CsCl densities were identical (1.39-1.40 g/ml), indicating the same protein:RNA ratio. Their proteins were found in the same molecular weight range, between 25 000 and 200 000. The major proteins of hnRNP from HeLa cells were present in hnRNP from adenovirus-infected cells. As 60% of the cellular RNA was replaced by adenovirus RNA in hnRNP, this in dicated that there was not stringent specificity in the RNA-protein interactions. The relative proportions of the proteins were identifical in both cases, suggesting that the hnRNP assembly was independent of nucleotide sequences at least for the major proteins. The hnRNP from infected and uninfected cells differed by the size of their RNA, which was larger after infection, and by the presence of six additional minor polypeptides after infection. However, it cannot be excluded that the presence of these polypeptides in hnRNP resulted from non-specific adsorption.

The effect of sodium chloride on the structure of ribonucleoprotein particles from rat liver nuclei

38S (monoparticles) and greater than 50--200S ribonucleoprotein particles (polyparticles) from rat liver nuclei were treated with increasing concentrations of sodium chloride. Treatment of 38S or greater than 50--200S particles, with 0.14, 0.25, 0.5, 1.0, and 2.0M NaCl resulted in a decrease of protein to RNA ratios from 8 to 3.1 for 38S particles and from 4.0 to 1.5 for greater than 20--200S particles. Correspondingly the densities in CsCl increased. Whereas the maximum of the sedimentation profile of polyparticles decreased from 90S to 50S after treatment with increasing NaCl concentrations, a discontinuous change was found in the case of monoparticles. It was shown by sodium dodecyl sulfate-polyacrylamide gel electrophoresis that the proteins which were dissociated by NaCl were in the molecular weight range of 30--45 000. Four of the 5 small molecular weight RNAs in the range of 4.5 to 8S remained tightly associated even after treatment of polyparticles with 2.0M NaCl. When 38S or 70--200S nRNP particles were exposed to increasing concentrations of NaCl (0.25, 0.5, 1.0, 2.0M), the molar ellipticity at 264 nm increased progressively to about 40%. Upon NaCl treatment of polyparticles and successive removal of the dissociated proteins by centrifugation the increase in the positive CD band at 264 nm was only 15%.

Two chromatin fractions with different metabolic properties of non-histone proteins and of newly synthesized RNA

Digestion of chromatin with micrococcal nuclease under mild conditions results in the release of a minor chromatin fraction showing an increased RNA and non-histone protein content, a fast turnover of the non-histone proteins and the presence of rapidly labelled heterogeneous nuclear RNA (hnRNA) with half-life of about 20 min. Further digestion of the chromatin leads to the elimination of about 19% of the initial chromosomal DNA, thus leaving a second chromatin fraction relatively resistant to nuclease attack. This fraction has a low protein and RNA content and contains only metabolically stable non-histone proteins. No differences in the histone complement of the two fractions was found except for a 40% deficiency of H1 in the minor fraction.

Rearrangements in the course of ribonuclease hydrolysis of pre-messenger ribonucleoproteins. A warning

A study of the action of ribonuclease on 30--50-S monoparticles prepared from pre-messenger ribonucleoprotein (pre-mRNA . protein) was started in order to elucidate the structure of monoparticles. A ribonucleoprotein complex containing mostly 30000--38000-Mr proteins of pI 7--9 (alpha class) persisted under conditions where other proteins (23000--110000 Mr, pI 5--8.5, beta class) were relased. An unexpected increase of sedimentation coefficient accompanied the formation of the ribonucleoprotein complex. The extent of increase varied with the initial size of the monoparticles, reaching 45% for 30-S monoparticles. The ribonucleoprotein complexes designated here as 40--45-S alpha-ribonucleoproteins were more homogeneous in size than the original monoparticles. Electron microscopic examination showed that the sedimentation shift corresponded to an increase of the actual size of the particles, not to flattening or change of shape. Therefore, the 40--45-S alpha-ribonucleoprotein is not a pre-existing unit of pre-mRNA . protein but arises from specific rearrangements probably between small alpha ribonucleoproteins formed by fragmentation of monoparticles. In addition to the 40--45-S alpha-ribonucleoproteins, large protein aggregates corresponding to 15% of the monoparticle proteins were formed upon ribonuclease hydrolysis. Their major proteins were neutral, suggesting that the aggregates might be precipitates of proteins at pH close to the pI. Ribonuclease being a widespread cellular enzyme, partial rearrangements may occur during preparation and handling of pre-mRNA . protein. It is particularly crucial to remark that the 40--45-S alpha-ribonucleoprotein which does not pre-exist might be mistaken for a pre-mRNA . protein unit.

Studies on the preparation and properties of ribonucleoprotein particles from rat liver nuclei

Ribonucleoprotein particles of 38 S were extracted from rat liver nuclei with isotonic salt buffer under concomitant sonication. The fate of the endogeneous nuclear RNAases assayed with poly(A), high molecular weight yeast RNA and rapidly labeled hnRNA was followed during the preparation of 38-S nuclear ribonucleoprotein (nRNP) particles. Essentially all the RNAase activity could be removed from the particle preparation. The effect of synthetic RNAase inhibitors on the nRNP particles was studied. Upon extraction of nuclei with 0.14 M NaCl, approximately 38% of the total nuclear radioactivity was found in the 38-S nRNP particles. By two successive extractions of the remaining chromatin with either isotonic or 0.22 and 0.3 M NaCl, an additional 25 and 9% of rapidly labeled hnRNA of 38 S particle were dissociated from chromatin, respectively. The chromatin components, DNA, nonhistone proteins, histones and RNA were determined after successive salt extractions. Particularly alterations in the nonhistone proteins and RNA were found. The protein patterns upon SDS-acrylamide gel electrophoresis of the salt-extracted chromatin preparations were compared with those of the 38-S nRNP particles. Particularly proteins in the molecular weight range of 32 000-43 000 were dissociated from chromatin after treatment with 0.22 or 0.3 M NaCl.

Protein composition of nuclear ribonucleoprotein particles isolated from liver of rats in the early stages of feeding of 3'-methyl-4-dimethylaminoazobenzene and from hepatoma induced by the same carcinogen

The feeding of carcinogenic 3'-methyl-4-dimethylaminoazobenzene (3'-MeDAB) in the early stages results in a change in the protein composition of the nuclear ribonucleoprotein particles of the rat liver. These particles are associated with newly synthesized RNA and it is assumed that they are involved in the processing and in the transport of this RNA. After 6 weeks of feeding of this azocarcinogen, the amount of one of the main polypeptides (apparent molecular weight 42 000) is decreased and after 10 weeks of feeding the particles are devoid of this polypeptide completely. Feeding of the non-carcinogenic p-aminoazobenzene (AB) is without any effect. The loss of this polypeptide is not characteristic for the malignant transformation. In the nuclear ribonucleoprotein particles isolated from hepatoma which has been induced by 3'-MeDAB this polypeptide is present in even higher proportion to other polypeptides than it is in particles isolated from liver cells of control animals. The 3'-MeDAB binds to the proteins of the liver nuclear ribonucleoprotein particles and interferes with the RNA processing. It is proposed that the changes in the composition of the protein moiety of the particles reflect changes in the population of liver cells leading finally to the selection of hepatoma cells which are resistant to the toxic effect of 3'-MeDAB on RNA processing.

Selective inhibition with sodium cyanate of protein synthesis in colon cancer cells

Sodium cyanate, which in its tautomeric acidic form, isocyanic acid, acts as a protein carbamylating reagent, has been previously shown to inhibit selectively both DNA and protein synthesis in a variety of solid tumors. We have now compared its effects on protein synthesis in normal colonic epithelium and in colon tumors induced by the administration of 1,2-dimethylhydrazine to rats. The incorporation of 3H-amino acids into cytoplasmic and nuclear protein fractions was suppressed to a much greater extent in the tumor tissue than in colonic epithelial tissue surrounding the tumors of cyanate-treated rats. Despite its effect on tumor protein synthesis in whole animals, cyanate had little or no effect on cultured cells (HT-29) derived from a human adenocarcinoma of the colon, nor on other malignant cell lines such as HeLa S3 cells, chick fibroblasts transformed by the Rous sarcoma virus, mouse Ehrlich ascites tumor cells, or rat Novikoff hepatoma cells. However, the administration of cyanate i.p. does suppress amino acid incorporation by Novikoff hepatoma cells in the peritoneal cavity of rats. The implication that the mechanism of cyanate inhibition of protein synthesis in tumors may require its in vivo metabolism or utilization to produce a postsynthetic modification of circulatory factors is discussed.

Serum stimulation of human fibroblasts: effect on non-histones of nuclear ribonucleoprotein and chromatin

In quiescent human fibroblasts stimulated to proliferate by fresh medium plus 15% serum, no changes were seen in the incorporation of 3H tryptophan into the protein of nuclear ribonucleoprotein during the first three hours following re-feeding. This was in contrast to non-histone chromosomal proteins where the incorporation increased by 90% within ten minutes. The density of the formaldehyde fixed nuclear ribonucleoprotein in CsCl was 1.43-1.44 g/ml and this also did not change following stimulation. The electrophoretic profile of the proteins of nuclear ribonucleoprotein on SDS gels exhibited a predominant band corresponding to a molecular weight of 44,000 closely trailed by a band at 47,000 and other bands at higher molecular weight. This pattern was not altered by serum stimulation and the same was true for the more complex electrophoretic profile of the chromatin proteins. Following a 10-minute pulse of 3H-tryptophan at ten minutes after stimulation, there was a selective increase in the labeling of non-histone chromosomal protein of molecular weight 59,000; no change was seen in the labeling of any protein of nuclear ribonucleoprotein.

Complexity of the structure of particles containing heterogeneous nuclear RNA as demonstrated by ribonuclease treatment

Brain ribonucleoprotein particles containing heterogeneous nuclear RNA (hnRNA) and a large number of polypeptides ranging from 23000 to 150000 molecular weight were treated with pancreatic and T1 ribonucleases at low (0.1 or 0.5 microng plus 5 or 25 units/ml), high (2 microng plus 100 units/ml) and very high (20 microng plus 1000 units/ml) concentrations. At low enzyme concentration, a large fraction of the particle material accumulated at 35-45 S. The accumulation was more marked for proteins in the 30000-38000 molecular weight range. Heterogeneous complexes containing a large spectrum of proteins with a characteristic distribution were disclosed between 60 and 200 S. At high ribonuclease concentration the total quantity of proteins at 35-45 S decreased, but the proteins of 30000-38000 molecular weight predominated. Heterogeneous complexes were also present. Finally at very high enzyme concentration, the particles were almost entirely hydrolyzed. Only a small amount of heterogeneous complexes subsisted at 30-190 S. The RNA content of the remaining ribonucleoprotein complexes as well as its size decreased upon ribonuclease treatment as shown by CsCl density determination and electrophoretic analysis. The results suggested that the stability of the complexes depended upon protein-protein as well as RNA-protein interactions. They also showed that sequences up to 200-300 nucleotides were protected by proteins against ribonuclease. The results were compatible with the existence of at least 3 constituents in the particles. The previously defined monoparticle population accumulating at 35-45 S was heterogeneous in respect to ribonuclease sensitivity and protein composition. The 30000-38000 molecular weight proteins accumulating at low ribonuclease and predominating afterwards were assumed to belong to monoparticles alpha. Monoparticles beta contained a larger range of proteins more easily released by the enzymes. The heterogeneous complexes were a third constituent whose relationship with the monoparticles war not established yet. A large fraction of the particle phosphoproteins was associated to these complexes. On the basis of our experiments in vitro it is assumed that monoparticle alpha can be preferentially isolated from the nuclei under conditions where endogeneous ribonuclease is high and (or) not inhibited. This might explain why, in certain cases, only one or a few proteins were described in nuclear particles instead of the complete set present in the native particles.

Dependence of the composition of the protein moiety of nuclear ribonucleoprotein particles on the extent of particle purification as studied by electrophoresis including a two-dimensional procedure

Extraction with 0.1 M NaCl in 0.01 M Tris-HCl buffer, pH 8.0 releases from liver nuclei 30-40-S ribonucleoprotein particles containing newly synthesized RNA. Separation of the protein moiety of these particles by acid-urea gel electrophoresis depends on the concentration of beta-mercaptoethanol in the buffer used for the solubilization of the particles. At low concentration or with short time of solubilization, only a polypeptide chain with apparent molecular weight 38 000 penetrates into the gel and can be detected by electrophoresis. By introduction of two-dimensional polyacrylamine gel electrophoresis, we succeeded to separate the protein moiety of these particles into a core group of 4 major and 6 minor polypeptides with molecular weights ranging from 38 000 to 50 000 and a second group of 19 polypeptides ranging in molecular weight from 50 000 to 120 000. The composition of the protein moiety of these particles is dependent on the extent of purification. Polypeptides with molecular weight below 50 000 represent 55% of the total protein of particles purified only by centrifugation through a 15-30% sucrose gradient. If the particles were first purified by gel filtration through Bio-Gel A-50m followed by centrifugation in sucrose gradient, the low molecular weight proteins represent 80% of all the proteins of the particles. The purification removed selectively the minor high molecular weight polypeptides without resulting in any extensive release of the four major polypeptides with molecular weight below 50 000 which form a stable core particle. By repeated purification it is possible to strip the particles of the high molecular weight polypeptides even further. An increase in the NaCl concentration of the extraction buffer to 0.35 M will extract additional 30-40-S particles associated with a newly synthesized RNA from the cell nucleus. These particles contain the same polypeptides as particles extracted at lower salt concentration. Extraction with 0.1 M and 0.35 M NaCl at pH 8.0 removed from the nucleus approximately 55% of all RNA labeled in 30 min after intraperitoneal injection of [3H] orotic acid to the rats.