Generation of cDNA libraries from RNP-derived regulatory noncoding RNAs.

Next-generation sequencing of noncoding RNA (ncRNA) libraries has become an essential tool for the profiling of ncRNAs and the identification of novel ncRNA species. Here, we describe the generation of a ncRNA-derived complementary DNA (cDNA) library by 3'-tailing of ncRNAs by CTP and poly(A) polymerase, followed by 5'-adapter ligation by T4 RNA ligase and reverse transcription of ncRNAs with an oligo-d(G) anchor primer. Preliminary selection of ncRNAs from ribonucleoprotein particles (RNPs) enables a strong enrichment of the generated libraries with functional regulatory ncRNAs compared to classical approaches.

[Internal epidemic influenza virus proteins: isolation and investigation].

The internal influenza virus proteins M1 and RNP free from surface protein impurities were isolated from subviral particles (virions free from HA and NA ectomenes). The spikeless particles had no propensity to aggregate in the solution at pH 5.0 as compared with native viruses. The subviral particles of B/Hong Kong/330/01 influenza virus, which belonged to B/Victoria/2/87-lineage, were obtained by proteolytic treatment with the enzyme bromelain under the same conditions as in cases of influenza B viruses of B/Jamagata/16/88 lineage. A chromatographic analysis of the tryptic hydrolyzates obtained for matrix (M1) proteins of A(H1N1) and A(H3N2) influenza viruses revealed differences that were greatest between the protein M1 molecules isolated from influenza viruses of different subtypes of hemagglutinine. These findings suggest there are variations in the structure of this conservative internal viral protein M1 during evolution.

The recessive epigenetic swellmap mutation affects the expression of two step II splicing factors required for the transcription of the cell proliferation gene STRUWWELPETER and for the timing of cell cycle arrest in the Arabidopsis leaf.

Generally, cell division can be uncoupled from multicellular development, but more recent evidence suggests that cell cycle progression and arrest is coupled to organogenesis and growth. We describe a recessive mutant, swellmap (smp), with reduced organ size and cell number. This defect is partially compensated for by an increase in final cell size. The mutation causes a precocious arrest of cell proliferation in the organ primordium and possibly reduces the rate of cell division there. The mutation proved to be an epigenetic mutation (renamed smp(epi)) that defined a single locus, SMP1, but affected the expression of both SMP1 and a second very similar gene, SMP2. Both genes encode CCHC zinc finger proteins with similarities to step II splicing factors involved in 3' splice site selection. Genetic knockouts demonstrate that the genes are functionally redundant and essential. SMP1 expression is associated with regions of cell proliferation. Overexpression of SMP1 produced an increase in organ cell number and a partial decrease in cell expansion. The smp(epi) mutation does not affect expression of eukaryotic cell cycle regulator genes CYCD3;1 and CDC2A but affects expression of the cell proliferation gene STRUWWELPETER (SWP) whose protein has similarities to Med150/Rgr1-like subunits of the Mediator complex required for transcriptional activation. Introduction of SWP cDNA into smp(epi) plants fully restored them to wild-type, but the expression of both SMP1 and SMP2 were also restored in these lines, suggesting a physical interaction among the three proteins and/or genes. We propose that step II splicing factors and a transcriptional Mediator-like complex are involved in the timing of cell cycle arrest during leaf development.

Two-step affinity purification of the hepatitis C virus ribonucleoprotein complex.

Positive-strand RNA viruses replicate their RNA genome within a ribonucleoprotein (RNP) complex that is associated with cellular membranes. We used a two-step method of purification to isolate hepatitis C virus (HCV) RNP complexes from human hepatoma cell line Huh7, which stably expresses HCV subgenomic replicons. The procedure involved hybridization of replicon-expressing cellular lysates with oligonucleotides tagged with biotin and digoxigenin at their respective termini complementary to subgenomic replicon RNA followed by avidin-agarose enrichment of the mixture and subsequent immunoprecipitation of biotin-eluted material with anti-digoxigenin antibody. The immunoprecipitates were immunoblotted with antisera against HCV nonstructural (NS) proteins. The analysis revealed the association of all the HCV NS proteins (NS3, NS4a, NS4b, NS5a, and NS5b) that are encoded by the subgenomic replicon RNA. The HCV RNP complex migrated in a native polyacrylamide gel with an approximate molecular mass of 450 kD. The association of these viral proteins in the RNP complex reinforces the widely acknowledged notion that RNA viruses accomplish replication within a membranous RNP complex.

Calreticulin enriched as an early-stage encapsulation protein in wax moth Galleria mellonella larvae.

To investigate the molecular mechanism of the early-stage encapsulation reaction in insects, we purified a 47kDa protein from injected beads into Galleria mellonella larvae. When a cDNA clone was isolated, the 47kDa protein showed high homology with Drosophila and human calreticulin. Western blotting analysis showed that the 47kDa protein was present in the hemocytes, but not in the plasma. When the early-stage encapsulated beads were coated with 47kDa protein antibody and reinjected into G. mellonella larvae, any further encapsulation reaction was inhibited. These results suggest that calreticulin is involved in non-self recognition in invertebrate cellular defense reactions.

Involvement of a cellular glycolytic enzyme, phosphoglycerate kinase, in Sendai virus transcription.

In vitro mRNA synthesis of Sendai virus is almost entirely dependent on the addition of cellular proteins (host factors). Previous studies indicated that the host factor activity from bovine brain was resolved into at least two complementary fractions, one of which may be tubulin. In this study, the host factor activity that stimulates the transcription in the presence of tubulin was further purified from bovine brain. This fraction was found to contain at least two complementary factors, and one of them was purified to a single polypeptide chain with an apparent M(r) of 46,000 (p46). From the amino acid sequence, biochemical, and immunological analyses, p46 was identified as a glycolytic enzyme, phosphoglycerate kinase (PGK). Purified native PGK from rabbit and yeast, and a recombinant human PGK substituted for p46. Although, as previously suggested, tubulin was involved in the transcription initiation complex formation by being integrated into the complex, p46 and its complementary factor had little effect on the complex formation. On the other hand, when p46 and the complementary factor were added to the RNA chain elongation reaction from the isolated initiation complex formed with tubulin, mRNA synthesis was dramatically stimulated. The enzymatic activity per se of PGK did not seem to be required for its activity. West-Western blot analysis showed that PGK could directly interact with tubulin. These data suggest that PGK stimulates Sendai virus mRNA synthesis at the elongation step, probably through its interaction with tubulin in the initiation complex.

Identification of chURP, a nuclear calmodulin-binding protein related to hnRNP-U.

In a screen for myosin-like proteins in embryonic chicken brain, we have identified a novel nuclear protein structurally related to hnRNP-U (heterogeneous nuclear ribonuclear protein U). We have called this protein chURP, for chicken U-related protein. In this screen, chURP was immunoreactive with two myosin antibodies and, in common with the unconventional myosins, bound calmodulin in vitro in both the presence and absence of calcium ions. Determination of 757 amino acids of the chURP sequence revealed that it shares 41% amino acid identity with human and rat hnRNP-U, although chURP and hnRNP-U appear not to be orthologous proteins. ChURP is ubiquitously expressed in the nuclei of all chick tissues and, as one of a growing number of calmodulin-binding proteins to be identified in the nucleus, further highlights the potential of calmodulin as a regulator of nuclear metabolism.

Functional conservation of calreticulin in Euglena gracilis.

Calreticulin is the major high capacity, low affinity Ca2+ binding protein localized within the endoplasmic reticulum. It functions as a reservoir for triggered release of Ca2+ by the endoplasmic reticulum and is thus integral to eukaryotic signal transduction pathways involving Ca2+ as a second messenger. The early branching photosynthetic protist Euglena gracilis is shown to possess calreticulin as its major high capacity Ca2+ binding protein. The protein was purified, microsequenced and cloned. Like its homologues from higher eukaryotes, calreticulin from Euglena possesses a short signal peptide for endoplasmic reticulum import and the C-terminal retention signal KDEL, indicating that these components of the eukaryotic protein routing apparatus were functional in their present form prior to divergence of the euglenozoan lineage. A gene phylogeny for calreticulin and calnexin sequences in the context of eukaryotic homologues indicates i) that these Ca2+ binding endoplasmic reticulum proteins descend from a gene duplication that occurred in the earliest stages of eukaryotic evolution and furthermore ii) that Euglenozoa express the calreticulin protein of the kinetoplastid (trypanosomes and their relatives) lineage, rather than that of the eukaryotic chlorophyte which gave rise to Euglena's plastids. Evidence for conservation of endoplasmic reticulum routing and Ca2+ binding function of calreticulin from Euglena traces the functional history of Ca2+ second messenger signal transduction pathways deep into eukaryotic evolution.

The class III POU factor Brn-4 interacts with other class III POU factors and the heterogeneous nuclear ribonucleoprotein U.

The class III POU proteins are expressed throughout the central nervous system, including the hypothalamus, where they are often co-localized. Presumably, these POU proteins (Brain-1, Brain-2, Brain-4 and SCIP) serve as transcriptional transactivators. That they are co-expressed in some neurons suggests that, if they were to form homomeric and heteromeric complexes with each other, depending on the particular combination, they might have different DNA-binding specificities and, thus, activate different genes. We used purified fusion proteins of the four class III POU proteins in far-western assays to show that the proteins can interact. We confirmed their interactions using a two-hybrid system. Both techniques indicate that the interaction occurs through the POU domain. The far-western technique also allowed us to identify a 120-kDa nuclear protein that interacts with Brain-4. Subsequent affinity purification and microsequencing identified the protein as the heterogeneous nuclear ribonucleoprotein U (hnRNP U). This result suggests another mechanism by which a POU protein can influence gene expression: by facilitating the processing of pre-mRNA whose transcription it has stimulated.

Strong expression of the calreticulin gene in the liver of Rana rugosa tadpoles, but not adult frogs.

In the present paper we report the purification of calreticulin (CLT) from livers of the frog, Rana rugosa, the cloning and sequencing of its cDNA, and the CLT gene expression. CLT with M(r) = 52 kDa, estimated by SDS-PAGE, was purified from frog livers. Using rat CLT cDNA as a probe, a 2.4-kilobase frog cDNA clone was isolated from a frog liver cDNA library. The cDNA encoded 419 amino acids including an 18-residue NH2-terminal signal sequence that was 76% homologous to the rat CLT sequence and was 84% homologous to the partial sequence of Xenopus laevis CLT (Treves et al. [1992] Biochem. J. 287:579-581). Phylogenetic relationships estimated from the amino acid sequence of CLTs showed no pronounced variation between the two frog species, R. rugosa and X. laevis. Northern blot analysis indicated that the CLT mRNA level was very high in the liver of tadpoles, but extremely low in adult frogs. Expression levels were also very high in the premature ovary, while moderate expression was observed in the testis and brain of adult frogs. However, there was little histological change in the liver of tadpoles during development. Furthermore, CLT was recognized by Western blot analysis of total proteins in the liver of adult frogs. Immunostaining showed that CLT was distributed in the cytoplasm of liver cells. These results suggest that the expression of the CLT gene is tissue-dependent in the frog, R. rugosa, and that CLT probably functions biochemically in liver cells even when its gene expression is low.

Overexpression of calreticulin increases the Ca2+ capacity of rapidly exchanging Ca2+ stores and reveals aspects of their lumenal microenvironment and function.

A molecularly tagged form of calreticulin (CR), a low affinity-high capacity Ca2+ binding protein that resides in the ER lumen, was transiently transfected into HeLa cells to specifically modify the Ca2+ buffering capacity of the intracellular Ca2+ stores. Fluorescence and confocal microscope immunocytochemistry revealed the tagged protein to be expressed by over 40% of the cells and to overlap in its distribution the endogenous CR yielding a delicate cytoplasmic network, i.e., the typical pattern of ER. In contrast, no signal was observed associated with the plasmalemma (marked by ConA) and within the nucleus. One- and two-dimensional Western blots revealed the transfected to exceed the endogenous CR of approximately 3.5-fold and to maintain its Ca2+ binding ability, whereas the expression of other ER proteins was unchanged. Ca2+ homeostasis in the transfected cells was investigated by three parallel approaches: (a) 45Ca equilibrium loading of cell populations; (b) [Ca2+]c measurement with fura-2 followed by quantitative immunocytochemistry of single cells and iii) [Ca2+]c measurement of cell population upon cotransfection with the Ca(2+)-sensitive photoprotein, aequorin. The three approaches revealed different aspects of Ca2+ homeostasis, yielding results which were largely complementary. In particular, the following conclusions were established: (a) both endogenous and transfected CR participate in Ca2+ buffering within the IP3-sensitive, rapidly exchanging, Ca2+ stores; the other pools of the cells were in contrast unaffected by CR transfection; (b) the Ca2+ capacity of the stores is not the main limiting factor of individual IP3-mediated Ca2+ release responses triggered by receptor agonists; (c) in control cells, the contribution of CR to Ca2+ buffering within the IP3-sensitive stores accounts for approximately 45% of the total, the rest being probably contributed by the other lumenal (and also membrane) Ca2+ binding proteins; (d) the free [Ca2+] within the lumen of the IP3-sensitive stores, revealed by the degree of Ca2+ binding to the transfected CR protein, amounts to values in (or approaching) the millimolar range; and (e) Ca2+ influx across the plasmalemma activated by depletion of the stores is directly dependent on the lumenal [Ca2+].

Human placental calreticulin: purification, characterization and association with other proteins.

Calreticulin is an intracellular protein known to be involved in calcium binding, but is also known to appear as an autoantigen in certain autoimmune diseases. The cDNA sequence is known but the protein has not yet been well characterized at the amino acid level. Owing to the possible involvement of this protein in autoimmune disease and with the aim of making monoclonal antibodies for use in assay development and immunohistochemistry, we have purified calreticulin using human placental material. Amino acid analysis of the purified protein confirmed the cDNA-derived composition, and only one discrepancy between the cDNA-predicted sequence and the amino acid sequence was found by peptide mapping and microsequencing. The protein contains one disulfide bridge and has one free SH group and the protein is neither glycosylated nor phosphorylated. Affinity chromatography of a placental protein extract on a column with immobilized calreticulin showed the existence of at least six proteins interacting with calreticulin. Using the purified calreticulin in Western blots, two out of eight patients with autoimmune disease diagnosed as having anti DNA antibodies in their serum were found also to contain autoantibodies to calreticulin in their serum.

Purification and characterization of ribonucleoproteins from pea chloroplasts.

RNA-binding proteins are known to mediate the post-transcriptional regulation of genes in many organisms. Recently they have been found to be important in the expression of plastid genes. We have purified a group of three single-stranded nucleic-acid-specific acidic proteins (33, 30 and 28 kDa) from chloroplast extracts of pea (Pisum sativum L.), using single-stranded DNA affinity chromatography. All of them have acidic amino termini but the amino acid sequences are unique to each polypeptide, with partial similarities to the recently reported ribonucleoproteins from tobacco chloroplasts. The pea proteins are also antigenically distinct, as shown by Western blot analysis using polyclonal antisera for purified proteins. Further, from their large nucleic-acid-binding domains and the polynucleotide substrate affinities, they are predicted to belong to a family of pea plastid ribonucleoproteins. In vivo radiolabeling of proteins in the presence of translational inhibitors as well as in vitro translation of leaf tissue RNA suggest that these proteins are encoded in the nucleus. Antibody cross-reactivity experiments reveal that their genes are conserved during plastid evolution.

Two-step affinity purification of U7 small nuclear ribonucleoprotein particles using complementary biotinylated 2'-O-methyl oligoribonucleotides.

U7 snRNP is a low-abundance small nuclear ribonucleoprotein particle essential for 3' processing of replication-dependent histone pre-mRNA. We have developed a two-step purification of the particle from TB21 mouse mastocytoma cell nuclear extracts, with about a 20% overall yield, using affinity binding to 2'-O-methyl oligoribonucleotides. The purified particle is homogeneous with respect to RNA content. SDS/PAGE of the U7 snRNP proteins revealed a full complement of the standard core proteins (B, DD', E, F, and G) found in the majority of snRNPs. In addition, two U7-specific polypeptides of 14 kDa and 50 kDa were identified. Summation of the molecular masses of the identified components of the U7 particle yields a particle mass of 249 kDa, in approximate agreement with estimates from sucrose gradient sedimentation (261 kDa) and nondenaturing gradient PAGE (217 kDa).

Assemblage of the prespliceosome complex with separated fractions isolated from HeLa cells.

The first ATP-dependent complex formed in pre-mRNA splicing is the prespliceosome, a 30 S complex. This reaction was investigated using partially purified fractions isolated from nuclear extracts of HeLa cells. Previous studies (Furneaux, H. M., Perkins, K. K., Freyer, G. A., Arenas, J., and Hurwitz, J. (1985) Proc. Natl. Acad. Sci. U. S. A. 82, 4351-4355) have shown that DEAE-cellulose chromatography of nuclear extracts yielded two fractions (fractions I and II, eluted at 0.2 and 1 M NaCl, respectively) which carried out pre-mRNA splicing only when combined. Fraction II, alone and in the presence of ATP, supported the formation of the 30 S complex. In this report, we have separated fraction II into ribonucleoprotein and protein-rich fractions by isopycnic banding in CsCl. The combination of these two fractions completely replaced fraction II in prespliceosome formation; when supplemented with fraction Ib (1 M NaCl Biorex fraction derived from fraction I), the preparations supported spliceosome formation; when supplemented with fraction I, they yielded spliced products. The CsCl fractions, like fraction II, efficiently converted pre-mRNA to the 30 S complex with high yields (30-70%). The 30 S complex was shown to contain pre-mRNA complexed to U2 small ribonucleoproteins and small amounts of U1 small ribonucleoproteins. The 30 S complex protected a 50-nucleotide region at the 3'-end of the intron from T1 RNase attack. This region included sequences spanning the branch site, the polypyrimidine stretch and the AG dinucleotide of the 3'-splice site. When the 30 S complex was first generated with partially purified fractions, followed by the addition of a large amount of poly(U) or unlabeled pre-mRNA, the 30 S complex could be chased into a 55 S spliceosome complex by the addition of fraction Ib. These results support the conclusion, initially derived from kinetic data, that the 30 S complex is a precursor of the 55 S complex.

Antisense probing of the human U4/U6 snRNP with biotinylated 2'-OMe RNA oligonucleotides.

We have used antisense 2'-OMe RNA oligonucleotides carrying four 5'-terminal biotin residues to probe the structure and function of the human U4/U6 snRNP. Nine oligonucleotides, complementary to multiple regions of U4 and U6 snRNAs, bound stably and specifically to U4/U6 snRNP. This allowed for efficient and selective removal of U4/U6 from HeLa cell nuclear extracts. Binding of oligonucleotides to certain snRNA domains inhibited splicing and affected the U4-U6 interaction. Pre-mRNA and splicing products could also be affinity-selected through binding of the oligonucleotides to U4/U6 snRNPs in splicing complexes. The results suggest that U4 snRNP is not released during spliceosome assembly.

Purification of the major UsnRNPs from broad bean nuclear extracts and characterization of their protein constituents.

Small nuclear ribonucleoprotein particles containing the five major nucleoplasmic snRNAs U1, U2, U4, U5 and U6 as well as two smaller sized snRNAs were purified from broad bean nuclear extracts by anti-m3G, monoclonal antibody, immunoaffinity chromatography. We have so far defined 13 polypeptides of approximate mol. wts. of 11 kd, 11.5 kd, 12.5 kd, 16 kd, 17 kd, 17.5 kd, 18.5 kd, 25 kd (double band), 30 kd, 31 kd, 35 kd, 36 kd and 54 kd. Upon fractionation of the UsnRNPs by anion exchange chromatography, essentially pure U5 snRNPs were obtained, containing the 11 kd, 11.5 kd, 12.5 kd, 16 kd, 17 kd, 17.5 kd, 35 kd and 36 kd polypeptides. These may therefore represent the common snRNP polypeptides and which may also be present in the other snRNPs. By immunoblotting studies, using anti-Sm sera and mouse monoclonal antibodies we show that the 35 kd and 36 kd proteins are immunologically related to the mammalian common B/B' proteins. The broad bean 16 kd and 17 kd proteins appear to share structural elements with the mammalian D protein. The three proteins of mol. wts. 11 kd, 11.5 kd and 12.5 kd probably represent the broad bean polypeptides E, F, and G. Cross-reactivity of proteins of mol. wts of 30 kd and 31 kd with Anti-(U1/U2)RNP antibodies suggests that they may represent the broad bean A and B" polypeptides. The 54 kd protein and the 18.5 kd protein could be candidates for the U1 specific 70 k and C polypeptides. Our results demonstrate a strong similarity between the overall structure of broad bean and mammalian snRNPs.

[Extraction of native preparations of mRNP-particles from the nuclei of kidney bean cells]. / Poluchenie nativnykh preparatov m-RNP-chastits iz iader kletok semian fasoli.

A soft technique is suggested for extracting the mRNP-particles from nuclei. It is based on the incubation of nuclei with ATP. Advantages of the technique, as compared with other described in literature, are as follows: contamination-free mRNP preparations without any DNP fragments are more homogeneous in respect to the CsCl gradient buoyant density and a higher percentage of poly(A)+-mRNP in the total quantity of RNP extracted from nuclei.

[Effect of the isolation method and staining procedure on the morphology of the virion ribonucleoprotein of Sendai virus]. / Vliianie metoda vydeleniia i sposoba kontrastirovaniia na morfologiiu virnionnogo ribonukleoproteida virusa Sendai.

Electron microscopic examinations of morphology of Sendai virus ribonucleoprotein (RNP) isolated from purified virions by two methods and simultaneous staining of the preparations with uranyl acetate and phosphotungstate acid (PTA) were carried out. The staining method was shown not to influence the kind of nucleoproteins which had been isolated from disrupted virions by sucrose density gradient centrifugation. With both strains RNP appeared as strongly helixed filaments. The staining method, however, strongly influenced morphology of RNP isolated from disrupted virions by equilibrium centrifugation in cesium chloride density gradient. After uranyl acetate staining RNP had an appearance of hard filaments whereas in the same preparation stained with PTA partially and completely unwound spirals of nucleocapsid were found alongside with strongly spiralized structures.

Masking of pleomorphic glycogen sites by methanolic uranyl acetate.

Rat liver tissue was fixed in 2.5% glutaraldehyde buffered with cacodylic acid (pH 7.3) for 2 hr, washed twice in buffer, and postfixed in 2% osmium tetroxide at 4 C for 1 hr. The tissue then was dehydrated, infiltrated with and embedded in Epon by routine procedures. The ultrathin sections from this tissue, when stained with spectroscopic grade methanol saturated with uranyl acetate (SMUA) for 1 min followed by aqueous lead citrate (PbCi) (Reynolds 1963) for 5 min at room temperature, showed a uniform staining of all major cellular components except glycogen. The SMUA appeared to be specific for ribonuceloprotein granules, rendering them more prominent in the cytoplasm due to the lack of glycogen staining. The question of glycogen removal from the sections due to SMUA treatment was evulated using various extractions and staining methods. It appeared that SMUA pretreatment alters the subsequent binding ability of lead salts, resulting in lack of glycogen staining, although it does not remove the glycogen from the sections.