Distribution of 5 s RNA in HeLa cells

Molecular mechanisms governing offspring metabolic programming in rodent models of in utero stress

The results of different human epidemiological datasets provided the impetus to introduce the now commonly accepted theory coined as 'developmental programming', whereby the presence of a stressor during gestation predisposes the growing fetus to develop diseases, such as metabolic dysfunction in later postnatal life. However, in a clinical setting, human lifespan and inaccessibility to tissue for analysis are major limitations to study the molecular mechanisms governing developmental programming. Subsequently, studies using animal models have proved indispensable to the identification of key molecular pathways and epigenetic mechanisms that are dysregulated in metabolic organs of the fetus and adult programmed due to an adverse gestational environment. Rodents such as mice and rats are the most used experimental animals in the study of developmental programming. This review summarises the molecular pathways and epigenetic mechanisms influencing alterations in metabolic tissues of rodent offspring exposed to in utero stress and subsequently programmed for metabolic dysfunction. By comparing molecular mechanisms in a variety of rodent models of in utero stress, we hope to summarise common themes and pathways governing later metabolic dysfunction in the offspring whilst identifying reasons for incongruencies between models so to inform future work. With the continued use and refinement of such models of developmental programming, the scientific community may gain the knowledge required for the targeted treatment of metabolic diseases that have intrauterine origins.

Chaperoning 5S RNA assembly

In this study, Madru et al. determined the structure of the ribosome-bound Rpf2–Rrs1 complex, a complex essential for the assembly of the 5S RNA in ribosomes, and characterized the free and 5S-bound structures. The findings show that Rpf2 and Rrs1 establish a network of protein–protein and protein–RNA interactions with the 5S RNA and specific preribosomes, thus providing novel insight into ribosome biogenesis.

In eukaryotes, three of the four ribosomal RNAs (rRNAs)—the 5.8S, 18S, and 25S/28S rRNAs—are processed from a single pre-rRNA transcript and assembled into ribosomes. The fourth rRNA, the 5S rRNA, is transcribed by RNA polymerase III and is assembled into the 5S ribonucleoprotein particle (RNP), containing ribosomal proteins Rpl5/uL18 and Rpl11/uL5, prior to its incorporation into preribosomes. In mammals, the 5S RNP is also a central regulator of the homeostasis of the tumor suppressor p53. The nucleolar localization of the 5S RNP and its assembly into preribosomes are performed by a specialized complex composed of Rpf2 and Rrs1 in yeast or Bxdc1 and hRrs1 in humans. Here we report the structural and functional characterization of the Rpf2–Rrs1 complex alone, in complex with the 5S RNA, and within pre-60S ribosomes. We show that the Rpf2–Rrs1 complex contains a specialized 5S RNA E-loop-binding module, contacts the Rpl5 protein, and also contacts the ribosome assembly factor Rsa4 and the 25S RNA. We propose that the Rpf2–Rrs1 complex establishes a network of interactions that guide the incorporation of the 5S RNP in preribosomes in the initial conformation prior to its rotation to form the central protuberance found in the mature large ribosomal subunit.

5S ribosomal RNA is an essential component of a nascent ribosomal precursor complex that regulates the Hdm2-p53 checkpoint

Recently, we demonstrated that RPL5 and RPL11 act in a mutually dependent manner to inhibit Hdm2 and stabilize p53 following impaired ribosome biogenesis. Given that RPL5 and RPL11 form a preribosomal complex with noncoding 5S ribosomal RNA (rRNA) and the three have been implicated in the p53 response, we reasoned they may be part of an Hdm2-inhibitory complex. Here, we show that small interfering RNAs directed against 5S rRNA have no effect on total or nascent levels of the noncoding rRNA, though they prevent the reported Hdm4 inhibition of p53. To achieve efficient inhibition of 5S rRNA synthesis, we targeted TFIIIA, a specific RNA polymerase III cofactor, which, like depletion of either RPL5 or RPL11, did not induce p53. Instead, 5S rRNA acts in a dependent manner with RPL5 and RPL11 to inhibit Hdm2 and stabilize p53. Moreover, depletion of any one of the three components abolished the binding of the other two to Hdm2, explaining their common dependence. Finally, we demonstrate that the RPL5/RPL11/5S rRNA preribosomal complex is redirected from assembly into nascent 60S ribosomes to Hdm2 inhibition as a consequence of impaired ribosome biogenesis. Thus, the activation of the Hdm2-inhibitory complex is not a passive but a regulated event, whose potential role in tumor suppression has been recently noted.

The JAK-STAT pathway at twenty

We look back on the discoveries that the tyrosine kinases TYK2 and JAK1 and the transcription factors STAT1, STAT2, and IRF9 are required for the cellular response to type I interferons. This initial description of the JAK-STAT pathway led quickly to additional discoveries that type II interferons and many other cytokines signal through similar mechanisms. This well-understood pathway now serves as a paradigm showing how information from protein-protein contacts at the cell surface can be conveyed directly to genes in the nucleus. We also review recent work on the STAT proteins showing the importance of several different posttranslational modifications, including serine phosphorylation, acetylation, methylation, and sumoylation. These remarkably proficient proteins also provide noncanonical functions in transcriptional regulation and they also function in mitochondrial respiration and chromatin organization in ways that may not involve transcription at all.

A Drosophila fragile X protein interacts with components of RNAi and ribosomal proteins

Fragile X syndrome is a common form of inherited mental retardation caused by the loss of FMR1 expression. The FMR1 gene encodes an RNA-binding protein that associates with translating ribosomes and acts as a negative translational regulator. In Drosophila, the fly homolog of the FMR1 protein (dFMR1) binds to and represses the translation of an mRNA encoding of the microtuble-associated protein Futsch. We have isolated a dFMR1-associated complex that includes two ribosomal proteins, L5 and L11, along with 5S RNA. The dFMR1 complex also contains Argonaute2 (AGO2) and a Drosophila homolog of p68 RNA helicase (Dmp68). AGO2 is an essential component for the RNA-induced silencing complex (RISC), a sequence-specific nuclease complex that mediates RNA interference (RNAi) in Drosophila. We show that Dmp68 is also required for efficient RNAi. We further show that dFMR1 is associated with Dicer, another essential component of the RNAi pathway, and microRNAs (miRNAs) in vivo, suggesting that dFMR1 is part of the RNAi-related apparatus. Our findings suggest a model in which the RNAi and dFMR1-mediated translational control pathways intersect in Drosophila. Our findings also raise the possibility that defects in an RNAi-related machinery may cause human disease.

Two novel RNA binding proteins from Trypanosoma brucei are associated with 5S rRNA

We have previously reported the identification of two closely related RNA binding proteins from Trypanosoma brucei which we have termed p34 and p37. The predicted primary structures of the two proteins are highly homologous with one major difference, an 18-amino-acid insert in the N-terminal region of p37. These two proteins have been localized to the nucleus based on immunofluorescence microscopy. To gain insight into their function, we have utilized UV crosslinking, coimmunoprecipitation, and sucrose density gradients to identify T. brucei RNA species that associate with p34 and p37. These experiments have demonstrated a specific interaction of both p34 and p37 with the 5S ribosomal RNA and indicate that other RNA species are unlikely to be specifically bound. This suggests a role for p34 and p37 in the import and/or assembly pathway of T. brucei 5S rRNA in ribosome biogenesis.

Analysis of the 5S RNA pool in Arabidopsis thaliana: RNAs are heterogeneous and only two of the genomic 5S loci produce mature 5S RNA

One major 5S RNA, 120 bases long, was revealed by an analysis of mature 5S RNA from tissues, developmental stages, and polysomes in Arabidopsis thaliana. Minor 5S RNA were also found, varying from the major one by one or two base substitutions; 5S rDNA units from each 5S array of the Arabidopsis genome were isolated by PCR using CIC yeast artificial chromosomes (YACs) mapped on the different loci. By using a comparison of the 5S DNA and RNA sequences, we could show that both major and minor 5S transcripts come from only two of the genomic 5S loci: chromosome 4 and chromosome 5 major block. Other 5S loci are either not transcribed or produce rapidly degraded 5S transcripts. Analysis of the 5'- and 3'-DNA flanking sequence has permitted the definition of specific signatures for each 5S rDNA array.

Release of ribosome-bound 5S rRNA upon cleavage of the phosphodiester bond between nucleotides A54 and A55 in 5S rRNA

Reticulocyte lysates contain ribosome-bound and free populations of 5S RNA. The free population is sensitive to nuclease cleavage in the internal loop B, at the phosphodiester bond connecting nucleotides A54 and A55. Similar cleavage sites were detected in 5S rRNA in 60S subunits and 80S ribosomes. However, 5S rRNA in reticulocyte polysomes is insensitive to cleavage unless ribosomes are salt-washed. This suggests that a translational factor protects the backbone surrounding A54 from cleavage in polysomes. Upon nuclease treatment of mouse 60S subunits or reticulocyte lysates a small population of ribosomes released its 5S rRNA together with ribosomal protein L5. Furthermore, rRNA sequences from 5.8S, 28S and 18S rRNA were released. In 18S rRNA the sequences mainly originate from the 630 loop and stem (helix 18) in the 5' domain, whereas in 28S rRNA a majority of fragments is derived from helices 47 and 81 in domains III and V, respectively. We speculate that this type of rRNA-fragmentation may mimic a ribosome degradation pathway.

Nucleolar targeting of 5S RNA in Xenopus laevis oocytes: somatic-type nucleotide substitutions enhance nucleolar localization

In Xenopus laevis oocytes, 5S RNA is stored in the cytoplasm until vitellogenesis, at which time it is imported into the nucleus and targeted to nucleoli for ribosome assembly. This article shows that throughout oogenesis there is a pool of nuclear 5S RNA which is not nucleolar-associated. This distribution reflects that of oocyte-type 5S RNA, which is the major 5S RNA species in oocytes; only small amounts of somatic-type, which differs by six nucleotides, are synthesized. Indeed, 32P-labeled oocyte-type 5S RNA showed a degree of nucleolar localization similar to endogenous 5S RNA (33%) after microinjection. In contrast, 32P-labeled somatic-type 5S RNA showed significantly enhanced localization, whereby 70% of nuclear RNA was associated with nucleoli. A chimeric RNA molecule containing only one somatic-specific nucleotide substitution also showed enhanced localization, in addition to other somatic-specific phenotypes, including enhanced nuclear import and ribosome incorporation. The distribution of 35S-labeled ribosomal protein L5 was similar to that of oocyte-type 5S RNA, even when preassembled with somatic-type 5S RNA. The distribution of a series of 5S RNA mutants was also analyzed. These mutants showed various degrees of localization, suggesting that the efficiency of nucleolar targeting can be influenced by many discrete regions of the 5S RNA molecule.

Distinct domains in ribosomal protein L5 mediate 5 S rRNA binding and nucleolar localization

Ribosomal protein L5, a 34-kDa large ribosomal subunit protein, binds to 5 S rRNA and has been implicated in the intracellular transport of 5 S rRNA. By immunofluorescence microscopy, L5 is detected mostly in the nucleolus with a fainter signal in the nucleoplasm, and it is known to also be a component of large ribosomal subunits in the cytoplasm. 5 S rRNA is transcribed in the nucleoplasm, and L5 is thought to play an important role in delivering 5 S rRNA to the nucleolus. Using RNA-binding assays and transfection experiments, we have delineated the domains within L5 that confer its 5 S rRNA binding activity and that localize it to the nucleolus. We found that the amino-terminal 93 amino acids are necessary and sufficient to bind 5 S rRNA in vitro, while the carboxyl-terminal half of the protein, comprising amino acids 151-296, serves to localize the protein to the nucleolus. L5, therefore, has a modular domain structure reminiscent of other RNA transport proteins where one region of the molecule serves to bind RNA while another determines subcellular localization.

Interaction of the ribosomal protein, L5, with protein phosphatase type 1

The two-hybrid system was used to screen for binding proteins of type 1 protein phosphatase. Two plasmids were constructed, one containing the cDNA of the delta isoform of the type 1 catalytic subunit and the other containing a chicken gizzard cDNA library. Yeast (Y190) were transformed with the plasmids and screened for interacting species. 35 positive clones were categorized into 19 gene groups. Most of these were not identified. One clone, however, contained a sequence identical to the C-terminal portion of the chicken ribosomal protein L5 and corresponded to nucleotide residues 606-975. L5 was isolated from rat liver ribosomes as the L5.5 S RNA complex. This activated phosphatase activity of a myosin-bound phosphatase and the isolated type 1 catalytic subunit using phosphorylated myosin light chains and phosphorylase alpha as substrates. In addition, it was found that phosphatase sedimented with ribosomal subunits containing L5 but did not sediment with those deficient in L5. These data indicate that L5 binds to the catalytic subunit of the type 1 protein phosphatase and may act as a target molecule for phosphatase in ribosomal function or other cell mechanisms.

Metabolic characteristics of rat liver cytosolic 5SRNA

5SRNA were purified from the cytosol, ribosomes, nucleoli and nucleoplasm of rat liver. The 5'-terminal and 3'-terminal sequences of these 5SRNA species were shown to be the same. The time course of changes in specific activities of these 5SRNA in rat liver, 20 min to 16 h after intraperitoneal injection of [14C]orotic acid, were investigated. The specific activity of cytosolic 5SRNA increased almost linearly for 3 h, without a lag, to a high value, then decreased rapidly. The specific activity of cytosolic 5SRNA was much higher than the specific activities of 5SRNA from the other cellular components over 45 min to 6 h after intraperitoneal injection, although at 20 min the specific activity was similar to that of nucleoplasmic 5SRNA. Thus, cytosolic 5SRNA of rat liver is characterized by a high rate of turnover, which was shown to be comparable to that of heterogeneous nuclear RNA. The specific activity of 5SRNA, 45 min to 6 h after intraperitoneal injection, was as follows; cytosolic > nucleoplasmic > nucleolar > ribosomal 5SRNA. The specific activity of nucleoplasmic RNA that migrated slightly slower than nucleoplasmic 5SRNA on PAGE was much higher than that of cytosolic 5SRNA or nucleoplasmic 5SRNA, and so may be the precursor of nucleoplasmic 5SRNA. Together, these results indicate that cytosolic 5SRNA is transferred from the nuclei to the cytosol immediately after maturation of the precursor of nucleoplasmic 5SRNA without entering the nucleoplasmic pool of 5SRNA.

Electron microscopic visualisation of the 5S rRNA-YL3 complex from Saccharomyces cerevisiae

The complex comprising 5S ribosomal RNA and the ribosomal protein YL3 (5S rRNP) was isolated from yeast (Saccharomyces cerevisiae), and positively contrasted preparations were imaged by transmission electron microscopy. The overall dimensions of the 5S rRNP complex in the micrographs were 10 nm by 6 nm. Three predominant projections were selected from several hundred putative particles for digitisation and computer averaging to yield two-dimensional constructions with reproducible spatial resolutions exceeding 2 nm. The enhanced projection images were compatible with structural models of this complex based on biochemical studies.

A Trypanosoma brucei small RNP particle containing the 5S rRNA

In mammalian cells, approximately 50% of the 5S rRNA is found in ribosomes, and the remainder in a small particle, the 5S rRNA/ribosomal protein L5 complex, which is thought to be a precursor in ribosome assembly. Trypanosoma brucei, an African trypanosome, is one of the most primitive eukaryotic organisms which have been studied, and it likewise possesses a 5S rRNA species, a small proportion of which is found in an apparent ribonucleoprotein-(RNP) complex. Like the mammalian RNP particle, the T. brucei particle has a sedimentation coefficient of about 7S in sucrose gradients; unlike its mammalian counterpart, the complex is not disrupted by high salt and can be fractionated in cesium sulfate density gradients at a density characteristic of RNP complexes (1.45 g ml-1). Our studies demonstrate the the T. brucei 7S RNP contains 5S rRNA in association with a 36-kDa rRNA binding protein which not only shares molecular size, but also immunological determinants, with the yeast ribosomal protein YL3, and its mammalian homologue, L5. These results indicate that the RNP complex formed between the 5S rRNA and the 36-kDa ribosomal protein is conserved throughout great evolutionary distances between eukaryotic species.

Post-transcriptional regulation of 5S rRNA synthesis following myoblast differentiation

Terminal differentiation of proliferating rat L6 myoblasts to syncytial multi-nucleated myotubes results in a decline in the cellular levels of 5S rRNA. This decrease parallels the drop in ribosome number and the reduction in 45S rRNA precursor gene transcription previously documented [Jacobs et al. (1985) Eur. J. Biochem. 150, 255]. The activity of RNA polymerase III in 100,000 x g supernatants from myoblasts and myotubes is similar suggesting the level of this enzyme does not limit 5S rRNA synthesis. Nuclear and cell-free transcription assays were used to measure 5S rRNA synthesis in myoblasts and myotubes. No differences were observed in the rate of 5S rRNA gene transcription, thus demonstrating that 5S rRNA levels in myotubes are not transcriptionally controlled. To determine whether RNA stability plays a role, the half-life of newly synthesized 5S rRNA was measured in vivo. The half-life of nuclear 5S rRNA was calculated to be 370 min and 65 min in myoblasts and myotubes, respectively, demonstrating that the decrease in 5S rRNA levels following terminal differentiation is regulated post-transcriptionally.

Characterization by human antibodies of two HeLa cell proteins which are related to Xenopus laevis transcription factor TFIIIA

The sera of two patients with autoimmune disorders recognize in HeLa cell extracts two proteins with apparent molecular masses of 37,000 (p37) daltons and 32,000 daltons (p32). These proteins are non covalently associated with 5S RNA and sediment as 7-10 S particles in sucrose density gradients. Both proteins are antigenetically related to TFIIIA, a previously described protein of Xenopus laevis, which is known as a 5S RNA transcription factor and occurs in oocytes as a noncovalent complex with 5S RNA. Like TFIIIA, HeLa cell proteins p37 binds in vitro to 5S RNA and to cloned 5S RNA genes. These results suggest that protein p37 fulfils in HeLa cells a function similar to that of TFIIIA in amphibian oocytes, ie control of 5S RNA transcription.

A 5S rRNA/L5 complex is a precursor to ribosome assembly in mammalian cells

A novel 5S RNA-protein (RNP) complex in human and mouse cells has been analyzed using patient autoantibodies. The RNP is small (approximately 7S) and contains most of the nonribosome-associated 5S RNA molecules in HeLa cells. The 5S RNA in the particle is matured at its 3' end, consistent with the results of in vivo pulse-chase experiments which indicate that this RNP represents a later step in 5S biogenesis than a previously described 5S*/La protein complex. The protein moiety of the 5S RNP has been identified as ribosomal protein L5, which is known to be released from ribosomes in a complex with 5S after various treatments of the 60S subunit. Indirect immunofluorescence indicates that the L5/5S complex is concentrated in the nucleolus. L5 may therefore play a role in delivering 5S rRNA to the nucleolus for assembly into ribosomes.

Heterogeneity of 5S RNA in fungal ribosomes

Neurospora crassa has at least seven types of 5S RNA genes (alpha, beta, gamma, epsilon, delta, zeta, and eta) with different coding regions. A high resolution gel electrophoresis system was developed to separate minor 5S RNA's from the major 5S RNA (alpha). A study of several Neurospora crassa strains, four other species in the genus Neurospora, members of two closely related genera, and three distantly related genera demonstrated that 5S RNA heterogeneity is common among fungi. In addition, different 5S RNA's are present in Neurospora ribosomes. The finding that fungal ribosomes are structurally heterogeneous suggests that ribosomes may be functionally heterogeneous as well.

Isolation and characterization of hnRNA-snRNA-protein complexes from Morris hepatoma cells

Of the RNA labelled after incubation of hepatoma cells with radioactive precursors for 20 and 150 min. 35% and 70%, respectively, can be isolated from nuclei by two consecutive extractions with 0.14 M NaCl at pH 8. The isolated RNA is complexed with nuclear proteins forming structures with sedimentation coefficients of less than 30 S to greater than 100 S. Similar complexes from rat liver isolated under the same experimental conditions show coefficients of 30-40 S. The RNA-associated proteins are similar, on the basis of sodium dodecyl sulphate/polyacrylamide gel electrophoresis, to the respective proteins of other cell types. The presence on these RNP complexes of six discrete small nuclear RNAs (snRNA) has been established. Experiments with a reversible inhibitor of RNA synthesis, D-galactosamine, demonstrated, differences in the turnover of hnRNA and snRNA. The half-lives of the six snRNA species has been determined, varying from 32 h for snRNA species a, b and d, to 22 h for snRNA species e and f and to 13 h for snRNA species c. Treatment of the nuclear extracts with 0.7 M and 1 M NaCl results in dissociation of hnRNA from the 'core' and other polypeptides, whereas snRNA remains complexed with polypeptides of Mr 54 000-59 000. Incubation of the nuclear extracts at 0 C with low doses of pancreatic R Nase (up to 1.5 micrograms/ml), which renders approximately 80% of the hnRNA acid-soluble and cleaves most of the snRNA, results in conversion of the high-molecular-weight hnRNPs to 30-S structures, without disrupting the 30-S RNP. Treatment of the nuclear extracts with higher doses of RNase (3 micrograms/ml) leads to disruption of the 30-S RNP and release of the hnRNA-associated proteins, underlining the importance of hnRNA-protein interaction for the retainment of the hnRNP structures.

Small nuclear RNAs from Drosophila KC-H cells; characterization and comparison with mammalian RNAs

Small molecular weight nuclear RNAs were extracted from cultured Drosophila KC-H cells and characterized by their electrophoretic mobilities in 5--15% gradient acrylamide gels or in 10% acrylamide-7 M urea gels. Comparison between the electrophoretic profiles of these SnRNAs with those from human and mouse cells revealed striking similarities and allowed for assignation of band nomenclatures as established for mammalian cells. Comparison of mobilities in the two gel systems also permitted correspondence between the different nomenclatures established by various groups for this class of RNAs, as well as an approximate estimate of their molecular sizes.

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.

Intracellular distribution of low molecular weight RNA species in HeLa cells

Intracellular distributions of the low molecular weight RNA species of HeLa cells were determined by a nonaqueous method of cell fractionation, in which lyophilized cells were homogenized and centrifuged in anhydrous glycerol. The nonaqueous method was used to avoid artifactual extraction of weakly bound nuclear RNA during cell fractionation. We found that the mature small RNA species K, A, C, and D were almost entirely (greater than 95%) nuclear, and that mature 4S tRNA was partially (5-10%) nuclear. Our results gave higher nuclear content of the mature species K, A, C, and 4S than was shown previously with conventional aqueous cell fractionation. The nonaqueous method also gave higher nuclear proportions of some short-lived precursors to mature small RNAs. We found that approximately one-half of recently synthesized pre-4S RNA and more than one-half of recently synthesized 5S RNA were nuclear, whereas these species had been thought to be cytoplasmic from previous work. The species C' and D', precursors to the stable nuclear species C and D respectively, were found to be partially nuclear, also in contrast to earlier work. The stable cytoplasmic species L (oncornavirus 7S RNA) was found to be mostly nuclear shortly after synthesis.

The addition of 5' cap structures occurs early in hnRNA synthesis and prematurely terminated molecules are capped

After cells were labeled by brief exposure to 3H-methyl-L-methionine, the majority of labeled 5' terminal cap I (m7GpppN1mpN2p) oligonucleotide structures were in nuclear RNA (hnRNA) molecules approximately 750 nucleotides or less in length. After longer label times, the proportion of cap I structures in nuclear molecules longer than mRNA rose to approximately 60% of the total, but approximately 40% of the cap I structures were still in molecules shorter than approximately 750 nucleotides. The cap I structures in both long and short hnRNA chains contained all four 2' methylated nucleotides in the N1 position in about the same proportion as in mRNA. None of the large hnRNA molecules could be demonstrated to contain 5' pppX p termini; the only such terminus in high molecular weight RNA was pppAp which was decreased markedly by low doses of actinomycin and is presumably the terminus of pre-rRNA. These results raise the possibilities that hnRNA chains can initiate with any of the four nucleotides, that capping occurs very close to or at the start of hnRNA chain synthesis and that approximately 40% of the hnRNA chains may be prematurely terminated.

Low molecular weight RNAs as components of nuclear ribonucleoprotein particles containing heterogeneous nuclear RNA

70-130 S polyparticles as well as 38 S monoparticles were isolated from rat liver nuclei and analyzed in respect to their RNA components by microgel polyacrylamide electrophoresis in formamide. In addition to the high molecular weight polydisperse hnRNA of polyparticles several low molecular weight RNAs (snRNA) were detected. There are at least six distinct snRNA species in polyparticles. Except for one species, which is missing, 38 S monoparticles showed a similar snRNA pattern. From densitometer tracings of microgels the snRNAs were estimated to represent about 11% of the total polyparticle RNA. The number of nucleotides for the various snRNAs were determined from a plot of relative electrophoretic mobility versus log number of nucleotides. The possibility that the snRNAs are degradation products of the hnRNA was excluded on the basis of the following findings. (1) The snRNA pattern was similar in mono- and polyparticles. (2) Whereas the hnRNA of polyparticles incubated at 37 degrees C was extensively degraded, the snRNA did not show a corresponding increase. (3) After a 30 min pulse with [3H]orotate the hn RNA was readily labeled; none of the snRNAs, however, incorporated radioactivity. The snRNAs were still found after treatment of polyparticles with 2 M NaCl excluding contamination by nucleoplasm.

Metabolism of low molecular weight ribonucleic acids in early sea urchin embryos

There are three major low molecular weight RNAs (150-300 nucleotides) larger than 5S rRNA present in sea urchin embryos. Two of these are localized in the nucleus and one is localized in the cytoplasm. The nuclear species contain "capped" 5' termini, with a cap I structure. These RNAs are synthesized starting in late cleavage and continuing through pluteus. Relative to 5S RNA there is a 10-fold change in the rate of synthesis of these RNAs, due primarily to a decrease in their rate of transcription after blastula. The RNAs are metabolically stable and the nuclear RNA genes are reiterated 50--100 times in the genome. Significant amounts of these RNAs are present in sea urchin eggs, enough to supply the embryo during early cleavage, prior to initiation of their synthesis.

Low molecular weight RNAs hydrogen-bonded to nuclear and cytoplasmic poly(A)-terminated RNA from cultured Chinese hamster ovary cells

A group of RNAs 90--100 nucleotides long were isolated by melting them from poly(A)-terminated nuclear or cytoplasmic RNA from cultured Chinese hamster ovary cells. Conditions that favor hydrogen bond formation allowed the reassociation of these low molecular weight RNAs with poly(A)-terminated RNA. The nuclear poly(A)-terminated molecules contained 1.3 moles of the low molecular weight RNAs per mole of poly(A), while the cytoplasmic poly(A)-terminated RNA contained only one seventh as much. These low molecular weight RNAs were also isolated from the total 4S RNA of either the nucleus or cytoplasm by polyacrylamide gel electrophoresis. They formed a prominantly labeled band of RNA in the gels after cells had been labeled with H(3)32PO4 for 4 hr. The low molecular weight RNAs melted from the nuclear poly(A)-terminated RNA were slightly different (although not necessarily in primary nucleotide sequence) from those melted from the cytoplasmic poly(A)-terminated RNA.

Maturation of ribosomes in yeast. II. Position of the low molecular weight rRNA species in the maturation process

Yeast protoplasts were pulse labelled with [5-3H] uridine and the labelling kinetics of the low molecular weight rRNA species were determined in order to gain more insight into the position of those small rRNAs in the process of ribosome maturation. 7-S RNA, the immediate precursor of 5.8-S rRNA, is found to be present only in the nucleus, indicating that the conversion of 7-S to 5.8-S RNA is a nuclear event. 5.8-S rRNA is observed in the cytoplasm almost immediately after its formation. This as well as the presence of only a small amount of 5.8-S RNA in the nucleus, shows that the ribosomal precursor particles of the large ribosomal subunit are very rapidly transported into the cytoplasm once 5.8-S rRNA is formed. Most of the newly synthesized 5-S RNA is found in the nucleus. This nuclear 5-S rRNA is mainly present in the ribosomal precursor particles. However, a small pool of free 5-S rRNA is probably also present.

Detailed analysis of the ribosomal RNA synthesis in yeast

In order to study the biosynthesis of ribosomal RNA in Saccharomyces carlsbergensis the labelling kinetics of the various precursor and mature rRNA species were determined using pulse-labelling of protoplasts with [5-3H] uridine at 15 degrees C. Label appears almost immediately in 37 S RNA, the precursor common to both 26 S and 17 S rRNA. Labelled 29 S and 18 S RNA, the immediate precursors of 26 S and 17 S rRNA respectively, were found to appear about 4 min and about 8 min after addition of the isotope respectively. These data indicate that the topography of the 37 S precursor RNA is: 5'-17 S -26 S-3'. The pool size of 29 S RNA is about twice as large as that of either 37 S or 18 S RNA, indicating that under the conditions used processing of 18 S to 17 S rRNA proceeds more rapidly than processing of 29 S to 26 S rRNA. The labelling kinetics of 5.8 S rRNA are in agreement with the existence of a 7 S precursor rRNA, the identity of which was previously established (Trapman, J., de Jonge, P. and Planta, R.J. (1975) FEBS Lett. 57, 26--30) and which, in turn, probably is derived from 29 S precursor rRNA. The labelling kinetics of 5 S rRNA suggest that 5 S RNA sequences, rather than also being part of the common 37 S precursor, are located on a separate primary transcription product. Whether this transcript still contains excess sequences remains to be determined. However, because of the rapid appearance of labelled 5 S RNA, such a precursor would have to be very short lived.

Low molecular weight RNA species from chromatin

Several methods of preparing low molecular weight RNA from chick embryo chromatin have been examined. Traditional methods for dissociating chromatin utilizing high concentrations of salt (greater than 2 M) followed by high-speed centrifugation resulted in very low yields of RNA. Increased yields of RNA were obtained by treating chromatin at lower salt concentration (0.2-0.5 M). By using low salt extraction and sodium dodecyl sulfate-phenol deproteinization, six to eight low molecular weight homogeneous RNA species were isolated from chick embryo chromatin and mouse myeloma chromatin. In the myeloma system, all these RNAs are metabolically stable. Each component is homogeneous as examined by gel electrophoresis and hybridizes with mouse DNA at a rate consistent with a single species. There are multiple gene copies for these RNA species in the mouse genome, varying from 100 to 2000 copies for the different species. One of these RNAs is identical with 5S rRNA. In addition, the redundancy of genes for 18S, 28S, and 5S rRNA and tRNA was determined. Approximately 300 copies for 18 and 28S rTRNA and 500 copies for 5S rRNA were found. tRNAs were on an average 110-fold redundant with about 55 different species measured.

The role of 5-S RNA in temperature-sensitive ribosomal RNA maturation

The synthesis of 5-S RNA was found to be unchanged at both the permissive (33.5 degrees C) and non-permissive (38.5 degrees C) temperatures in a temperature-sensitive Baby Hamster Kidney cell line (BHK 21 ts 422 E) as measured relative to synthesis of 18-S rRNA. The 5-S RNA is shown to be associated with nucleolar ribonucleoprotein particles even though rRNA processing does not yield a functional 28-S rRNA at the non-permissive temperature. The amount of 5-S RNA found associated with the 80-S ribonucleoprotein particles was the same at the permissive and non-permissive temperatures, indicating that an aberrant 5-S RNA contribution to rRNA processing is not a primary cause for the temperature-sensitive lesion of rRNA maturation in this mutant cell line. The amount of 5-S RNA in nucleolar 80-S RNA particles indicated that the association of 5-S RNA with the rRNA precursor particle occurs before the cleavage step at which 32-S precursor RNA is produced.

Increased synthesis of low-molecular-weight nuclear ribonucleic acids of rat liver after gamma irradiation and hepatectomy

Incorporation of [3H]orotic acid into low-molecular-weight nRNA of rat liver, fractionated on polyacrylamide gels, increased 6-12h after partial hepatectomy and 6h after gamma-irridation at 2000 R. The incorporation of orotic acid was particularly increased into the 4.5S, 5S and approx. 10S nRNA fractions. If the irradiation was given after 6h of regeneration and RNA was isolated from the nucleus 12h after hepatectomy then the incorporation of orotic acid into these low-molecular-weight nRNA components was greater than after hepatectomy or irradiation alone.

Stimulation by insulin of RNA synthesis in chick fibroblasts

After the addition of insulin to monolayers of chick fibroblasts previously incubated in serum-free medium, the rates of protein and RNA synthesis increase continuously during the first 8-10 h. Little stimulation of DNA synthesis or mitosis results with the addition of insulin alone in contrast to the addition of fresh serum which stimulates both markedly. The stimulation in RNA synthesis does not result from expansion of the nucleotide pool but is correlated with increases in RNA polymerase activity. All major classes of RNA are stimulated; processing of preribosomal RNA to 28S and 18S and the association of this mature RNA with ribosomes appear to occur normally. The kinetics of stimulation of 5S RNA differ from those of the synthesis of 4S and of ribosomal RNA. Insulin and serum appear to affect the synthesis or stability of certain transcripts differentially.

Control of 5S RNA synthesis during early development of anucleolate and partial nucleolate mutants of Xenopus laevis

Ribosomes of all eukaryotes contain a single molecule of 5S, 18S, and 28S RNA. In the frog Xenopus laevis the genes which code for 18S and 28S RNA are located in the nucleolar organizer, but these genes are not linked to the 5S RNA genes. Therefore the synthesis of the three ribosomal RNAs provides a model system for studying interchromosomal aspects of gene regulation. In order to determine if the synthesis of the three ribosomal RNAs are interdependent, the relative rate of 5S RNA synthesis was measured in anucleolate mutants (o/o), which do not synthesize any 18S or 28S RNA, and in partial nucleolate mutants (p(l-1)/o), which synthesize 18S and 28S RNA at 25% of the normal rate. Since the o/o and p(l-1)/o mutants have a complete and partial deletion of 18S and 28S RNA genes respectively, but the normal number of 5S RNA genes, they provide a unique system in which to study the dependence of 5S RNA synthesis on the synthesis of 18S and 28S RNA. Total RNA was extracted from embryos labeled during different stages of development and analyzed by polyacrylamide gel electrophoresis. Quite unexpectedly it was found that 5S RNA synthesis in o/o and p(l-1)/o mutants proceeds at the same rate as it does in normal embryos. Furthermore, 5S RNA synthesis is initiated normally at gastrulation in o/o mutants in the complete absence of 18S and 28S RNA synthesis.