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PubMed2004

The structural basis for the interaction between nonsense-mediated mRNA decay factors UPF2 and UPF3.

Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons. Three 'up-frameshift' proteins, UPF1, UPF2 and UPF3, are essential for this process in organisms ranging from yeast to human. We present a crystal structure at a resolution of 1.95 A of the complex between the interacting domains of human UPF2 and UPF3b, which are, respectively, a MIF4G (middle portion of eIF4G) domain and an RNP domain (ribonucleoprotein-type RNA-binding domain). The protein-protein interface is mediated by highly conserved charged residues in UPF2 and UPF3b and involves the beta-sheet surface of the UPF3b RNP domain, which is generally used by these domains to bind nucleic acids. We show that the UPF3b RNP does not bind RNA, whereas the UPF2 construct and the complex do. Our results advance understanding of the molecular mechanisms underlying the NMD quality control process.

Amino Acid Sequence↗

PubMed1999

Changes in side-chain and backbone dynamics identify determinants of specificity in RNA recognition by human U1A protein.

The ribonucleoprotein (RNP) domain is one of the most common eukaryotic protein domains, and is found in many proteins involved in recognition of a wide variety of RNAs. Two structures of RNA complexes of human U1A protein have revealed important aspects of RNP-RNA recognition, but have also raised intriguing questions concerning how RNP domains discriminate between different RNAs. In this work, we extend the investigation of U1A-RNA recognition by comparing the dynamics of U1A protein both free and in complex with RNA. We have also investigated the trimolecular complex between two U1A proteins and the complete polyadenylation inhibition element to study the effect of RNA-dependent protein-protein interactions on protein conformational flexibility. We report that changes in backbone dynamics upon complex formation identify regions of the protein where conformational exchange processes are quenched in the RNA-bound conformation. Furthermore, amino acids whose side-chains experience significant changes in conformational flexibility coincide with residues particularly important for the specificity of the U1A protein/RNA interaction. This study adds a new dimension to the description of the coordinated changes in structure and dynamics that are critical to define the biological specificity of U1A and other RNP proteins.

Amino Acid Sequence↗

PubMed1986

Association of RNA with the cytoskeleton and the nuclear matrix.

Heteronuclear RNA (hnRNA) is preferentially associated (76%) with the nuclear matrix in mammalian cells. Active mRNA, in the form of polyribosomes, is associated (greater than 97%) with the cytoskeletal framework. In this report, we present evidence that the association of both hnRNA and mRNA with structural networks of the cell may be essential features of gene expression. To study the association of polyribosomes with the cytoskeletal framework, cytochalasin D was used to release mRNA from the cytoskeletal framework. Protein synthesis was inhibited by cytochalasin D in direct proportion to the release of mRNA. The released mRNA is unaltered in its translatability as measured in vitro but is no longer translated in the cytochalasin-treated HeLa cells. The residual protein synthesis occurs on polyribosomes that are reduced in amount but display a normal sedimentation distribution. The results support the hypothesis that mRNA binding to the cytoskeletal framework is necessary, though not sufficient, for translation. Further fractionation of the cytoskeletal framework separates nuclear constituents into three distinct protein fractions. Chromatin proteins and 94% of the DNA are released by 0.25 M-ammonium sulphate after inter-nucleosomal DNA is cut with DNase I. The resulting structure retains 76% of the hnRNA in the form of ribonucleoprotein and is designated the RNP-containing nuclear matrix. The proteins of hnRNP complex are those associated with the nucleus only if RNA is intact. These proteins and 97% of the hnRNA are released after brief digestion with RNase A. Visualizing the nuclear matrix using resinless sections shows that nuclear RNA plays an important role in the organization of the nuclear matrix. Electron micrographs of resinless sections show the interior of the matrix to be a three-dimensional network of thick filaments bounded by the nuclear lamina. The filaments are densely covered with 20-30 nm electron-dense particles, which may contain the hnRNA. The RNP-depleted matrix is disordered and the interior fibres aggregated. These results suggest that hnRNA is involved in the spatial organization of the interior of the nuclear matrix.

Animals↗

PubMed1988

Histone H4 mRNA is stored as a small cytoplasmic RNP during the G2 phase in Physarum polycephalum.

In Physarum polycephalum the triggering of histone H4 gene transcription occurs in G2 phase. The rate of synthesis of histone H4 mRNA was measured by in vivo pulse-labeling experiments. We show that it begins to increase in mid-G2. During the second part of G2 it increases approximately 20 fold over its minimum value and reaches a maximum at the end of G2. After entry of the cells in S, histone H4 gene transcription rate begins to decrease and reaches a minimum value in early G2. The histone H4 mRNA which accumulates in G2 is not translated immediately into proteins but is stored in an inactive form until the beginning of the next S phase. Immediately after its transcription the H4 mRNA is transported to the cytoplasm where it is stored and stabilized as an inactive mRNP complex. This was shown by fractionation of cytoplasmic RNP in sucrose gradients and blot hybridization of subcellular fractions.

Cytoplasm↗

PubMed1986

A solid-phase radioimmunoassay for the detection of nRNP immune complexes.

We developed a solid-phase radioimmunoassay for complement (C)-fixing nuclear ribonucleoprotein (nRNP):anti-nRNP immune complexes (nRNP ICs). The assay was based on the ability of the C-fixing nRNP ICs to bind strongly to immobilized F(ab')2 anti-C3. The extent of binding was quantified by incubating the C-fixing nRNP ICs bound to anti-C3 with 125I-labeled anti-nRNP-specific IgG. The interaction between anti-C3 and C-fixing nRNP ICs was rapid, time- and concentration-dependent and sensitive over a broad range of nRNP IC concentrations in an antigen-antibody ratio of 8 : 1 (9.8-5000 ng of human aggregated IgG equivalent per ml). We found that the assay also detected an immunoreactive U1-RNP antigen in Sm : anti-Sm immune complexes but did not detect SSA : anti-SSA immune complexes. The assay was preliminary applied for serum samples obtained from patients with mixed connective tissue disease (MCTD), and elevated concentrations of nRNP immune complexes were found in 3 out of 5 patients with MCTD. This assay appears to be applicable to the detection and quantification of circulating nRNP ICs in patients with MCTD.

Adult↗

PubMed1979

Antibody penetration into living cells. II. Anti-ribonucleoprotein IgG penetrates into Tgamma lymphocytes causing their deletion and the abrogation of suppressor function.

We have previously shown that an anti-ribonucleoprotein (RNP) IgG can penetrate into live human mononuclear cells (MNC) having receptors for the Fc portion of IgG. Because T cells with such receptors (Tgamma cells) seem to behave as suppressor cells in immune regulation and because this suppressor function is diminished in diseases where antinuclear antibodies appear, we considered the possibility that antinuclear IgG antibody could penetrate Tgamma cells and affect them. Herein we show that fluorescein-labeled anti-RNP IgG can penetrate into Tgamma cells, enriched by either mitogenic stimulation or separation with a subpopulation of T cells with low affinity for sheep erythrocytes. Incubation of MNC with anti-RNP IgG before carrying out the separation procedures resulted in apparent loss of Tgamma cells at the end of separation. To confirm that deletion had actually occurred, we performed a cytotoxicity assay using 51Cr-labeled T cells. Anti-RNP IgG had a significantly higher cytotoxic effect that normal IgG on T cells, particularly on those with low affinity for sheep erythrocytes that include most Tgamma cells. Suppressor cell function studied in a system where it was expanded, by either 7-day culture or incubation with concanavalin A, and detected in a reverse plaque-forming cell assay with rabbit anti-human immunoglobulin-developing antibody was found to be abrogated by the addition of anti-RNP IgG to the suppressor function-expanding cultures. Controls in Ig-free medium, or medium supplemented with normal human IgG, aggregated normal human IgG, BSA-anti-BSA immune complexes, or F(ab')2 fragments of the anti-RNP IgG, did not abrogate suppressor cell function. This indicates that the abrogation of suppressor cell function by anti-RNP IgG is due to its penetration into Tgamma cells. Suppressor cell loss and/or dysfunction caused by penetration of antinuclear antibodies into Tgamma cells may lead to the self-perpetuation of autoimmune disease.

Animals↗

PubMed1991

Formation of a small ribonucleoprotein particle between Tat protein and trans-acting response element in human immunodeficiency virus-infected cells.

The trans-acting response element (TAR) within the long terminal repeat of human immunodeficiency virus (HIV) is present in all 5' termini of HIV mRNAs and is recognized by the viral Tat protein. Now we describe that the 59-nucleotide-long TAR-RNA exists as a ribonucleoprotein particle in polysomal and heterogeneous nuclear RNP fractions of HIV-1-infected HeLa-T4+ cells. Applying an immunoprecipitation technique this Tat.TAR complex could be isolated from total cell extracts as well as from polysomal or heterogeneous nuclear RNP fractions. The chain length and the identity of the TAR-RNA were established by RNase protection assays while the Tat protein was confirmed by Western blotting technique. The TAR-RNA in this complex was sequenced and found to comprise nucleotides +2 to +61 and hence includes the 3-nucleotide bulge (nucleotides +23 to +25) and the loop sequence of the TAR stem-and-loop structure. The Tat.TAR complex is present in cells at low abundance (12.5 x 10(3) copies/cell). In contrast to the TAR-containing mRNAs, which decay very rapidly after incubation of cells with actinomycin D (half-life of approximately 120 min) the half-life of TAR in the Tat.TAR complex is greater than 180 min. Alignment studies revealed that TAR-RNA (positive strand) has a potential binding ability to the U5 region within the long terminal repeat (DNA negative strand; nucleotides +107 to +147); a complementary binding with a continuous homology of 16 nucleotides was identified. It is proposed that the Tat.TAR complex functions as a small ribonucleoprotein particle during transcription initiation of HIV mRNA.

Base Sequence↗

PubMed1981

Purification and characterization of a simple ribonucleoprotein particle containing small nucleoplasmic RNAs (snRNP) as a subset of RNP containing heterogenous nuclear RNA (hnRNP) from HeLa cells.

A ribonucleoprotein complex whose RNA complement consists exclusively of small nuclear RNA species (snRNA) has been purified from particles containing heterogenous nuclear RNA (hnRNP) from HeLa cells. This was accomplished by taking advantage of their ability to band at a density of about 1.43 g/cm3 in plain cesium chloride as well as in cesium chloride gradients containing 0.5% sarkosyl without prior aldehyde fixation. After these two steps of equilibrium density centrifugation, these snRNPs were still largely contaminated by free proteins (and especially phosphoproteins). A final step of purification by velocity sedimentation in a sucrose gradient containing 0.5 M cesium chloride and 0.5% sarkosyl was efficient in completely eliminating all free proteins. U1, U2, U4, U5 and U6 species according to the nomenclature of Lerner et al. (Nature, (1980) 283, 220-224) were found in these purified snRNPs, while a significant part of U6 and a small amount of U2 were found in the bottom fraction. 5S species behaved entirely as free RNA and is presumably a contaminant of cytoplasmic origin. Electrophoresis of proteins from snRNP labeled in vivo with (35S) methionine, revealed four bands with migrations corresponding to molecular weights ranging between 10,000 and 14,000 daltons.

Base Sequence↗

PubMed2002

A new conformational epitope generated by the binding of recombinant 70-kd protein and U1 RNA to anti-U1 RNP autoantibodies in sera from patients with mixed connective tissue disease.

OBJECTIVE: To establish an enzyme-linked immunosorbent assay (ELISA) using a complex of in vitro-transcribed U1 RNA and recombinant 70-kd, A, and C proteins (C-ELISA) to detect anti-U1 RNP antibodies reactive in double immunodiffusion (DID), but not in ELISA using the proteins alone (P-ELISA). METHODS: Sera from 196 patients with mixed connective tissue disease were used to test reactivity in P- and C-ELISAs, and the specificity of the sera was also tested by DID and immunoprecipitation (IP). RESULTS: In P-ELISA, 15 of 196 sera positive for anti-U1 RNP in DID did not react, while all sera reacted in C-ELISA. The reactivity of 15 sera to the U1 RNA was tested by IP and ELISA, and only 3 sera reacted with the U1 RNA. These results indicated that the increased reactivity in C-ELISA was not due to the U1 RNA itself. We confirmed that the 70-kd and A proteins were bound directly to the U1 RNA by IP using antibodies to His-tag, and we tested the reactivity of the sera to the U1 RNA-70-kd protein complex and the U1 RNA-A protein complex by IP. All sera reacted with the U1 RNA-70-kd protein complex, and 1 sample reacted with the U1 RNA-A protein complex. CONCLUSION: These results suggest that some anti-U1 RNP-positive sera specifically recognize the conformational structure altered by the binding of U1 RNA to the proteins, and the ELISA using U1 RNA and recombinant proteins is as useful as the DID method for detecting anti-U1 RNP antibodies.

Autoantibodies↗

PubMed2006

The crystal structure of mouse Nup35 reveals atypical RNP motifs and novel homodimerization of the RRM domain.

The nuclear pore complex mediates the transport of macromolecules across the nuclear envelope (NE). The vertebrate nuclear pore protein Nup35, the ortholog of Saccharomyces cerevisiae Nup53p, is suggested to interact with the NE membrane and to be required for nuclear morphology. The highly conserved region between vertebrate Nup35 and yeast Nup53p is predicted to contain an RNA-recognition motif (RRM) domain. Due to its low level of sequence homology with other RRM domains, the RNP1 and RNP2 motifs have not been identified in its primary structure. In the present study, we solved the crystal structure of the RRM domain of mouse Nup35 at 2.7 A resolution. The Nup35 RRM domain monomer adopts the characteristic betaalphabetabetaalphabeta topology, as in other reported RRM domains. The structure allowed us to locate the atypical RNP1 and RNP2 motifs. Among the RNP motif residues, those on the beta-sheet surface are different from those of the canonical RRM domains, while those buried in the hydrophobic core are highly conserved. The RRM domain forms a homodimer in the crystal, in accordance with analytical ultracentrifugation experiments. The beta-sheet surface of the RRM domain, with its atypical RNP motifs, contributes to homodimerization mainly by hydrophobic interactions: the side-chain of Met236 in the beta4 strand of one Nup35 molecule is sandwiched by the aromatic side-chains of Phe178 in the beta1 strand and Trp209 in the beta3 strand of the other Nup35 molecule in the dimer. This structure reveals a new homodimerization mode of the RRM domain.

Amino Acid Motifs↗

PubMed2001

Structure of the C-terminal RNA-binding domain of hnRNP D0 (AUF1), its interactions with RNA and DNA, and change in backbone dynamics upon complex formation with DNA.

Heterogeneous nuclear ribonucleoprotein (hnRNP) D0 has two ribonucleoprotein (RNP) -type RNA-binding domains (RBDs), each of which can specifically bind to the UUAG-sequence. hnRNP D0 also binds specifically to single-stranded d(TTAGGG)(n), the human telomeric DNA repeat. We have already reported the structure and interactions with RNA of the N-terminal RBD (RBD1). Here, the structure of the C-terminal RBD (RBD2) determined by NMR is presented. It folds into a compact alpha beta structure comprising an antiparallel beta-sheet packed against two alpha-helices, which is characteristic of RNP-type RBDs. In addition to the four beta-strands commonly found in RNP-type RBDs, an extra beta-strand, termed beta 4(-), was found just before the fourth beta-strand, yielding a five-stranded beta-sheet. Candidate residues of RBD2 involved in the interactions with RNA were identified by chemical shift perturbation analysis. Perturbation was detected on the beta-sheet side, not on the opposite alpha-helix side, as observed for RBD1. It is notable that the beta 4(-) to beta 4 region of RBD2 is involved in the interactions in contrast to the case of RBD1. The chemical shift perturbation analysis also showed that RBD2 interacts with DNA in essentially the same way as with RNA. Changes in the backbone dynamics upon complex formation with DNA were examined by means of model free analysis of relaxation data. In free RBD2, the beta 4(-) to beta 4 region exhibits slow conformational exchange on the milli- to microsecond time scale. The exchange is quenched upon complex formation. The flexibility of free RBD2 may be utilized in the recognition process by allowing different conformational states to be accessed and facilitating induced fit. Additionally, faster flexibility on the nano- to picosecond time scale was observed for loop 3 located between beta 2 and beta 3 in free RBD2, which is retained by the complex as well.

Amino Acid Sequence↗

PubMed2002

Nuclear estrogen receptor II (nER-II) is involved in the estrogen-dependent ribonucleoprotein transport in the goat uterus: II. Isolation and characterization of three small nuclear ribonucleoprotein proteins which bind to nER-II.

Three proteins of a goat uterine small nuclear ribonucleoprotein (snRNP) fraction, which bind to nuclear estrogen receptor-II (nER-II) have been isolated and purified. These are the p32, p55, and p60 of which p32 is the major nER-II binding protein. Indirect evidence reveals that p32 binds to the nuclear export signal (NES) on the nER-II. nER-II is a snRNA binding protein while p32 does not bind to the RNA. nER-II along with p32 and p55 form an effective Mg(++)ATPase complex, the activation of which appears to be the immediate reason behind the RNP exit from the nuclei following estradiol exposure. The three nER-II binding proteins bind to the nuclear pore complex; nER-II does not possess this property.

Adenosine Triphosphatases↗

PubMed1975

Evidence for tertiary structural RNA-RNA interactions within the protein S4 binding site at the 5'-end of 16S ribosomal RNA of Escherichia coli.+.

Evidence is presented for tertiary structural interaction(s) (interactions(s) between two regions of an RNA molecule that are widely separated in the RNA sequence) within the 5'-one third of the 16S ribosomal RNA of Escherichia coli that constitutes the binding site of protein S4. The two main interacting RNA regions were separated by about 120 nucleotides (sections Q to M) of the 16S RNA sequence. A second, smaller gap, of 13 nucleotides, occurred within section C". The two main interacting regions contain about 150 nucleotides (sections H" to Q) and 160 nucleotides (sections M to C"). They are folded back on one another and, especially in the presence of protein S4, are strongly protected against ribonuclease digestion. The intermediate region (sections Q to M), however, is relatively accessible to ribonucleases in the S4-RNP. By partial removal of subfragments from the RNA complex it was possible to localise the two main interacting sites within sections H" - H and sections I" - C". Three main criteria for the specificity of the RNA-RNA interactions were invoked and satisfied. The possibility of other tertiary structural RNA-RNA interactions occurring in other regions of the 16S RNA is discussed. Finally, all the structural information on the S4-RNP is summarised and a tentative model is proposed.

Base Sequence↗

PubMed1990

Human U1-70K ribonucleoprotein antigen gene: organization, nucleotide sequence, and mapping to locus 19q13.3.

We have isolated and sequenced the gene encoding the human U1-70K snRNP protein. U1-70K is an RNA-binding protein that is a specific component of the U1 small nuclear ribonucleoprotein complex (snRNP) and constitutes the major anti-(U1) RNP autoimmune antigen. We have mapped the U1-70K gene to the distal portion of chromosome 19, at band q13.3. The gene is greater than 44 kb in size and consists of 11 exons. The general structure of the gene has been completely conserved during vertebrate evolution and accounts for the production of several different U1-70K mRNA species by alternative pre-mRNA splicing. Comparison of the predicted amino acid sequences of animal U1-70K proteins reveals a high degree of conservation, particularly in the region of the RNP consensus domain. Even more striking is the complete conservation of the nucleotide sequence of an alternative included/excluded exon containing an in-frame translational termination codon. This conservation also includes significant portions of the downstream intervening sequence. This extraordinary conservation at the nucleotide sequence level suggests that alternative splicing of this exon serves an important function, perhaps in regulating the production of functional U1-70K protein.

Amino Acid Sequence↗

PubMed2002

Nuclear export of 5S rRNA-containing ribonucleoprotein complexes requires CRM1 and the RanGTPase cycle.

In Xenopus oocytes, 5S rRNA is exported out of the nucleus in the context of two ribonucleoprotein complexes (RNPs): complexed with transcription factor IIIA as the 7S RNP or as the 5S RNP with ribosomal protein L5. 5S rRNA-containing RNP export takes place at a slow rate in comparison to that of nuclear export signal-containing proteins and the U1 snRNP. Using oocyte microinjection assays we found that the export of 5S RNPs requires nuclear RanGTP and RanGTP hydrolysis and is leptomycin B-sensitive, indicating the process is mediated by the export receptor CRM1. A novel nuclear export signal motif is characterised in a region of L5 also possessing a nuclear import signal, thus identifying a shuttling domain for this protein. This same motif in L5 is found to be required for interaction with CRM1 in vitro and for export in vivo.

Active Transport, Cell Nucleus↗

PubMed2001

Interaction of the influenza virus nucleoprotein with the cellular CRM1-mediated nuclear export pathway.

Influenza virus transcription occurs in the nuclei of infected cells, where the viral genomic RNAs are complexed with a nucleoprotein (NP) to form ribonucleoprotein (RNP) structures. Prior to assembly into progeny virions, these RNPs exit the nucleus and accumulate in the cytoplasm. The mechanisms responsible for RNP export are only partially understood but have been proposed to involve the viral M1 and NS2 polypeptides. We found that the drug leptomycin B (LMB), which specifically inactivates the cellular CRM1 polypeptide, caused nuclear retention of NP in virus-infected cells, indicating a role for the CRM1 nuclear export pathway in RNP egress. However, no alteration was seen in the cellular distribution of M1 or NS2, even in the case of a mutant virus which synthesizes greatly reduced amounts of NS2. Furthermore, NP was distributed throughout the nuclei of infected cells at early times postinfection but, when retained in the nucleus at late times by LMB treatment, was redistributed to the periphery of the nucleoplasm. No such change was seen in the nuclear distribution of M1 or NS2 after drug treatment. Similar to the behavior of NP, M1 and NS2 in infected cells, LMB treatment of cells expressing each polypeptide in isolation caused nuclear retention of NP but not M1 or NS2. Conversely, overexpression of CRM1 caused increased cytoplasmic accumulation of NP but had little effect on M1 or NS2 distribution. Consistent with this, NP bound CRM1 in vitro. Overall, these data raise the possibility that RNP export is mediated by a direct interaction between NP and the cellular CRM1 export pathway.

Animals↗

PubMed1993

Mammalian U6 small nuclear RNA undergoes 3' end modifications within the spliceosome.

Mammalian U6 small nuclear RNA (snRNA) is heterogeneous with respect to the number of 3' terminal U residues. The major form terminates with five U residues and a 2',3' cyclic phosphate. Because of the presence in HeLa cell nuclear extracts of a terminal uridylyl transferase, a minor form of U6 snRNA is elongated, producing multiple species containing up to 12 U residues. In this study we have used glycerol gradients to demonstrate that these U6 snRNA forms are assembled into U6 ribonucleoprotein (RNP), U4/U6 snRNPs, and U4/U5/U6 tri-snRNP complexes. Furthermore, glycerol gradients combined with affinity selection of biotinylated pre-mRNAs led us to show that elongated forms of U6 snRNAs enter the spliceosome and that some of these become shortened with time to a single species having the same characteristics as the major form of U6 snRNA present in mammalian nuclear extracts. We propose that this elongation-shortening process is related to the function of U6 snRNA in mammalian pre-mRNA splicing.

Base Composition↗

PubMed2002

Functional specialization within the cat red nucleus.

Magnocellular (RNm) and parvicellular (RNp) divisions of the cat red nucleus (RN) project to the cervical spinal cord. RNp projects more heavily to upper cervical levels and RNm projects more heavily to lower levels. The cells in RN are active during reaching and grasping, and the differences in termination suggest that the divisions influence different musculature during this behavior. However, the spinal termination may not reflect function because most rubrospinal terminations are to interneuronal regions, which can influence motor neurons at other spinal levels. To test for functional differences between RNm and RNp, we selectively stimulated RNm and RNp as well as the efferent fibers from each region. Electromyographic activity was recorded from seven muscles of the cat forelimb during reaching. The activity from each muscle was averaged over several thousand stimuli to detect influences of stimulation on muscle activity. Stimulation within the RN produced a characteristic pattern of poststimulus effects. The digit dorsiflexor, extensor digitorum communis (edc), was most likely to show facilitation, and several other muscles showed suppression. The pattern of activation did not differ between RNm and RNp. In contrast, stimulation of RNp fibers favored facilitation of shoulder muscles (spinodeltoideus and supraspinatus), and stimulation of RNm fibers favored facilitation of digit and wrist muscles (edc, palmaris longus, and extensor carpi ulnaris). Fiber stimulation produced few instances of poststimulus suppression. The results from fiber stimulation indicate that the physiological actions of RNm and RNp match their levels of spinal termination. The complex pattern of facilitation and suppression seen with RN stimulation may reflect synaptic actions within the nucleus.

Animals↗