Correlation of messenger RNA function with adenylate-rich segments in the genomes of single-stranded RNA viruses

A novel fluorescent probe with high photostability for imaging distribution of RNA in living cells and tissues

Herein, we have firstly developed a novel fluorescent probe based on 2,2′-bithiophene for imaging distribution of RNA in living cells and tissues.

RNA-responsive fluorescent carbon dots for fast and wash-free nucleolus imaging

RNA as a carrier of genetic information plays a critical role in various physiological processes. RNA-rich nucleolus is usually employed as an important biomarker for many malignant diseases. Herein, RNA-responsive fluorescent carbon dots (CDs) were synthesized by a simple microwave method. Due to the presence of cationic benzothiazolium groups in the CDs, a "turn-on" fluorescence signal was achieved between CDs and RNA. The CDs exhibit excellent RNA selectivity and a good linear relationship with a detection limit of 0.62 μg/mL. The small particle size, polarity sensitivity and RNA response behavior of CDs realized fast and wash-free nucleolus imaging effectively. Overall, these CDs provide a powerful potential tool for monitoring cell nucleus activity and elucidating RNA dynamics.

A ratiometric fluorescent composite nanomaterial for RNA detection based on graphene quantum dots and molecular probes

RNA plays a central role in controlling cellular functions. Research of the content and distribution of RNA in living cells is of great significance to both biochemistry and biomedicine. However, ratiometric fluorescent probes for the detection of RNA in the cytoplasm and nucleoli are still rarely reported. We herein present the first example of a novel ratiometric fluorescent composite nanomaterial by using graphene quantum dots (GQDs) and a fluorescent probe molecule for the sensitive and selective detection of RNA. HVC-6 was selected as the detection group. The fluorescence was excited at 365 nm and the fluorescence emission at 470 and 610 nm increased gradually with the addition of RNA. The fluorescence intensity ratio of I₆₁₀/I₄₇₀ displayed a linear response to RNA. Furthermore, the developed nanomaterial HVC-6@GQDs showed potential for utilization as a fluorescent RNA probe in living cells.

Fluorescence behavior of a unique two-photon fluorescent probe in aggregate and solution states and highly sensitive detection of RNA in water solution and living systems

In this work, we developed a unique fluorescent probe HVC-6 for highly sensitive detection of RNA in pure water systems and living systems by aggregation–disaggregation of the probe for the first time.

Sindbis virus mutants selected for rapid growth in cell culture display attenuated virulence in animals

Mutants of Sindbis virus were selected for rapid growth in baby hamster kidney (BHK) cell cultures and screened for attenuation of virulence in suckling mice. Comparisons among independently isolated virulent and attenuated strains, as well as a classical reversion analysis, showed that accelerated penetration of BHK cells was correlated with attenuation in vivo. Both phenotypic changes resulted from a reorganization of virion structure as detected by monoclonal antibodies. These results suggest that mutants selected for rapid growth in cell culture may be useful as attenuated vaccines and for studies of the molecular basis of virus pathogenesis.

Reduced synthesis of Sindbis virus negative strand RNA in cultures treated with host transcription inhibitors

Host cell involvement in Sindbis virus (SB) RNA synthesis was examined in cells which had been treated before infection with actinomycin D or alpha-amanitin (alpha-A). Overall synthesis of SB RNA was reduced significantly in CHO cells treated for 18 h before infection with alpha-A. However, SB RNA was produced at near normal levels in CHOama-1 cells, a line which contains an alpha-A-resistant RNA polymerase II. In BHK or CHO cells infected with SBamr, a mutant which replicates normally in cells pretreated with either actinomycin D or alpha-A, viral RNA synthesis was not decreased. The levels of negative strand RNA and of replicative forms I, II, and III in SB-infected cells were progressively reduced with increasing times of pretreatment with host transcription inhibitors, indicating fewer functional replicative intermediates in treated cells. Replicative events after replicative intermediate formation also were inhibited but only to the extent predicted by the reduction in replicative intermediates. Similarly, events preceding negative strand synthesis, adsorption, penetration, uncoating, and translation of nonstructural proteins, apparently were not impeded in treated cells. Therefore, our results are consistent with the involvement of a host component after translation of the nonstructural proteins but before or during the synthesis of SB negative strand RNA.

Bluegill virus is a ribovirus of positive-strand polarity

RNA was extracted from purified Bluegill virus (BGV) and fractionated onto a poly (U)-Sepharose-4 B column. More than 70 per cent of this RNA became bound and could be subsequently eluted from the column. By polynucleotide phosphorylase digestion, the poly (A) sequences were located at the 3'-terminus of the RNA. This RNA and purified BGV RNA were infectious as shown by plaque assay titration of the virus produced. Furthermore, we were unable to detect RNA polymerase activity in preparations of BGV. These results indicate that the genome in the BGV particle is a positive-strand RNA.

Evidence that the genome of hepatitis A virus consists of single-stranded RNA

Nucleic acid was extracted from purified hepatitis A virus, radiolabeled with 125I, and shown to consist of single-stranded RNA which sediments at 35S and contains sequences of polyadenylic acid. These findings are consistent with hepatitis A virus being a member of the genus Enterovirus within the family Picornaviridae.

Induction of N-acetylglucosamine-catabolic pathway in spheroplasts of Candida albicans

Synthesis of N-acetylglucosamine-catabolic enzymes, namely permease (high-affinity uptake system), kinase and deaminase was studied in the spheroplasts of the yeast Candida albicans. The presence of N-acetylglucosamine as inducer is essential for the induced synthesis of these enzymes in the spheroplasts, which were active for at least 8--9 h. However, some of the newly synthesized kinase and deaminase leaked out from the spheroplasts into the medium during induction. Experiments with inhibitors of RNA and protein synthesis indicate that the appearance of new enzyme activities is dependent on concomitant new protein synthesis and the inducer operates at a transcriptional level. However, inhibitors of DNA synthesis, e.g. mitomycin-C and hydroxyurea, had no effect on the synthesis of these enzymes.

Strandedness of Pichinde virus RNA

The Pichinde virus RNA did not possess the following characteristics of eucaryotic mRNA: polyadenylic acid sequence, capped methylated structure, and ability to direct protein synthesis in vitro. Polysomal RNA extracted from cells infected with Pichinde virus reannealed with 32P-labeled virus RNA, protecting about 60% of the latter against RNase degestion. The polyadenylic acid-containing polysomal RNA also reannealed to the 32P-labeled virus RNA to approximately the same extent. These indicate that the major part of the genomic RNA of Pichinde virus is negative stranded.

Presence of infectious polyadenylated RNA in coronavirus avian bronchitis virus

Avian infectious bronchitis virus (IBV) was radiolabeled for its nucleic acid component by growth in deembryonated chicken eggs. Purified virions of IBV have a buoyant density in linear sucrose gradients of 1.17-1.18 g/cm3 and contain approximately 4% RNA by weight. The genomic ribonucleic acid of IBV shows the following characteristic: (1) It consists of one size class of single-stranded RNA having a molecular weight of 5.5-5.7 x 108 and a sedimentation coefficient of about 48 S; (2) no evidence for subunit structure is apparent since the RNA resolves as a single species with the same electrophoretic mobility in polyacrylamide gels before and after heat denaturation; (3) at least 20–30% of the RNA molecules extracted from purified virions contain sequences of polyadenylic acid of approximately 4 S size; (4) RNA obtained from detergent-disrupted virus particles by phenol-chloroform extraction is infectious for cultures of chick embryo fibroblasts, giving rise to progeny virus which is lethal for embryonated eggs. These findings, together with the observation that IBV virions do not exhibit detectable transcriptase activity, support the conclusion that the genome of this coronavirus acts directly as a messenger RNA in eukaryotic cells.

Effect of cordycepin on the replication of western equine encephalitis virus

Cordycepin (3'-deoxyadenosine) inhibited viral RNA synthesis in the replication of western equine encephalitis virus, thereby causing a reduction of virus production. The rate of inhibition of viral RNA synthesis was dependent on drug concentration and the period of treatment with the drug. These results suggest that the virus RNA synthesizing system is sensitive to the drug.

Size and location of poly (A) in encephalomyocarditis virus RNA

Encephalomyocarditis (EMC) virus RNA contains a covalently bound sequence of polyriboadenylic acid (poly(A). This was determined by two-dimensional gel electrophoresis of complete T1 and pancreatic RNase digests of formamidesucrose gradient-purified RNA and subsequent analysis of the product by alkaline hydrolysis. The size of the EMC virus genomic poly(A) sequence was estimated by formamide-polyacrylamide gel electrophoresis of the RNase-resistant product, or by [3H-]poly(U) hybridization to freshly purified virion RNA, to be, on average, 40 nucleotides in length. The evidence obtained from [3H-]isoniazid labelling and other experiments would indicate that the poly(A) sequence is located at the 3'-terminus of EMC virus RNA.

Polyadenylate sequences of human rhinovirus and poliovirus RNA and cordycepin sensitivity of virus replication

The polyadenylate [poly(A)] content of the genome RNA of human rhinovirus type 14 (HRV-14) is nearly twice as large as that of the genome RNA of poliovirus type 2. The poly(A) content of viral RNA was determined to be the RNase-resistant fraction of 32P-labeled viral RNA extracted from purified virions. Polyacrylamide gel electrophoresis indicated that the poly(A) sequences of HRV-14 are more heterogenous and on an average larger than those of poliovirus RNA. On the basis of susceptibility to micrococcal polynucleotide phosphorylase the rhinovirus genome terminates in poly(A). Replication of both viruses is almost totally inhibited by cordycepin at 50 mug/ml. At lower concentrations, rhinovirus replication is more sensitive to cordycepin than poliovirus replication. Addition of cordycepin (75 mug/ml) to infected culture prior to or during viral RNA replication results in more or less complete inhibition of virus-specific RNA synthesis. The results do not indicate that cordycepin sensitivity of either virus is due to preferential inhibition of viral poly(A) synthesis by this antibiotic.

Polyadenylic acid in the genomic RNA of mengovirus

The polyadenylic acid contained in 35S mengovirus RNA produced in infected BHK-21 cells contained approximately 94% AMP and was estimated to contain an average of 50 to 55 nucleotides. The polyadenylic acid is placed at the 3'-end of the genomic RNA based on the presence of significant levels of [3H]adenosine in complete alkali or RNase T2 digests of polyadenylic acid from [3H]adenosine-labeled 35S viral RNA.

Association of the polyadenylate segment of messenger RNA with other polynucleotide sequences in mouse sarcoma 180 polyribosomes

Limited digestion of polysomal RNA with pancreatic ribonuclease releases a structure consisting of poly(A) associated with other polyribonucleotide sequences. This complex can be purified by oligo(dT)-cellulose chromatography. Heating for formamide treatment causes the dissociation of fragments free of poly(A) from the poly(A)-containing components. The two types of fragments tend to reassociate under annealing conditions, and this association is prevented by poly(U). Control experiments indicate that this structure is not an artifact generated during the manipulations. The same structure can be obtained by limited RNase digestion of polyribosomes, followed by deproteinization. The results suggest that the mRNA in polyribosomes may have a defined configuration caused by the interaction of the poly(A) sequence with another segment of the RNA.

Messenger RNA metabolism of animal cells. Possible involvement of untranslated sequences and mRNA-associated proteins

The past several years have seen a virtual revolution in the study of eukaryotic mRNA. Among the notable recent achievements are the positive identification of mRNA precursors in HnRNA, the enumeration of the DNA sequences from which mRNA is transcribed, and the finding that mRNA in cultured cells is much more stable than was previously believed. One of most far-reaching discoveries has been the finding that mRNA in eukaryotes contains poly A. This discovery, aside from providing a powerful tool for mRNA isolation, has generated a large body of research into the properties and metabolism of poly A itself. In addition, the finding of a poly A-associated protein has given a renewed stimulus to the study of proteins associated with mRNA. This review is devoted to a discussion of these and related achievements, and some of their implications

Polyriboadenylate sequences at the 3'-termini of ribonucleic acid obtained from mammalian leukemia and sarcoma viruses

The location of poly(A) sequences in the RNA of mammalian RNA-tumor viruses was determined by enzymatic analyses. The 56-64S viral genomic RNAs, the 20-40S viral subunit RNAs, and the 4-5S poly(A) sequences excised from these viral RNAs were subjected to either hydrolysis with a 3'-OH specific exoribonuclease from Ehrlich ascites tumor cells or phosphorolysis from the 3'-termini with polynucleotide phosphorylase from Micrococcus luteus. Purified adenosine-labeled poly(A) fragments, excised from genomic viral RNAs by RNase A and T(1) digestion, were hydrolyzed with the 3'-OH specific exoribonuclease for various periods of time. Poly(U) filter binding studies of the residual poly(A) indicated that 97% of the poly(A) fragments were hydrolyzed. Adenosine-labeled genomic and subunit viral RNAs and excised poly(A) fragments were phosphorolyzed from their 3'-termini for various periods of time with polynucleotide phosphorylase. The degree of phosphorolysis was monitored by poly(U) filter binding studies, and CCl(3)COOH insolubility and solubility determinations. There was an initial preferential rate of phosphorolysis of the poly(A) sequences of genomic and subunit viral RNAs as compared to the total adenosine-labeled viral RNAs. The data from these two different enzymatic mechanisms of action indicated conclusively that the poly(A) sequences were located at the 3'-termini of genomic and subunit viral RNAs.

Translational properties of rabbit globin mRNA after specific removal of poly(A) with ribonuclease H

Highly purified RNase H (RNA.DNA hybrid ribonucleotidohydrolase, EC 3.1.4.34) from calf thymus was used to specifically remove the poly(A) sequences of purified rabbit globin mRNA after its hybridization with poly(dT). The deadenylylated globin mRNA was repurified by a one-step procedure including a nitrocellulose column. The poly(A) size and the content of unmodified mRNA were determined by hybridization with [(3)H]-poly(U), and it could be shown that the RNase H digestion method effectively removes this terminal poly(A) sequence. No difference in activity was found between mRNAs with and without poly(A) to initiate, elongate, terminate, and release newly synthesized globin chains in exogenous-mRNA-dependent, cell-free, protein-synthesizing systems from wheat embryo, ascites Krebs II cells, and rat liver. Furthermore, poly(A)-free globin mRNA competed with the same efficiency as authentic globin mRNA against chick ovalbumin mRNA when translated under total mRNA saturation conditions. It is apparent that the 3'-terminal poly(A) sequence is not necessary to maintain the translationally active secondary and tertiary configuration of the globin mRNA molecule. Preincubation of intact and deadenylylated globin mRNA in the Krebs II ascites translational system indicates that the presence of the poly(A) sequence may stabilize the translationally active mRNA molecule.

Effects of cytosine arabinoside on differential gene expression in embryonic neural retina. I. Accumulation of glutamine synthetase with suppression of macromolecular synthesis

The analogue of cytidine, cytosine arabinoside (Ara-C), elicited a significant increase in the level of glutamine synthetase (GS) in embryonic chick neural retina in the absence of the steroid inducer of the enzyme. The increase was due to de novo synthesis of GS and was mediated by RNA which accumulated in the presence of the effective concentration of Ara-C. Accumulation of GS did not result from the inhibition of DNA synthesis for which Ara-C is best known. This new effect of Ara-C involves differential suppression of macromolecular synthesis in this system: the concentration of Ara-C which caused maximum GS accumulation suppressed overall protein and RNA syntheses 65-75% without inhibiting the transcription and translation of templates essential for GS synthesis. Withdrawal of Ara-C resulted in restoration of RNA synthesis and cessation of GS accumulation, even though preformed templates for the enzyme were present; however, if all RNA synthesis was arrested with actinomycin D at the time of Ara-C withdrawal, GS continued to accumulate. The results are consistent with the hypothesis that Ara-C differentially affects the activity of structural and regulatory genes involved in the regulation of GS levels in the retina: Ara-C allows transcription of the enzyme-specific templates, but reversibly inhibits the expression of regulatory genes which limit the accumulation of GS.

Poliovirus infection and poly(A) sequences of cytoplasmic cellular RNA

The influence of polio infection on Poly(A) sequences of cellular cytoplasmic RNA was investigated. In the presence of guanidine, cellular protein synthesis was still shut off after poliovirus infection, although there was no viral RNA synthesis. The Poly(A) of these cells was unchanged with respect to quantity, size, and linkage to cellular cytoplasmic RNA. This finding strongly suggests that the shut off of cellular protein synthesis is not caused by a change of the Poly(A) sequences of cellular mRNA.

Characterization of a protein species isolated from HeLa cell cytoplasm by affinity chromatography on polyadenylate-sepharose

Chromatography of different soluble extracts from HeLa cells on poly(A)-Sepharose columns has allowed the isolation of a protein fraction eluted by 0.2 M NaCl and localized predominantly in the cytoplasmic supernatant and in the 0.5 M KCl ribosomal wash. This fraction is present in large amounts (around 3% of total cytosolic proteins) and appears to contain a major protein species that is acidic on electrofocusing (pI around 4.5) and phosphorylated. It runs on glycerol gradients and Sephadex G-200 chromatography close to the aldolase marker (158,000 daltons) and dissociates into apparently identical subunits of 38,000 +/- 2,000 daltons on sodium dodecyl sulfate-acrylamide gels, suggesting a tetrameric structure.

Polyadenylylation and transcription following fertilization

Polyadenylylated RNA from sea urchin embryos concomitantly labeled with [(3)H]adenosine and [(14)C]uridine between fertilization and the four-cell stage was used to determine whether the RNA primers prerequisite to the massive polyadenylylation known to occur after fertilization are synthesized during oogenesis or subsequent to fertilization. Characterization of this RNA and unlabeled RNA via retention on nitrocellulose membranes and poly(U)-impregnated filters, molecular hybridization with [(3)H]poly(U), RNase resistance, oligo(dT)-cellulose chromatography, and size-distribution studies indicates that the poly(A) tracts synthesized after fertilization are predominantly appended to preexisting cytoplasmic primers of oogenic origin. Hence, if polyadenylylation is involved in the selective editing of presumptive genetic messages, this process is not confined to the nucleus unless a given codogenic transcript can undergo more than one cycle of adenylylation.

Preliminary observations pertaining to polyadenylation of rhinovirus RNA

Human rhinovirus type 14 contained polyadenylated RNA. Virus growth in HeLa cells was inhibited by cordycepin or polyuridilic acid and stimulated by polyadenylic acid. Polyadenylic acid also reversed cordycepin inhibition of virus-induced cytopathology of infected HeLa cells.

Identification of discrete polyadenylate-containing RNA components transcribed from HeLa cell mitochondrial DNA

Polyacrylamide gel electrophoresis and sedimentation analysis under denaturing conditions of poly(A)-containing RNA from the polysome region of the sedimentation pattern of a HeLa-cell mitochondrial lysate has revealed the occurrence of a discrete RNA component, which sediments in the native state with a sedimentation constant of about 7 S. From the sedimentation behavior under native and denaturing conditions and the poly(A) content, a molecular weight of about 9 x 10(4) has been estimated for this component. RNA.DNA hybridization experiments have indicated that this component is coded for by the light strand of mitochondrial DNA. Evidence for the occurrence of a poly(A)-containing RNA component sedimenting at about 9 S and coded for by the heavy strand has also been obtained.

Phosphorylated proteins of Sindbis virus

The capsid and two membrane proteins of Sindbis virus, grown in chicken cells, contain 0.03 to 0.1 mol of phosphate per mol of protein.

Inhibition of murine leukemia virus replication by poly(vinyluracil) and poly(vinyladenine)

Poly(1-vinyluracil) and poly(9-vinyladenine), as well as the corresponding polynucleotides poly(uridylate) and poly(adenylate), inhibit acute murine leukemia virus infection in mouse-embryo cells, but they do not significantly inhibit the replication of Sindbis and vesicular stomatitis viruses. The polymers were most effective as inhibitors when added during an early stage of virus replication. Effects of vinyl polymers on the RNA-dependent DNA polymerase from the virions of murine leukemia virus were also observed.