Short, synthetic and selectively 13C-labeled RNA sequences for the NMR structure determination of protein–RNA complexes

We report an optimized synthesis of all canonical 2′-O-TOM protected ribonucleoside phosphoramidites and solid supports containing [¹³C₅]-labeled ribose moieties, their sequence-specific introduction into very short RNA sequences and their use for the structure determination of two protein–RNA complexes. These specifically labeled sequences facilitate RNA resonance assignments and are essential to assign a high number of sugar–sugar and intermolecular NOEs, which ultimately improve the precision and accuracy of the resulting structures. This labeling strategy is particularly useful for the study of protein–RNA complexes with single-stranded RNA in solution, which is rapidly an increasingly relevant research area in biology.     

Appearance of rapidly labeled, high molecular weight RNA in nuclear ribonucleoprotein. Release from chromatin and association with protein.

Chromatin and nuclear ribonucleoprotein (nRNP) have been prepared from a human carcinoma cell line. Following a 1-hour (3H)uridine pulse, 60 to 70% of the nuclear radioactivity, after removal of nucleoli, was found in the chromatin, the balance in nRNP. This was true whether the chromatin and nRNP were separated by velocity centrifugation or by isopycnic centrifugation on Metrizamide gradients. Radioactivity in chromatin and nRNP was found in high molecular weight RNA, with mean sedimentation coefficients of 20 S and 15 S, respectively, as determined on sodium dodecyl sulfate-sucrose gradients. Experiments on the kinetics of appearance of radioactivity in the RNA of the two fractions suggest that some of the chromatin-associated RNA is precursor to nRNP-RNA. The proteins of nRNP are complex as revealed by sodium dodecyl sulfate gel electrophoresis. The contamination by chromatin protein was estimated to be 5%. Experiments involving short pulses of (3H)tryptophan, and pulse-chase, suggested that the rapidly turning over proteins of nRNP were not complexed with RNA while still associated with chromatin. However, it was also shown that the radioactivity in nRNP following short pulses of (3H)tryptophan did not correspond to the major bands seen on stained sodium dodecyl sulfate gels. It is therefore concluded that the protein of nRNP consists of two classes: species present in large amounts, possibly common to all RNA in nRNP, which are relatively stable and may be complexed to RNA still associated with chromatin; and a large number of rapidly turning over species, each present in small amounts and associated with nRNP only after its release from chromatin.     

Small nuclear RNA and VA RNA in nuclear ribonucleoprotein fibrils from adenovirus-2 infected HeLa cells

The small RNA of hnRNP¹ were studied in HeLa cells infected with adenovirus-2. At 15 h post-infection, when 50–60 % of the hnRNA was of viral origin, all the small nuclear RNA of hnRNP from non-infected cells were present in hnRNP from infected cells. The small, virus-encoded VA RNA could not be detected by staining like the snRNA but only after labeling. It represented less than 1 % of the small nuclear RNA in hnRNP. The low level of VA RNA in hnRNP as compared to that of the small nuclear RNA does not favor the hypothesis of a similar function for these 2 classes of small RNA.     

Autoradiographic Studies of Uridine-5-H3 Uptake in Entamoeba histolytica in the CLG Medium1

SYNOPSIS. Using uridine-5-H³, “long-term” labeling experiments over a 72 hr growth cycle were done with E. histolytica strain K9 grown in CLG medium with penicillin-inhibited Bacteroides. Autoradiographic analysis revealed that tritium occurs primarily in cytoplasm and rarely the nucleus of amebae. The most extensive cytoplasmic activity was observed during the initial 0–24 hr growth period of amebae as compared to later labeling periods. RNase or RNase followed by DNase extracted a large amount but not all label from amebae. These nucleases were least effective during the initial 24 hr period of growth. Thus it appears that tritium from uridine-5-H³ is not highly specific for RNA in amebae. However, the possibility that such label is associated with RNase-resistant RNA cannot be ruled out. More recent cytochemical studies do indicate the presence of RNase-resistant RNA in the cytoplasm of amebae. The activity found in penicillin-inhibited Bacteroides after uridine-5-H³ labeling and their reaction to the various digestive procedures was similar to amebae at corresponding labeling periods. Therefore at least some of the RNase-resistant material present in the cytoplasm of amebae may be derived from the ingested bacteria; this has been further found by appropriate experiments in which amebae were fed prelabeled bacteria. Nuclear activity when observed (always after 24 hrs growth) was associated either with the periphery of the nucleus and/or the endosome. It was not seen in the nuclear stroma. Some of this activity is RNase-resistant, perhaps representing double or multi-stranded RNA. It therefore appears that RNA is not distributed in the nuclear stroma in “long-term” labeling experiments.     

Rates of synthesis of major classes of RNA in Drosophila embryos.

We have been successful in labeling to high specific activity (3 × 10⁵ dpm/μg) the RNA synthesized by large numbers of Drosophila embryos. Embryos of various developmental stages were rendered permeable with octane and labeled with [³H]uridine for 1 hr. At each stage the total dpm incorporated into RNA and the specific activity of the UTP pool were measured and used to calculate the absolute rate of RNA synthesis per embryo. This rate increases during embryonic development, from 1 pmole UTP/hr at 2 hr after oviposition to 6 pmoles UTP/hr at 15 hr. The rates of synthesis of nuclear and cytoplasmic poly(A)^? and poly(A)⁺ RNAs were determined by analyzing the fractionated RNAs from each stage by sucrose gradient sedimentation. There is a significant activation of nuclear RNA synthesis at the blastoderm stage (approximately 2 hr after oviposition). After blastoderm, the rates of synthesis of nuclear and cytoplasmic poly(A)^? and poly(A)⁺ RNA per embryo increase continuously; the rate of synthesis of each of these classes per nucleus, however, remains fairly constant. After making corrections for turnover during the labeling period, we find that the rates of synthesis of the major classes of RNA per nucleus at the gastrula stage are: cytoplasmic poly(A)⁺ RNA, 0.06 fg/nucleus-min; hnRNA, 0.86 fg/nucleus-min; and ribosomal RNA, 0.46 fg/nucleus-min. These rates are compared to rates of RNA synthesis in sea urchin embryos.     

Nanosecond electric pulses penetrate the nucleus and enhance speckle formation

Nanosecond electric pulses generate nanopores in the interior membranes of cells and modulate cellular functions. Here, we used confocal microscopy and flow cytometry to observe Smith antigen antibody (Y12) binding to nuclear speckles, known as small nuclear ribonucleoprotein particles (snRNPs) or intrachromatin granule clusters (IGCs), in Jurkat cells following one or five 10 ns, 150 kV/cm pulses. Using confocal microscopy and flow cytometry, we observed changes in nuclear speckle labeling that suggested a disruption of pre-messenger RNA splicing mechanisms. Pulse exposure increased the nuclear speckled substructures by ∼2.5-fold above basal levels while the propidium iodide (PI) uptake in pulsed cells was unchanged. The resulting nuclear speckle changes were also cell cycle dependent. These findings suggest that 10 ns pulses directly influenced nuclear processes, such as the changes in the nuclear RNA-protein complexes.     

Membrane-associated protein synthesis of mammalian cells. II. Isopycnic separation of membrane-bound polyribosomes

The membrane-bound ribosomes of HeLa cells were analyzed in CsCl buoyant-density gradients. There exist two classes: a heavy class with a density of 1.55 g/ cm³ and a light class heterogeneously distributed with a mean density of 1.49 g/cm³. The lower density of the light class is due to an increased ratio of protein to RNA. This additional protein is not removed with increased ionic strength. Both classes of ribosomes incorporate amino acids at a rate comparable to non-membrane-bound ribosomes. The heavy and light ribosomes appear to correspond to the EDTA-sensitive and the EDTA-resistant ribosomes, respectively.     

Effects of cordycepin on the synthesis of nuclear and cytoplasmic RNAs in embryonic cells of Xenopus laevis

Effects of cordycepin on the incorporation of [3H] guanosine into embryonic Xenopus cells were examined. Cordycepin inhibited the labeling not only of poly(A) + RNA, but of all the other major classes of RNAs. Cellular fractionation showed that this inhibition was much stronger in the labeling of cytoplasmic RNAs than of nuclear RNAs. [3H]Cordycepin was incorporated into both poly(A) + RNA and other RNA species.     

LOCALIZATION OF MACROMOLECULES IN ESCHERICHIA COLI : II. RNA and its Site of Synthesis

The distribution of RNA in cells of E. coli 15 T^-U^- labeled with uridine-H³ was studied by methods involving the analysis of radioautographic grain counts over random thin cross-sections and serial sections of the cells. The results were correlated with electron microscope morphological data. Fractionation and enzyme digestion studies showed that a large proportion of the label was found in RNA uracil and cytosine, the rest being incorporated as DNA cytosine. In fully labeled cells the distribution of label was found to be uniform throughout the cell. The situation remained unchanged when labeled cells were subsequently treated with chloramphenicol. When short pulses of label were employed a localization of a large proportion of the radioactivity became apparent. The nuclear region was identified as the site of concentration. Similar results were obtained when cells were exposed to much longer pulses of uridine-H³ in the presence of chloramphenicol. If cells were subjected to a short pulse of cytidine-H³, then allowed to grow for a while in unlabeled medium, the label, originally concentrated to some extent in the nuclear region, was found dispersed throughout the cell. The simplest hypothesis which accounts for these results is that a large fraction of the cell RNA is synthesized in a region in or near the nucleus and subsequently transferred to the cytoplasm.     

Labeling of non poly(A) associated RNA in the rabbit cerebral cortex 24 hours after a single electroconvulsive shock

The labeling pattern of non poly(A) associated (poly(A)^–) RNA of rabbit cerebral cortex was studied 24 hr after a single electroconvulsive shock (ECS). The animals were injected subarachnoidally with [³H]uridine and sacrificed 1 hr later. The fractionation pattern of labeled nuclear poly(A)^– RNA in the cerebral cortex of ECS treated animals was identical to that of the controls. However, microsomal poly(A)^– RNA from the treated animals showed an increased labeling of 18S ribosomal RNA. Also 28S RNA displayed a higher labeling but the effect was not statistically significant. These results indicate a more efficient production of ribosomal RNA in the late post-ECS period which might be in relationship with an increased activity of brain protein synthesis machinery.     

Structure and metabolism of adenovirus RNAs containing sequences from the fiber gene

The body of adenovirus fiber messenger RNA is specified by viral r-strand co-ordinates 86.2 to 91.2. Since this mRNA is transcribed from the major late promoter at map position 16, nuclear precursors to the mRNA could be as large as 84% of the length of the 35,000 nucleotide genome. This study identified and characterized polyadenylated nuclear RNAs that contain fiber sequences and therefore are possible processing intermediates. These nuclear RNAs were characterized by hybridization of [³H]RNA preparations and by electron microscopy of RNA-DNA hybrids. Three size classes of RNAs containing fiber sequences were identified: (1) a 22 S species maps from 86.2 to 90.3. This RNA has essentially the same co-ordinates as fiber mRNA. (2) Two 28 S species have co-ordinates of 80.1 to 90.4 and 85.9 to 96.9, respectively. Thus one species has a 5′ terminus coincident with that of the mRNA body, and one has a 3′ terminus coincident with that of the 3′ end of the mRNA body. The polyadenylated terminus at 96.9 does not coincide with the 3′ end of any known mRNA. (3) There are at least two 35 S species. The 3′ end of one species is coincident with that of fiber mRNA. The 3′ terminus of the second RNA is at approximately 96.9.The labeling kinetics of each of these polyadenylated nuclear RNAs were investigated. In continuous label experiments, the two 35 S RNAs and the 85.9 to 96.9 28 S RNA became uniformly labeled in approximately 60 minutes. The 22 S RNA and the 80.1 to 90.4 28 S species continued to accumulate for at least several hours. These results are consistent with a precursor function for the 35 S RNAs and the 85.9 to 96.9 28 S species. The structures of the putative precursors imply that processing of the 3′ end is not a prerequisite for 5′ cleavage.     

The labeling of polysomes and rough microsomal membranes by 5-fluoroorotic acid

Using [2-¹⁴C]fluoroorotic acid for the selective labeling of rat liver messenger RNA, strikingly different levels of radioactivity appeared in the bound and free classes of polysomes (free > bound, ～ 3:1) well-washed rough microsomal membrane preparations, contained 5X more radioactivity than their own bound polysomes.     

Catabolism of Tritiated Thymidine by Aquatic Microbial Communities and Incorporation of Tritium into RNA and Protein

The incorporation of tritiated thymidine by five microbial ecosystems and the distribution of tritium into DNA, RNA, and protein were determined. All microbial assemblages tested exhibited significant labeling of RNA and protein (i.e., nonspecific labeling), as determined by differential acid-base hydrolysis. Nonspecific labeling was greatest in sediment samples, for which ≥95% of the tritium was recovered with the RNA and protein fractions. The percentage of tritium recovered in the DNA fraction ranged from 15 to 38% of the total labeled macromolecules recovered. Nonspecific labeling was independent of both incubation time and thymidine concentration over very wide ranges. Four different RNA hydrolysis reagents (KOH, NaOH, piperidine, and enzymes) solubilized tritium from cold trichloroacetic acid precipitates. High-pressure liquid chromatography separation of piperidine hydrolysates followed by measurement of isolated monophosphates confirmed the labeling of RNA and indicated that tritium was recovered primarily in CMP and AMP residues. We also evaluated the specificity of [2-³H]adenine incorporation into adenylate residues in both RNA and DNA in parallel with the [³H]thymidine experiments and compared the degree of nonspecific labeling by [³H]adenine with that derived from [³H]thymidine. Rapid catabolism of tritiated thymidine was evaluated by determining the disappearance of tritiated thymidine from the incubation medium and the appearance of degradation products by high-pressure liquid chromatography separation of the cell-free medium. Degradation product formation, including that of both volatile and nonvolatile compounds, was much greater than the rate of incorporation of tritium into stable macromolecules. The standard degradation pathway for thymidine coupled with utilization of Krebs cycle intermediates for the biosynthesis of amino acids, purines, and pyrimidines readily accounts for the observed nonspecific labeling in environmental samples.     

PERSISTENCE OF ALTERED RNA SYNTHESIS IN RAT CEREBRAL CORTEX 12h AFTER A SINGLE ELECTROCONVULSIVE SHOCK

The effect of electroshock (ECS) on RNA synthesis in nuclei and cytoplasm of rat cerebral cortex was examined using a double label technique by intraventricular injection of [³H] and [¹⁴C]orotate. At t h after ECS, the incorporation into nuclear RNA was 80% of the control rate and the appearance of newly synthesized RNA in the cytoplasm was only 27.6%. Analysis on composite polyacrylamide-agarose gels of purified RNA showed that the ³H/¹⁴C ratio of each gel slice slowly increased with decreasing M.W. of the RNA. This has been interpreted as an inhibition in the rate of processing of nuclear RNA. When the nuclear RNA was subjected to denaturation with 50% dimethyl sulphoxide (DMSO) this effect was enhanced. In a similar experiment, rats were injected, treated to ECS and killed 12 h later. The overall incorporation into nuclear and cytoplasmic RNA was increased to 174%, and 137.5% respectively. Analysis on gels showed very little variation in the ³H/¹⁴C ratio of the steady state levels of nuclear RNA. They compared well with a control experiment where rats were injected with [³H] and [¹⁴C]orotate as described above but no ECS was applied to the [¹⁴C] labelled animals. However a 1 h pulse label given 11 h after ECS treatment revealed that the rate of incorporation into nuclear RNA still showed a decrease of 81% of the control. The nuclear RYA fractionated on gels clearly showed that the inhibition of the processing rate of nuclear RNA was still occurring. This effect was again magnified on denaturation of the RNA with DMSO. This suggests that ECS may disturb RNA metabolism in nervous tissue for much longer periods than previously realised.     

Pushing the (nuclear) envelope into meiosis

A recent study shows that a short isoform of a mammalian nuclear lamin is important for homologous chromosome interactions during meiotic prophase in mice.Meiosis is the specialized cell division process required for sexual reproduction. As cells enter meiotic prophase, a relatively long period preceding the two chromosome divisions, nuclei and chromosomes undergo remodeling to promote interactions between homologous chromosomes. Each chromosome must find and identify its unique partner within the volume of the nucleus, a process that obviously involves large-scale chromosome movements.Over 100 years ago, cytological analysis of meiotic cells revealed a unique chromosome configuration termed the meiotic ''bouquet'', in which chromosome ends seem to be attached to the nuclear periphery, frequently in a tight cluster. The presence of the bouquet was found to coincide with the stage during which homologous chromosomes undergo pairing and synapsis. This was the first indication that interactions between the chromosomes and the nuclear envelope might be important for meiotic pairing. More recent analysis in diverse model systems has revealed that the bouquet is a consequence of interactions between chromosomes and cytoskeletal elements - microtubules or actin cables - via a protein bridge that spans the nuclear envelope. A study recently published in PLOS Genetics [1] has shed further light on the role of the nuclear lamina in meiotic progression by studying the role of a meiosis-specific isoform of a nuclear lamin protein.In metazoans the nuclear envelope is fortified by the nuclear lamina, a meshwork of intermediate filament proteins (lamins) and associated proteins that underlies the inner nuclear membrane. The lamina confers structural rigidity to nuclei and also interacts with a wide variety of nucleoplasmic, transmembrane and chromosome-associated proteins. The composition of the lamina in metazoans shows tissue-specific variability and developmental regulation. Most differentiated mammalian cells express both A-type lamins (lamins A and C, which are generated by alternative splicing of the LMNA gene) and B-type lamins (encoded by two different genes), whereas some invertebrates express only a single lamin protein. Stem cells typically lack A-type lamins, which are also dispensable for early development in mice.Among the nuclear envelope components that interact with lamins are LINC (linker of nucleoskeleton and cytoskeleton) complexes. These versatile networks involve a pair of SUN/KASH proteins that bridge both membranes of the nuclear envelope. SUN domain proteins traverse the inner membrane, with their amino termini projecting into the nucleus and their SUN domains in the lumen between the two membranes. Their partners have membrane-spanning regions adjacent to their carboxy-terminal KASH domains, short peptides that bind to the SUN domains. Using a variety of interaction modules, LINC complexes create connections between nuclear structures such as the lamina or chromosomes and cytoskeletal elements such as actin filaments or microtubules. Throughout the eukaryotes, they have essential roles in diverse processes, including the positioning and migration of nuclei within cells and anchorage of centrosomes to the nuclear envelope. During meiosis, specific LINC complexes are recruited to interact with chromosomes through the expression of meiosis-specific proteins that bind to telomeres or, less frequently, to other specialized loci [2]. These connections, probably in conjunction with meiosis-specific modifications to the cytoskeleton and motor proteins, lead to large-scale chromosome motions that facilitate homologous chromosome pairing. These movements involve dramatic motion of the LINC proteins within the nuclear membrane, sometimes involving movements of up to several micrometers that occur within a few seconds [3]. This stands in sharp contrast to the behavior of some of the same protein complexes in somatic or premeiotic cells, in which they show highly constrained motion and minimal turnover [3].In the new PLOS Genetics study [1], groups led by Manfred Alsheimer and Ricardo Benavente, both of the University of Würzburg, have now engineered a disruption of an exon in the mouse LMNA gene that is specific to the meiotic isoform lamin C2 to generate C2-deficient mice (C2^-/- mice). These collaborators have previously provided important insights into the regulation and functions of cell-type specific lamin isoforms, particularly during meiosis. Using antibodies, they characterized the lamin isoforms present in rat spermatocytes [4]. Immunolocalization revealed that a truncated isoform of lamin C (lamin C2) was localized in a patchy pattern along the nuclear envelope, along with a short B-type lamin (lamin B3) [4]. Because these short isoforms lack domains implicated in interactions between lamin subunits, they and others proposed that these proteins might form a more flexible network. This idea was supported by experiments in which meiosis-specific lamin C2 was ectopically expressed in fibroblasts and found to be more mobile within the nuclear envelope than full-length lamin C [5]. Expression of lamin C2 also resulted in aberrant localization of Sun1 in these cells. The collaborators also demonstrated that spermatogenesis was disrupted in Lmna^-/- mice, although oocyte meiosis was not obviously perturbed [6]. Although defects in meiosis-specific processes were observed in the knockout mice, it was not possible to rule out an indirect effect of lamin depletion in somatic cells on meiosis in spermatocytes, prior to the new study.An important feature of the new research [1] is that the C2^-/- mice show normal expression of all other A-type lamins. The C2^-/- males recapitulate the meiotic failure seen in Lmna^-/- mice. Nevertheless, their chromosomes frequently fail to synapse and they engage in heterologous associations or show aberrant telomere-telomere interactions; all of these defects are rare in wild-type spermatocytes. As a result of extensive apoptosis and failure of sperm maturation, the males are completely infertile. However, females are fertile, despite some evidence for pairing defects in C2^-/- oocytes.These sex-specific differences in the effects of lamin C2 loss are somewhat surprising. They could in part reflect differential implementation of meiotic checkpoints, which cull defective spermatocytes more ruthlessly than oocytes [7]. However, analysis of homologous pairing and synapsis in the C2^-/- mutant mice also revealed more severe defects in males. Both male and female mice lacking Sun1 protein are completely sterile and show synaptic failure during meiotic prophase [8]. This suggests that LINC-mediated chromosome dynamics are essential for homolog interactions during meiosis in both sexes. The milder defects caused by loss of lamin C2 in both male and female meiosis suggest that it has a less direct role in mediating chromosome movement than Sun1. This is consistent with the idea that expression of short lamin isoforms during meiosis acts primarily to increase the mobility of proteins within the nuclear envelope, relative to somatic cells. It seems likely that the dynamics of pairing, synapsis and recombination differ dramatically between spermatocytes, which are produced continually during the adult life of the male, and oocytes, which undergo meiotic prophase during fetal development. Such differences might render male meiosis more sensitive to changes in nuclear envelope organization or dynamics.The modifications made to the mouse nuclear envelope during meiosis are likely to be conserved in concept, if not in detail, in other taxa. As mentioned above, the isoforms and expression patterns of lamin proteins have diverged rapidly among the metazoa, as have the structures and functions of LINC complexes. For example, amphibians lack lamin C (and lamin C2), suggesting that its meiotic role in mammals is a recent innovation. Furthermore, the mouse Sun1 protein has a C2H2 zinc finger lacking in primate orthologs, which might suggest that it has evolved a distinct way to connect with meiotic chromosomes. It is thus not currently clear which aspects of meiotic lamina remodeling in mice can be extrapolated to other species.In Caenorhabditis elegans, meiotic chromosome dynamics are probably mediated by post-translational modification of the amino-terminal (nucleoplasmic) domain of sun-1 [9]. It is not yet known how this modification contributes to the function of the meiotic LINC complex. Direct observation has indicated that the motion of LINC complexes within the nuclear envelope becomes much less constrained as cells enter meiosis [3]. Phosphorylation of sun-1 may weaken interactions between the LINC complexes and the lamina to increase their mobility within the nuclear envelope, and/or promote interactions between LINC complexes to create high load-bearing aggregates of these proteins necessary to drive chromosome movement. It is not currently known whether the lamina itself is modified in C. elegans meiotic nuclei, but it is easy to imagine that phosphorylation could also be used to tweak protein-protein interactions within the lamina to optimize its properties during meiosis and other specialized cellular processes. It is likely that metazoans have evolved a wide range of mechanisms to modify their nuclear envelopes to meet the special demands of meiotic prophase.Homologous chromosome pairing remains one of the most mysterious aspects of meiosis. This new work in mice [1] adds an important piece of the puzzle by illuminating how the nuclear lamina can be modified to facilitate meiotic chromosome dynamics. To understand this process will clearly require looking beyond the chromosomes, and even beyond the nucleus, to the cellular networks connected by LINC complexes.     

Drug-induced migration of cytoplasmic ornithine decarboxylase into rat liver nucleus in not related to increased RNA polymerase activity

1-Methyl-3-isobutylxantine (MIX) caused rapid increases in cytoplasmic and nuclear ornithine decarboxylase (ODC) activity as well as increases in RNA polymerases I and II. MIX also significantly increased labeling of nuclear proteins with [³H]-leucine while causing only a slight rise in the labeling of the cytoplasm. Cycloheximide prevented the MIX-induced increases in cytoplasmic ODC, RNA polymerases I and II, and radioactive labeling of cytoplasmic and nuclear proteins. Cycloheximide did not prevent the MIX-induced change in nuclear ODC. These data suggest that cytoplasmic ODC migrated in to the nucleus after MIX treatment but this migration was not correlated with increased RNA polymerase activity.