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Complementary change in cis determinants and trans factors in the evolution of an mRNP stability complex.

RNA-protein (RNP) complexes play significant roles in the fate and expression of mRNAs. The prolonged half-life of human alpha-globin mRNA, a major determinant of normal erythroid differentiation, is dependent on the assembly of a sequence-specific 3'-untranslated region (3'UTR) RNP (alpha-complex). We demonstrate that the stability of murine alpha-globin mRNA is controlled by a parallel mechanism. Unexpectedly, however, the respective 3'UTR RNP complexes that stabilize the h(alpha)- and m(alpha)-globin mRNAs differ in structure. While the cis determinants in both species are encoded in polypyrimidine tracks, the human determinant is C-rich (CCUCC motif) while the mouse alpha-3'UTR consists of an equal distribution of Cs and Us (CCUUCU motif). The protein components of the corresponding human and murine alpha-complexes differ in a complementary manner: the previously described 39 kDa poly(C) binding protein (PCBP) present in the human alpha-complex is replaced in the mouse alpha-complex by a 48 kDa cytoplasmic poly(CU) binding protein (CUBP). These results reveal that drift in the primary sequences of the alpha-globin mRNA 3'UTR polypyrimidine tracks in a comparison between mouse and human is paralleled by an alteration in the composition of the corresponding trans-acting components. Surprisingly, these structurally distinct complexes appear to perform the identical function of stabilizing the corresponding alpha-globin mRNAs.

Animals↗

Purification of ribonucleoproteins by a novel approach: isolation of the SSB1 ribonucleoprotein from yeast and demonstration that it has no role in mRNA splicing.

A novel approach is described to purify potential ribonucleoproteins (RNP) of yeast. The method assays a yeast RNP complex, assembled in vitro on actin pre-mRNA, by low-ionic strength acrylamide gel electrophoresis. The minimal protein components of this RNP complex were three proteins, one of 30 kDa and two at 42-44 kDa, defined by formation of the complex on biotinylated-RNA, binding of this complex to avidin-agarose, and salt elution of the protein in the biotinylated-RNP complex. Using the assay for RNP complex formation, an RNP protein was purified to homogeneity on the basis of its affinity towards single-stranded DNA and RNA. This RNP protein turned out to be identical to a known RNP protein, the single-stranded binding protein 1 (ssb1) of yeast, on the basis of identical gel electrophoretic migration, antibody cross-reactivity, and identical properties on the gel complex formation assay. In vitro mRNA splicing was normal in extracts made from a yeast strain missing ssb1 (ssb1- strain). Addition of anti-ssb1 antibody to splicing extracts made from a wild type strain did not inhibit or diminish splicing. Instead, mRNA splicing was reproducibly stimulated several fold, indicating competition between ssb1 and splicing factors for binding to single-stranded RNA in the extracts. RNP complexes still formed in the ssb1- strain, demonstrating that it would be possible to purify other RNP proteins from this strain using the gel complex formation assay.

Actins↗

[Ribonucleoprotein mRNA-containing cytoplasmic particles from mouse lymphocytes before and after injection of antigen].

In mouse spleen lymphocytes mRNA was discovered not only in poliribosomes but also in lighter RNP complexes having sedimentation coefficients of 80--120S and buyoant density of 1,40--1,52 g/cm3. The incorporation of 14C-pulse aminoacid lable has shown that the most active polypeptide synthesis takes place in light RNP-complexes and not in polyribosomes. The pattern and the contents of labeled mRNA-containing particules in spleen cytoplasm changed within different periods after the antigen injection. The greatest contents of these particles have been discovered on the second day after the antign injection, 3H- and 14C-radioactivity of RNP-complexes with higher sedimentation coefficients, and that of polyribosomes was increased; the optical density of polyribosomes peak was also increased. On the 4th day after the antigen injection contents of light RNP-complexes with higher sedimentation coefficients were decreased. On the 5th day the decrease of RNP-complexes contents was more pronounced. The changes of radioactive RNP-complexes contents in spleen cytoplasm at different periods of the immune response, which can be discovered during determined period of labling, are probably due to acceleration and then to retardation of the transition of light RNP complexes into polyribosomes. It, probably, reflects the existens in spleen lymphocytes mechanisms of translation regulation, irrespective of mRNA stability which are realized during immune reaction. Periods of the translation increasing or inhibiting in immune lymphocytes don't correspond to periods of increasing or decreasing of number of antibody synthesising cells in spleen.

Animals↗

Nuclear ribonucleoprotein complexes containing U1 and U2 RNA.

Nuclear ribonucleoprotein (RNP) complexes that contain the U1 and U2 RNA of chromatin of Novikoff hepatoma cells were extracted with 0.01 M Tris-HCl (pH 8.0) after the nuclei were initially washed with 0.075 M NaCl and 0.025 M EDTA (pH 8.0). These RNP complexes were purified by chromatography on Sepharose 6B columns and centrifugation on sucrose density gradients. The identity of the U1 and U2 RNA in these particles was established by their electrophoretic mobility in polyacrylamide gels and their T1 RNase fingerprints which were identical with those of authentic U1 and U2 RNA (R. Reddy et al. (1974), J. Biol. Chem.249, 6486-6494; H. Shibata et al. (1974), Mol. Cell. Biochem. 4, 3-19). The nuclear riboncleoproteins had a buoyant density of 1.47 g/ml in CsCl gradients. Two-dimensional polyacrylamide gel electrophoresis of their proteins showed these RNP complexes contain 10 polypeptide spots, of which two are phosphorylated in vivo.

Animals↗

Isolation and characterization of a virus-specific ribonucleoprotein complex from reticuloendotheliosis virus-transformed chicken bone marrow cells.

Chicken bone marrow cells transformed by reticuloendotheliosis virus (REV) produce in the cytoplasm a ribonucleoprotein (RNP) complex which has a sedimentation value of approximately 80 to 100S and a density of 1.23 g/cm3. This RNP complex is not derived from the mature virion. An endogenous RNA-directed DNA polymerase activity is associated with the RNP complex. The enzyme activity was completely neutralized by anti-REV DNA polymerase antibody but not by anti-avian myeloblastosis virus DNA polymerase antibody. The DNA product from the endogenous RNA-directed DNA polymerase reaction of the RNP complex hybridized to REV RNA but not to avian leukosis virus RNA. The RNA extracted from the RNP hybridized only to REV-specific complementary DNA synthesized from an endogenous DNA polymerase reaction of purified REV. The size of the RNA in the RNP is 30 to 35S, which represents the subunit size of the genomic RNA. No 60S mature genomic RNA was found within the RNP complex. The significance of finding the endogenous DNA polymerase activity in the viral RNP in infected cells and the maturation process of 60S virion RNA of REV are discussed.

Animals↗

Probing the RNA structure within the yeast 5 S RNA.L1a protein complex by fluorescence and enzymatic digestion.

Conformational states of the ribosomal 5 S RNA molecule and its associated protein L1a in the yeast RNA-protein (RNP) complex were determined using controlled RNase T1 digestion in conjunction with fluorescence probes, ethidium bromide and bisanilinonaphthalenesulfonic acid. Fluorescence measurements indicated that the RNA molecule in the RNP complex appeared to exhibit a slightly lower degree of secondary structure than that in the free form. Controlled digestion of the intact RNP complex with RNase T1 resulted in an initial increase in ethidium fluorescence followed by a gradual decrease. In free RNA, a similar profile, except that a larger increase in ethidium fluorescence at the initial stage of digestion, was observed. During digestion of the RNP complex, increases in bisanilinonaphthalenesulfonic acid fluorescence and in light scattering were observed. These findings implied that as regions of the 5 S RNA molecule were perturbed, hydrophobic regions in the protein became exposed. Polyacrylamide gel analysis of the digestion products revealed a temporal appearance of discrete RNA fragments. Sequence analysis of these fragments generated information about the structural arrangement of the RNA molecule within the RNP complex. Results from the present investigation indicate that interactions between the 5 S RNA and protein L1a can stabilize functionally relevant conformations of the components that are individually labile. Properties of the separated components also suggest that special conditions, such as those suggested by Steitz et al. (Steitz, J. A., Berg, C., Hendrick, J. P., LaBranche-Chabot, H., Metspalu, A., Rinke, J., and Yario, T. (1988) J. Cell Biol. 106, 545-556) may be involved for these components to associate during ribosomal assembly.

Base Sequence↗

Purification of a glucose-binding protein from rat liver nuclei. Evidence for a role in targeting of nuclear mRNP to nuclear pore complex.

A nuclear carbohydrate-binding protein with a molecular mass of 67 kDa (CBP67), which is specific for glucose residues, was purified to essential homogeneity from rat liver nuclear extracts. This protein could also be isolated from nuclear ribonucleoprotein (RNP) complexes by extraction in the presence of 0.6 M or 2 M NaCl, but it was absent in polysomal RNP complex. The binding of the purified protein, which has an isoelectric point of 7.3, to glucose-containing glycoconjugates depends on the presence of Ca2+ and Mg2+. Using closed nuclear envelope vesicles as a system to study nuclear transport of RNA, it was shown that both entrapped polysomal mRNA and nuclear RNA precursors are readily exported from the vesicles in an ATP-dependent manner. The transport was unidirectional and strongly promoted by the poly(A) segment attached to these RNAs. In contrast, nuclear RNP complexes entrapped into the vesicles together with glucose-conjugated bovine serum albumin or nucleoplasmin, or bird nest glycoprotein, were not exported into the extravesicular space. However, transport of nuclear RNP complexes could be achieved in the presence of glucose or after co-addition of a glucose-recognizing lectin from Pellina semitubulosa. In Western blots, radioiodinated CBP67 binds to an 80-kDa polypeptide both in isolated rat liver nuclear envelopes and pore-complex laminae. From these results we postulate that CBP67 may direct nuclear RNP complexes to the nuclear pore.

Animals↗

Neuronal tissue-specific ribonucleoprotein complex formation on SOD1 mRNA: alterations by ALS SOD1 mutations.

Amyotrophic lateral sclerosis (ALS) is a fatal disease of unknown etiology. Mutations in copper/zinc superoxide dismutase (SOD1) are the most commonly associated genetic abnormality. Given that SOD1 is ubiquitously expressed, the exclusive vulnerability of motor neurons is one of the most puzzling issues in ALS research. We here report that wild-type SOD1 mRNA forms ribonucleoprotein (RNP) complexes with protein homogenates of neuronal tissue but not with homogenates of non-neuronal tissues. 3' Untranslated region of SOD1 mRNA-dependent RNP complexes functioned to stabilize SOD1 mRNA. Moreover, SOD1 mRNAs harboring ALS-associated mutations, including silent mutations, were deficient in forming RNP complexes. In contrast, SOD1 mRNAs harboring artificial mutations, not known to be associated with ALS, demonstrated preserved RNP complex formation. This paper reports RNP complex formation on SOD1 mRNA as a neuronal tissue-specific and ALS-associated mutation sensitive feature.

Humans↗

[Functional properties of prosomal protein 39 kappaDa from Datura stramonium leaves infected with Potato Virus X].

Free cytoplasmic informosomes isolated from Datura stramonium plants infected by PVX contain a low-molecular ribonucleoprotein complex (RNP). This complex as to its main physico-chemical parameters (sedimentation coefficient 10S, buoyant density in CsSO4 1.31 g/cm3, stability to 1% lauroylsarcosinate-Na) corresponds to the prosome (inhibitory RNP). Prosomes isolated from free mRNP of D. stramonium plants infected by PVX contain the protein of 39 kDa. This protein was shown to be capable to phosphorylate in vitro in the composition of informosomes and prosomes. It is possible that this protein can be the protein-repressor, since it is absent in the translated polysome-associated form of mRNP. The label incorporation has shown that the protein of 39 kDa is able to reduce in vitro the template activity of genomic RNA PVX to 40% and RNA TMIV--to 30%. Moreover, the protein 39 of kDa has the protease activity. It affects substrate-case in like trypsin. It is supposed that it can participate in splitting the intracellular proteins as well as in the expression of the virus genome, it can also influence the template activity of cell RNAs.

Datura stramonium↗

The structure of ribonucleoprotein particles from rat liver nuclei.

During or immediately after transcription of chromatin the high molecular weight pre-mRNA is complexes with proteins and low molecular weight RNA (lmwRNA). In the presence of a cytosolic RNase inhibitor pre-mRNA-protein complexes, designated as polyparticles, can be isolated from rat liver nuclei. The polyparticles are characterized by a maximum of their sedimentation coefficient of around 90 S, a protein to RNA ratio of 4.1, and a density in CsCl of 1.4 g/cm3. A set of 6--10 basic proteins of molecular weights between 30 and 45 kd as well as a multitude of polypeptides of higher molecular weights is associated with the rapidly labeled, polydisperse, high molecular weight RNA and several lmwRNA species. In order to study the structure of these very complex nuclear RNP complexes, the polyparticles were incubated at various concentrations of sodium chloride, urea or proteinases of different specificities (trypsin, chymotrypsin, proteinase K), recentrifuged through a sucrose layer and analyzed with respect to their sedimentation behavior, their protein to RNA ratios and their protein- and RNA components. Rhe results of these experiments led us to the proposal of a structural model which is presented here.

Animals↗

Isolation and proteomic characterization of the major proteins of the nucleolin-binding ribonucleoprotein complexes.

Nucleolin (NCL) is one of the most abundant nucleolar proteins of exponentially growing eukaryotic cells. It is known to interact only transiently with rRNA and preribosomal particles and not to be detectable in mature cytoplasmic ribosomes, and is believed to function as multi-protein complexes during ribosome biogenesis and maturation. However, those multiprotein complexes remain only partially characterized due to the difficulty of conventional protein analysis methods. Here we report isolation of NCL-binding protein complex and its proteomic characterization with the use of an analytical method based on matrix-assisted laser desorption/ionization-time of flight analysis coupled with searching peptide mass databases. The NCL-binding protein complex was isolated by immunoprecipitation with anti-Flag antibody from human kidney 293 cells that were transfected with the Flag-tagged NCL gene, and showed RNA integrity for holding their protein constituents. Interaction between NCL and its binding complex was disrupted by an RNA oligonucleotide with a NCL recognition element, indicating that NCL binds to the ribonucleoprotein (RNP) complex mainly through the sequence specific protein-RNA interaction. We confirmed that an RNA-binding domain of NCL alone was sufficient to hold the entire NCL-binding RNP complex, indicating the strict binding specificity of NCL to the isolated RNP complex in 293 cells. We identified forty ribosomal proteins from both the large and small subunits, and twenty nonribosomal proteins. These results together suggest that the isolated NCL-binding RNP complex is a preribosomal particle present in the nucleolus of 293 cells.

Blotting, Western↗

Cellular protein hnRNP-A1 interacts with the 3'-end and the intergenic sequence of mouse hepatitis virus negative-strand RNA to form a ribonucleoprotein complex.

We previously showed that several cellular proteins specifically bind to the 3'-end and the intergenic sequences of the negative-strand RNA of mouse hepatitis virus (MHV), and proposed that these distant RNA sequences can be brought together by cellular and viral proteins (Furuya and Lai, 1993; Zhang et al., 1994; Zhang and Lai, 1995). The cellular protein p35 has been identified as a heterogeneous nuclear ribonucleoprotein (hnRNP) A1. We have now expressed hnRNP-A1 as a glutathione-S-transferase (GST) fusion protein and demonstrated that the amino terminal two-thirds of hnRNP-A1 interacted with the two MHV regulatory RNA sequences (3'-end and intergenic sequences) through protein-RNA interaction while its carboxy-terminal glycine-rich domain mediated homomeric (protein-protein) interactions. In a partially reconstituted reaction, in which the two MHV RNA fragments and the purified GST-hnRNP-A1 fusion protein were mixed, an RNP complex was formed. Depletion of either hnRNP-A1 or one of the RNA components abolished the complex formation. These results indicate that hnRNP-A1 can mediate the formation of an MHV RNP complex, which includes both the negative-strand leader and intergenic sequences. Site-directed mutagenesis revealed that mutations in the MHV intergenic sequences, which inhibited MHV RNA transcription, also inhibited the RNP complex formation. Deletion analysis showed that the amino terminal RNA-binding domains of hnRNP-A1 is essential for the RNP complex formation while the carboxy-terminal protein-binding domain enhanced the complex formation by 90-fold. These findings provide direct evidence demonstrating that the negative-strand leader RNA and intergenic sequences can form an RNP complex mediated by cellular protein hnRNP-A1.

Animals↗

Thymidylate synthase protein and p53 mRNA form an in vivo ribonucleoprotein complex.

A thymidylate synthase (TS)-ribonucleoprotein (RNP) complex composed of TS protein and the mRNA of the tumor suppressor gene p53 was isolated from cultured human colon cancer cells. RNA gel shift assays confirmed a specific interaction between TS protein and the protein-coding region of p53 mRNA, and in vitro translation studies demonstrated that this interaction resulted in the specific repression of p53 mRNA translation. To demonstrate the potential biological role of the TS protein-p53 mRNA interaction, Western immunoblot analysis revealed nearly undetectable levels of p53 protein in TS-overexpressing human colon cancer H630-R10 and rat hepatoma H35(F/F) cell lines compared to the levels in their respective parent H630 and H35 cell lines. Polysome analysis revealed that the p53 mRNA was associated with higher-molecular-weight polysomes in H35 cells compared to H35(F/F) cells. While the level of p53 mRNA expression was identical in parent and TS-overexpressing cell lines, the level of p53 RNA bound to TS in the form of RNP complexes was significantly higher in TS-overexpressing cells. The effect of TS on p53 expression was also investigated with human colon cancer RKO cells by use of a tetracycline-inducible system. Treatment of RKO cells with a tetracycline derivative, doxycycline, resulted in 15-fold-induced expression of TS protein and nearly complete suppression of p53 protein expression. However, p53 mRNA levels were identical in transfected RKO cells in the absence and presence of doxycycline. Taken together, these findings suggest that TS regulates the expression of p53 at the translational level. This study identifies a novel pathway for regulating p53 gene expression and expands current understanding of the potential role of TS as a regulator of cellular gene expression.

Animals↗

Isolation and characterization of intranuclear ribonucleoprotein complexes associated with double-stranded RNA adenosine deaminase from brain cells: implications for RNA-editing and hypermutation of viral RNA in the CNS.

Double-stranded RNA adenosine deaminase (DsRAD), which converts adenosine in duplex RNA to inosine, has been implicated in editing of cellular mRNA and hypermutation of viral RNA in the central nervous system (CNS). We used subcellular fractionation to show that DsRAD in bovine brain tissues is associated with high-molecular-weight ribonucleoprotein (RNP) complexes in the nuclei. DsRAD-associated RNP complexes have apparent molecular mass of up to 500 kDa and buoyant density of 1.35 to 1.42 g cc-1 in CsCl solution. In human glioma cells, DsRAD is also found exclusively in intranuclear RNP complexes that co-sediment with the largest RNA species. These DsRAD-associated RNP complexes are dissociated by RNase A or high salt. The RNA component is not essential for DsRAD activity, and the protein component can be separated by dsRNA-affinity column, gel filtration column, and glycerol gradient into enzymatically active protein species with apparent molecular mass ranging from 120 kDa to 70 kDa in polyacrylamide gel. The bovine brain DsRAD has no apparent requirement for low-molecular-weight cofactors or metal ions. These results provide insight into the native state of DsRAD in brain cells and have interesting implications for its putative roles in RNA-editing and hypermutation of viral RNA in the CNS.

Adenosine Deaminase↗

Association of nonribosomal nucleolar proteins in ribonucleoprotein complexes during interphase and mitosis.

rRNA precursors are bound throughout their length by specific proteins, as the pre-rRNAs emerge from the transcription machinery. The association of pre-rRNA with proteins as ribonucleoprotein (RNP) complexes persists during maturation of 18S, 5.8S, and 28S rRNA, and through assembly of ribosomal subunits in the nucleolus. Preribosomal RNP complexes contain, in addition to ribosomal proteins, an unknown number of nonribosomal nucleolar proteins, as well as small nucleolar RNA-ribonucleoproteins (sno-RNPs). This report describes the use of a specific, rapid, and mild immunopurification approach to isolate and analyze human RNP complexes that contain nonribosomal nucleolar proteins, as well as ribosomal proteins and rRNA. Complexes immunopurified with antibodies to nucleolin-a major nucleolar RNA-binding protein-contain several distinct specific polypeptides that include, in addition to nucleolin, the previously identified nucleolar proteins B23 and fibrillarin, proteins with electrophoretic mobilities characteristic of ribosomal proteins including ribosomal protein S6, and a number of additional unidentified proteins. The physical association of these proteins with one another is mediated largely by RNA, in that the complexes dissociate upon digestion with RNase. Complexes isolated from M-phase cells are similar in protein composition to those isolated from interphase cell nuclear extracts. Therefore, the predominant proteins that associate with nucleolin in interphase remain in RNP complexes during mitosis, despite the cessation of rRNA synthesis and processing in M-phase. In addition, precursor rRNA, as well as processed 18S and 28S rRNA and candidate rRNA processing intermediates, is found associated with the immunopurified complexes. The characteristics of the rRNP complexes described here, therefore, indicate that they represent bona fide precursors of mature cytoplasmic ribosomal subunits.

Animals↗

Identification of the Ro and La antigens in the endoribonuclease VII--ribonucleoprotein complex.

45 S RNP (ribonucleoprotein) particles from calf thymus or L5178y mouse lymphoma cells contain the poly(A)-modulated and oligo(U)-binding endoribonuclease VII [Bachmann, Zahn & Müller (1983) J. Biol. Chem. 258, 7033-7040]. From these particles a 4.5 S RNA was isolated that possesses an oligo(U) sequence. By using monospecific and non-cross-reacting antibodies directed against the La or Ro antigen, both proteins were identified in the endoribonuclease VII-RNP complex after phosphorylation in vitro. In a second approach, endoribonuclease VII activity was identified in immunoaffinity-purified Ro RNPs after preparative isoelectric focusing. Therefore we conclude that the 4.5 S RNA belongs to the Ro RNAs. The results indicate a possible function of endoribonuclease VII in activating stored mRNAs.

Animals↗

Stepwise molding of a highly selective ribonucleopeptide receptor.

The structural characteristics of RNA-peptide (RNP) complexes are suitable for molding of a ligand-binding pocket of the RNP complex in a stepwise manner. The first step involves molding of the RNA subunit by in vitro selection of an RNP pool originating from an RNA library and the peptide, as previously reported for the construction of an ATP-binding RNP complex from an RRE RNA-Rev peptide complex. The second step involves selection from an RNP library consisting of Rev peptides with randomized amino acid residues and the RNA subunit selected in the first molding. The ATP-binding pocket produced by sequential molding of RNA and peptide subunits shows higher affinity to ATP and a distinct specificity for ATP versus dATP as compared to the ATP-binding RNP receptor in which only the RNA subunit has been molded. The second step selection from the peptide-based RNP library allows expansion of the ATP recognition surface, consisting of both RNA and peptide subunits, to enhance the affinity and selectivity to discriminate ATP against dATP. Our approach of stepwise molding offers the advantage of increasing the diversity of the RNP library by utilizing characteristics of different biopolymers. The ribonucleopeptide-based, multi-subunit approach is also extendable to other biomacromolecular assemblies, which may yield artificial receptors and enzymes with increased specificity and more diverse chemical activities.

Adenosine Triphosphate↗

Formation of a ribonucleoprotein complex of mouse hepatitis virus involving heterogeneous nuclear ribonucleoprotein A1 and transcription-regulatory elements of viral RNA.

The heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) specifically binds to two transcription-regulatory elements, i.e., the leader and intergenic sequence, of the negative-strand (template-strand) RNA of mouse hepatitis virus (MHV) and may play a role in viral RNA transcription. Previous studies based on the defective-interfering RNAs of MHV suggested that these two RNA elements may interact with each other during transcription, although they do not have complementary sequences. In this study, we showed by an in vitro reconstitution assay that hnRNP A1 could mediate the formation of an RNP complex involving these two RNA elements. Both the RNA-binding domains and protein-interacting domain of hnRNP A1 contributed to the efficient formation of the RNP complex; however, the presence of the two RNA-binding domains alone, without the protein-interacting domain, also resulted in some RNP formation. Omission of hnRNP A1 in the reconstitution reaction abolished the RNP formation, and mutations of the IG sequences significantly inhibited the RNP formation. These findings suggest that the two cis-acting transcription-regulatory sequences of MHV RNA can interact with each other through the formation of an RNP complex involving a cellular protein hnRNP A1. This RNP complex may participate in MHV RNA transcription.

Animals↗