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PubMed1996

Epitopes exposed on hepatitis delta virus ribonucleoproteins.

A total of 17 antibodies, raised in several nonhuman species and specific for different regions on the delta antigen (delta Ag), were used to map, via immunoprecipitation, those domains exposed on the surface of the viral ribonucleoprotein (RNP). These studies showed that the domains for the nuclear localization signal and the C-terminal extension, unique to the large form of delta Ag, are exposed. Also exposed is the C-terminal region of the small form of delta Ag. In contrast, reactivity was not found with the coiled-coil domain needed for protein dimerization. When the hepatitis delta virus (HDV) RNA was released by treatment of viral RNP with vanadyl ribonucleoside complexes, no change in the pattern of delta Ag epitope presentation was detected, consistent with the interpretation that a multimeric protein structure persists in the absence of RNA. These RNP studies have implications not only for understanding of the process of HDV assembly but also for evaluation of the immune responses of an infected host to HDV replication.

Animals↗

PubMed1990

Reconstitution of influenza virus RNA-nucleoprotein complexes structurally resembling native viral ribonucleoprotein cores.

Reconstitution of influenza virus nucleoprotein (NP)-RNA complexes was performed with segment 8 RNA, which was synthesized in vitro from cDNA, and NP purified from virions. Under optimum conditions established using a filter binding assay and a gel retardation assay, NP was found to bind any RNA longer than 15 nucleotides. NP-RNA complexes formed at 30 degrees C are more resistant to high concentrations of NaCl than those formed at 0 degrees C. Treatment of NP with N-ethylmaleimide gave no effect on its RNA binding activity, whereas treatment with alkaline phosphatase enhanced its RNA binding activity. The newly developed "reverse-printing" method of RNase V1-treated complexes revealed that reconstituted NP-RNA complexes carry RNase V1-sensitive sites as do native ribonucleoprotein (RNP) cores (RNA polymerase-NP-RNA complexes), implying that RNA-NP complexes structurally similar to native RNP cores are reconstituted from isolated components.

Alkaline Phosphatase↗

PubMed1981

Arrangement of 30S heterogeneous nuclear ribonucleoprotein on polyoma virus late nuclear transcripts.

Heterogeneous nuclear ribonucleic acid (hnRNA) molecules in eucaryotic cell nuclei associate with a well-defined group of abundant, highly conserved proteins to form heterogeneous nuclear ribonucleoproteins (hnRNP). The exact manner in which these 30S complexes assemble on nuclear transcripts, however, has not been well documented. To determine whether any site selectivity in the formation of hnRNP can be detected (e.g., preferential recognition of intervening sequences or of premessage regions), we investigated the distribution of 30S hnRNP on a particular nuclear RNA, the polyoma virus late transcript. Hybridization studies showed not only that the majority of polyoma late nuclear RNA sequences can be isolated in the form of 30S complexes, but that the RNP were located equally on intervening sequences and premessage portions of the transcript. The latter conclusion was confirmed by ribonuclease T1 oligonucleotide fingerprint analysis of polyoma virus-specific RNA recovered from native 30S complexes. However, fingerprint analysis of the small segments of viral RNA in the 30S fraction that survived extensive ribonuclease treatment revealed that oligonucleotides corresponding to intervening sequences were preferentially lost. We discuss these findings in relation to the structure of 30S hnRNP and their function in RNA biogenesis.

Heterogeneous-Nuclear Ribonucleoproteins↗

PubMed1975

Electron microscopic observations on the poly(A)-RNP component of the pre-mRNA containing nuclear complexes.

The nuclear ribonucleoprotein particles containing polyadenylic acid were prepared from rat liver nuclear extract by treatment with RNase I. The sedimentation coefficient of the particles was approximately 14 S. These particles represent a component of the pre-mRNA containing ribonucleoprotein complexes of the nucleus. The submicroscopic morphology of the particles was examined in preparations pretreated by platinum-palladium shadowing and by various negative staining methods as well as in ultrathin sections. The 14 S particles are globular structures, 120-140 A in diameter. The particles are characterized by a strong tendency to aggregation. The results are discussed with respect to mRNA transport.

Animals↗

PubMed2006

Compartmentalization directs assembly of the signal recognition particle.

Many ribonucleoprotein complexes assemble stepwise in distinct cellular compartments, a process that usually involves bidirectional transport of both RNA and proteins between the nucleus and cytoplasm. The biological rationale for such complex transport steps in RNP assembly is obscure. One important example is the eukaryotic signal recognition particle (SRP), a cytoplasmic RNP consisting of one RNA and six proteins. Prior in vivo studies support an "SRP54-late" assembly model in which all SRP proteins, except SRP54, are imported from the cytoplasm to the nucleus to bind SRP RNA. This partially assembled complex is then exported to the cytoplasm where SRP54 binds and forms the SRP holocomplex. Here we show that native SRP assembly requires segregated and ordered binding by its protein components. A native ternary complex forms in vitro when SRP19 binds the SRP RNA prior to binding by SRP54, which approximates the eukaryotic cellular pathway. In contrast, the presence of SRP54 disrupts native assembly of SRP19, such that two RNA-binding loops in SRP19 misfold. These results imply that SRP54 must be sequestered during early SRP assembly steps, as apparently occurs in vivo, for proper assembly of the SRP to occur. Our findings emphasize that spatial compartmentalization provides an additional level of regulation that prevents competition among components and can function to promote native assembly of the eukaryotic SRP.

Active Transport, Cell Nucleus↗

PubMed2001

Nuclear DNA helicase II/RNA helicase A binds to filamentous actin.

Nuclear DNA helicase II (NDH II), also designated RNA helicase A, is a multifunctional protein involved in transcription, RNA processing, and transport. Here we report that NDH II binds to F-actin. NDH II was partially purified from HeLa nuclear extracts by ion-exchange chromatography on Bio-Rex 70 and DEAE-Sepharose. Upon gel-filtration chromatography on Sepharose 4B, partially purified NDH II resolved into two distinct peaks. The first NDH II peak, corresponding to the void volume of Sepharose 4B, displayed coelution with an abundant 42-kDa protein that was subsequently identified as actin. Several nuclear proteins such as RNA polymerase II, the U5 small nuclear ribonucleoprotein (RNP)-associated WD40 protein, and heterogeneous nuclear RNPs (hnRNPs) copurified with NDH II. However, only hnRNPs A1 and C were found together with NDH II and actin polymers during gel filtration. NDH II and hnRNP C from the HeLa nuclear extract coeluted with F-actin on Sepharose 4B in an RNase-resistant manner, whereas hnRNP A1 was nearly completely removed from F-actin-associated hnRNP complexes following RNA digestion. The association of NDH II and hnRNP C with F-actin was abolished by gelsolin, an F-actin-depolymerizing protein that fragments actin polymers into oligomers or monomers. Furthermore, NDH II co-immunoprecipitated with F-actin and hnRNP C, respectively. In vitro translated NDH II coeluted with F-actin on Sepharose 4B, whereas no coelution with F-actin was observed for in vitro translated hnRNP A1 or C1. Binding to F-actin requires an intact C terminus of NDH II and most likely a native protein conformation. Electron microscopy indicated a close spatial proximity among NDH II, hnRNP C, and F-actin within the HeLa nucleus. These results suggest an important function of NDH II in mediating the attachment of hnRNP-mRPP RNP complexes to the actin nucleoskeleton for RNA processing, transport, or other actin-related processes.

Actins↗

PubMed1987

Nature of immune complexes in autoimmune chronic active hepatitis.

Immune complexes containing antinuclear antibodies have been observed in autoimmune chronic active hepatitis. Using a library of nuclear constituents (deoxyribonucleic acid, small nuclear ribonucleoproteins, and histones), we analyzed the antigens involved in formation of immune complexes. Immune complexes were defined in dissociation experiments, and after separation under dissociating conditions. Immune complexes composed of histones and immunoglobulin G were observed in four of nine immune complex-positive autoimmune chronic active hepatitis sera. Immune complexes containing the small nuclear ribonucleoprotein U1-RNP and immunoglobulin G were observed in two additional samples. Kidney eluates obtained from 2 patients with autoimmune chronic active hepatitis and membranous glomerulonephritis revealed enrichment of anti-U1-RNP, suggesting specific deposition of this antibody in complexed form. Circulating immune complexes containing histones were observed only in patients with autoimmune chronic active hepatitis-associated sicca syndrome; those containing U1-RNP were restricted to patients with autoimmune chronic active hepatitis associated with kidney disease.

Antibodies, Antinuclear↗

PubMed1979

Fractionation of constituents of ribonucleoproteins containing heterogeneous nuclear ribonucleic acid.

A method of fractionation of hnRNP constituents adaptable to large-scale preparation is presented. It is based on differential resistance to salt dissociation of the two classes of units of hnRNP, the 30--50S monoparticles and the heterogeneous complexes. The monoparticle proteins were released from hnRNP by 0.4 M NaCl. They were separated from the salt-resistant RNP corresponding to the heterogeneous complexes in three steps: chromatography on DEAE-cellulose, high-speed centrifugation, and Bio-Gel chromatography. The latter chromatography permitted a first fractionation of monoparticle proteins according to molecular weight. Such fractions may serve for purification of individual proteins of molecular weight below 80 000. After the two first steps, two fractions of salt-resistant RNP were obtained. In addition to heterogeneous RNA up to 30 S, small nuclear RNAs were detected which represented 6% of total RNA. The protein pattern was complex, and no clear-cut segregation of groups of proteins could be observed between the two fractions. They were both highly enriched in phosphoproteins as compared to nomoparticle proteins. In another fraction corresponding to the void volume of Bio-Gel chromatography, one-third of the RNA was small nuclear RNA. It is suggested that this fraction contains snRNP in addition to free proteins of molecular weight above 80 000 and to salt-resistant RNP similar to those described above but of small size.

Animals↗

PubMed2004

Human UP1 as a model for understanding purine recognition in the family of proteins containing the RNA recognition motif (RRM).

Heterogeneous ribonucleoprotein A1 (hnRNP A1) is a prototype for the family of eukaryotic RNA processing proteins containing the common RNA recognition motif (RRM). The region consisting of residues 1-195 of hnRNP A1 is referred to as UP1. This region has two RRMs and has a high affinity for both single-stranded RNA and the human telomeric repeat sequence d(TTAGGG)(n). We have used UP1's novel DNA binding to investigate how RRMs bind nucleic acid bases through their highly conserved RNP consensus sequences. Nine complexes of UP1 bound to modified telomeric repeats were investigated using equilibrium fluorescence binding and X-ray crystallography. In two of the complexes, alteration of a guanine to either 2-aminopurine or nebularine resulted in an increase in K(d) from 88nM to 209nM and 316nM, respectively. The loss of these orienting interactions between UP1 and the substituted base allows it to flip between syn and anti conformations. Substitution of the same base with 7-deaza-guanine preserves the O6/N1 contacts but still increases the K(d) to 296nM and suggests that it is not simply the loss of affinity that gives rise to the base mobility, but also the stereochemistry of the specific contact to O6. Although these studies provide details of UP1 interactions to nucleic acids, three general observations about RRMs are also evident: (1) as suggested by informatic studies, main-chain to base hydrogen bonding makes up an important aspect of ligand recognition (2) steric clashes generated by modification of a hydrogen bond donor-acceptor pair to a donor-donor pair are poorly tolerated and (3) a conserved lysine position proximal to RNP-2 (K(106)-IFVGGI) orients the purine to allow stereochemical discrimination between adenine and guanine based on the 6-position. This single interaction is well-conserved in known RRM structures and appears to be a broad indicator for purine preference in the larger family of RRM proteins.

Base Sequence↗

PubMed1980

Stimulation by aminoacyl-tRNA of the GTPase and ATPase activities of rat liver 5S RNA protein particles in the presence of EF-2.

The GTP- and ATP-hydrolyzing activities of the rat liver 5S RNA-L5 (according to the proposed common nomenclature (1) protein complex designated as 5S RNP were stimulated by pig liver elongation factor 2 (EF-2) plus aminoacyl-tRNA, both of which were required for the stimulation. The stimulative effect of aminoacyl-tRNA on GTP hydrolysis by the complete system containing 5S RNP and EF-2 was dependent on the concentration of aminoacyl-tRNA. Aminoacyl-tRNA also stimulated ATP hydrolysis by the complete system but did not stimulate the ATP hydrolysis by 5S RNP alone or EF-2 alone. While deacylated tRNA stimulated the ATPase activity of the complete system, it had no effect on the GTPase activity. Preincubated tRNA lacking the 3'-terminal CCA moiety had little effect on the GTPase and ATPase activities of the complete system. Fusidic acid inhibited the GTPase and the ATPase activities of the complete system with and without aminoacyl-tRNA, although the extent of the inhibition was larger in the presence of aminoacyl-tRNA. These results suggest that 5S RNP may be a component of the GTPase center of rat liver 60S subunits.

Adenosine Triphosphatases↗

PubMed1979

Late transcription and simultaneous replication of simian adenovirus 7 DNA as revealed by spreading lytically infected cell cultures.

Miller's technique of spreading DNA was applied to monkey cells productively infected with simian adenovirus 7. This permitted the visualization of cellular DNA transcription, both nucleolar and non-nucleolar, and of late transcription and replication of virus. Virus double-stranded DNA, thin fibres with very few nucleosome-like particles, were observed carrying either transcription or replication complexes. In addition, both RNP transcripts and replication forks were found on some virus duplex DNA. Virus single-stranded DNA replicative intermediates were identified on the basis of their increased thickness and contrast which results from the presence of a DNA binding protein.

Adenoviridae↗

PubMed1994

Immunocytochemical characterization of nuclear ribonucleoprotein fibrils in cells of the central nervous system of the rat.

Nucleoplasmic structural constituents observed in partially decondensed nuclei of the central nervous system of the rat were analyzed by postembedding immunoelectron microscopy using antibodies specifically recognizing heterogenous nuclear ribonucleoprotein (hnRNP) and small nuclear ribonucleoprotein (snRNP) complexes and DNA. Fibrogranular RNP structures (polyparticles) were found in close proximity to DNA containing fibrillar areas resulting from partial dispersion of compact chromatin. The polyparticle-type fibrils are labeled by antibodies recognizing hnRNP core proteins as well as snRNPs (Sm antigen or 70 kDa protein of U1snRNP) or the m3G-cap structure of snRNAs. These observations suggest that such polyparticle-type fibrils correspond to extended perichromatin fibrils. Partially decondensed perichromatin granules are rarely labeled by anti-snRNP or snRNA antibodies. When labeling occurs it is restricted to the periphery of the granules. However, anti-hnRNP antibodies frequently label these granules. Our results favor the idea, previously proposed for Balbiani ring granules, that perichromatin granules are formed by the folding of hnRNP containing perichromatin fibrils (polyparticles) in the process of splicing, and that mature perichromatin granules contain already spliced messenger RNA.

Animals↗

PubMed1979

Analysis of a 5S RNA-protein complex isolated from the ribosomes of rye embryos.

Rye embryo ribosomes were dissociated into subunits and the large subunit fraction was treated with formamide. A low molecular weight complex of RNA and protein (RNP) was released. Electrophoresis of the RNP in polyacrylamide gels containing sodium dodecyl sulphate yielded an RNA band and a single protein band. The protein had a molecular weight of approximately 41 000 and the RNA of the complex was shown to be 5S ribosomal RNA. Embryos were germinated in the presence of [32P]orthophosphate and the labelled RNP was isolated from their ribosomes. The RNA component was partially digested with pancreatic A ribonuclease and the parts protected from degradation by the protein were determined by sequence analysis. Although the whole 5S RNA molecule was shielded to some extent, the portion most protected was between nucleotides 68 and 108. This is, therefore, probably the part of plant cytosol 5S RNA which is primarily involved in the interaction with protein in the complex and possibly in the ribosome as well.

Base Sequence↗

PubMed1980

Cytochemical studies on the relation of nucleoside triphosphatase activity to ribonucleoproteins in isolated rat liver nuclei.

Cytochemical tests for nucleosidetriphosphatase (NTPase) and Bernhard's preferential staining for ribonucleoproteins (RNP) were applied to isolated rat liver nuclei. The strongest and most easily reproducible positive reaction for NTPase was detected at pH 7.7 with ATP and GTP. This reaction was activated by Mg2+ and Ca2+ and inhibited by Be2+, Zn2+, quercetin, and ribonuclease. The major sites of enzyme reaction were intranuclear RNA-containing structures. Incubation of nuclei in ATP-stimulated RNA-release medium eliminated a considerable part of the material showing both NTPase reaction and staining for RNP; the perichromatin granules disappeared, while interchromatin granules remained. NTPase activity in the nuclear envelope seems to be associated with the annular part of nuclear pore complexes (permanent component) and with RNP particles translocated through nuclear pores or attached to the surface of nuclei (transitional component). From a morphological point of view, these observations support previous biochemical data suggesting the existence of a connection between NTPase activity and the translocation of RNP particles through the nuclear envelope.

Adenosine Triphosphatases↗

PubMed1984

Ultrastructural distribution of nuclear ribonucleoproteins as visualized by immunocytochemistry on thin sections.

The ultrastructural distribution of nuclear ribonucleoproteins (RNP) has been investigated by incubation of thin sections of mouse or rat liver, embedded in Lowicryl K4M or prepared by cryoultramicrotomy, with antibodies specific for RNP. The antibodies were localized by means of a protein A-colloidal gold complex. Anti-small nuclear (sn)RNP antibodies, specific for determinants of the nucleoplasmic snRNP species containing U1, U2, U4, U5, and U6 RNAs, were found associated preferentially with perichromatin fibrils, interchromatin granules, and coiled bodies. This indicates an early association of snRNP with structural constituents containing newly synthesized heterogeneous nuclear RNA. It also suggests a possible structural role of some snRNPs in nuclear architecture. Antibodies against the core proteins of heterogeneous nuclear RNP particles associate preferentially with the border regions of condensed chromatin, and in particular with perichromatin fibrils and some perichromatin granules. These results are discussed in view of recent knowledge about the possible role of nucleoplasmic RNP-containing components in the functions of the cell nucleus.

Animals↗

PubMed1997

Nucleocytoplasmic transport of 5S ribosomal RNA.

Nucleocytoplasmic transport of 5S ribosomal RNA in Xenopus oocytes occurs in the context of small, non-ribosomal RNPs. The complex with the zinc finger protein TFIIIA (7S RNP) is exported from the nucleus and stored in the cytoplasm, whereas the complex with the ribosomal protein L5 (5S RNP) shuttles between the nucleus and the cytoplasm. Nuclear import- and export-signals appear to reside within the protein moiety of these RNPs. Import of TFIIIA is inhibited by RNA binding, whereas nuclear transfer of L5 is not influenced by RNA binding. We propose that the export capacity of both, TFIIIA and L5, is regulated by the interaction with 5S ribosomal RNA.

Journal Article↗

PubMed1980

Electron microscopy of vesicular stomatitis virus replicative ribonucleoproteins.

The objective of this investigation was to examine by electron microscopy the replicative ribonucleoprotein (RNP) structures synthesized in vesicular stomatitis virus-infected HeLa cells. Pulse-labeled in vivo products of vesicular stomatitis virus replication and transcription can be separated by centrifugation in Renografin gradients. Transcription complexes are dissociated, allowing nascent messenger RNPs to remain at the top of the gradient, whereas RNPs biochemically consistent with replication complexes sediment to the middle of the gradient. Examination of these structures by electron microscopy revealed that all exist as coiled or helical RNPs having dimensions of approximately 20 by 700 nm. These structures can be further subdivided into three major morphological classes: (i) linear forms (20 by 769 +/- 158 nm), which have both ends free; (ii) circular forms (20 by 679 +/- 95 nm), which appear to have both ends joined; and (iii) complex forms, which include those structures which are branched replicative complexes as well as those which are random. To distinguish random complexes and possible transcriptive complex contaminants from replicative complexes, it was necessary to uncoil the RNP structures with EDTA so that length measurements could be made relating the nascent strand length to its position on the template. After EDTA treatment, the linear RNPs uncoiled (10 by 4,035 +/- 3,802 nm), and the circular morphology virtually disappeared. However, a new form appeared which was one-half the length and double the width (20 by 2,103 +/- 306 nm) of full-length RNPs and contained a loop at one end and two free ends at the other (alpha-form RNP). The distribution and length analysis of these structures, plus and minus EDTA, suggest that the alpha-form RNPs arise by EDTA-induced uncoiling of circular forms held together at the ends. Close scrutiny of uncoiled complex RNPs revealed no single-strand RNP templates with single-strand nascents. However, several complexes were observed which appeared to contain alpha-form templates with single-strand nascent RNPs. Length measurements suggest these complexes are neither random nor transcriptive, but are replicative. These experiments suggest that replication may, in part, occur on circular coiled RNP templates.

Edetic Acid↗

PubMed1978

[Post-transcriptional association of RNP particles with chromatin in Zajdela ascities hepatoma cells].

The interrelationship between nuclear RNP particles and chromatin in Zajdela hepatoma cells double labelled with 3H-thymidine and 14C-uridine was investigated by three independent methods (Nucleoprotein-Celite chromatography, sucrose density and CsCl band centrifugations). All nuclear RNP particles were found to be associated with the chromatin. Some of chromatin-associated RNA molecules are polyadenylated, thus indicating the post-transcriptional character of this association. DNA and RNA molecules in these complexes are bound through protein rather than being connected directly. The site of contact between RNP particle and chromatin is relatively resistant to the action of DNase I and pancreatic RNase. The experiments with exogeneous labelled RNP particles added to isolated nuclei do not reveal the formation of artificial RNP-chromatin complexes. The results obtained are discussed in the light of current views on the nucleus-to-cytoplasm transport of RNA molecules.

Animals↗