Double-stranded RNA as an inhibitor of protein synthesis and as a substrate for a nuclease in extracts of Krebs II ascites cells

Components of the multifactor complex needed for internal initiation by the IRES of hepatitis C virus in Saccharomyces cerevisiae

Interaction between the 40S ribosomal subunit and the IRES of hepatitis C virus (HCV) is thought to be independent of initiation proteins, while joining of the 60S ribosomal subunit, and initiation of translation is dependent upon components of the translation machinery. An established in vivo functional assay for internal initiation mediated by the HCV IRES was used to identify proteins needed for IRES dependent translation in Saccharomyces cerevisiae strains possessing alterations of the translation machinery. Internal initiation dependent upon the HCV IRES was abrogated in strains lacking eIF5B, and reduced in strains with altered eIF3, either lacking the Hcr1p subunit, a component of eIF3 not previously known to interact with HCV RNA, or possessing an amino acid change in the Rpg1p subunit. The HCV RNA-induced conformational change in the 40S subunit might affect positioning of eIF3 and lead to different interactions between the ribosome, eIF3, and the multifactor complex. HCV IRES dependent initiation was unaffected in strains in which the concentration of the initiating tRNA was reduced. Alteration of the δ subunit of eIF2B, which leads to inefficient recycling, or substitution of aspartic acid for serine 51 of eIF2α had no effect on internal initiation. Production of human Pkr inhibited HCV IRES dependent initiation in yeast. The synthesis of Pkr in yeast is known to result in high levels of eIF2α phosphorylation, increased Gcn4p synthesis, and reduced ribosomal protein production. These alterations may explain the effect of Pkr synthesis on HCV IRES dependent initiation in yeast.

Anti-mitogenic function of interferon-induced (2'-5')oligo(adenylate) and growth-related variations in enzymes that synthesize and degrade this oligonucleotide

Addition of (2'5')ApApA to concanavalin-A-stimulated mouse spleen lymphocytes strongly inhibits the large increase in RNA and protein synthesis which takes place 24-48 h after stimulation. The inhibitory effect on protein synthesis precedes the effect on RNA synthesis and takes at least 6 h to be detected. Histone synthesis is preferentially inhibited at 48 h. No effect on protein synthesis was detected in unstimulated resting lymphocytes, or in stimulated lymphocytes during the first 24 h after concanavalin A treatment. The anti-mitogenic effect of the (2'-5')oligo(adenylate) seems to result, therefore, from inhibition of protein synthesis taking place before initiation of DNA replication. The mitogenic stimulus produced by the lectin enhances, in lymphocytes, the level of the 2'-phosphodiesterase which degrades (2'-5')oligo(adenylate). Enhancement of the 2'-phosphodiesterase was also observed after serum stimulation of confluent monkey kidney cells. Furthermore, the ratio of (2'-5')oligo(adenylate) synthetase to 2'-phosphodiesterase is ten-times lower in fast-growing kidney cells than in quiescent serum-starved cells. A model for the role of (2'-5')oligo(adenylate) synthesis and degradation in the regulation of cell proliferation by interferon and by mitogens is presented.

Evidence that vesicular stomatitis virus produces double-stranded RNA that inhibits protein synthesis in a reticulocyte lysate

Cell-free protein synthesis by reticulocyte lysates was inhibited by a polyadenylated RNA fraction extracted from HeLa cells infected with vesicular stomatitis virus (VSV) but not by polyadenylated RNA from mock-infected HeLa cells. A similar inhibitor of cell-free protein synthesis was found in a polyadenylated fraction of RNA transcribed in vitro by VSV but not in untranscribed nucleocapsids. Fractionation of the VSV transcription product showed that the translation inhibitor segregated with nucleocapsids containing newly transcribed polyadenylated or non-polyadenylated RNA, as determined by oligodeoxythymidylate-cellulose chromatography. The inhibitors present in VSV-infected HeLa cells and in VSV in vitro transcripts both appeared to be double-stranded RNA, as judged by the characteristics for inhibition of reticulocyte cell-free protein synthesis described by Hunter et al. (J. Biol. Chem. 250:409-417, 1975). The double-stranded nature of the VSV RNA inhibitor was supported by the finding that the translational inhibitory effect was inactivated by melting the inhibitor in the absence of salt and by micrococcal nuclease.

Double-stranded RNA

High molecular weight, fully double-stranded RNA (dsRNA) has been recognized as the genetic material of many plant, animal, fungal, and bacterial viruses (Diplornaviruses): virusspecific dsRNA is also found in cells infected with single-stranded RNA viruses. DsRNA has identified in a variety of apparently normal eucaryotic cells and is associated with the "killer" character of certain strains of Saccaromyces cerevisiae.

Specific RNA-cleaving activities from HeLa cells

Subcellular fractionation of HeLa cells was carried out under gentle conditions to isolate enzymes that cleave RNA precursors in a specific manner. Four separate activities--cleavage of HeLa cell heterogeneous nuclear RNA, the HeLa cell 45S rRNA precursor, RNA . DNA hybrids (RNase H), and the Escherichia coli tRNATyr precursor (RNase P)--were revealed by these studies. The specificity and limited nature of these cleavages suggest that they are due to eukaryotic RNA-processing enzymes. The virtual absence of random nucleases from these enzymes was demonstrated by their inability to cleave the 8000-base early mRNA precursor of bacteriophage T7, E. coli 30S rRNA precursor, or HeLa cytoplasmic poly(A)-containing RNA.

Poliovirus single-stranded RNA and double-stranded RNA: differential infectivity in enucleate cells

The ability of poliovirus virion RNA and double-stranded RNA (replicative form) to replicate in enucleate mouse L cells was investigated. Virion RNA replicated successfully in the absence of the cell nucleus, whereas replicative form infection did not produce any detectable progeny in enucleate cells. The results provide direct evidence of a nuclear requirement early in the infection initiated by replicative form RNA.

Unwinding protein specific for mRNA translation fractionated together with rabbit reticulocyte initiation factor 3 complex

Experiments with a rabbit reticulocyte cell-free system dependent on the addition of initiation factor 3 (eIF-3) and mRNA were carried out. In this system, using ribosomal subunits, AUG(U)(n) can direct polyphenylalanine synthesis in the absence of eIF-3 at 3 mM MgCl(2). Globin mRNA was not translated under similar conditions; its translation requires the addition of eIF-3. Moreover, the maximal rate of globin synthesis was achieved when the molar ratio of eIF-3 to ribosomes was approximately 1. This was taken to indicate that some ribosomal proteins were fractionated with eIF-3 and functioned in reconstitution of salt-washed ribosomes. In our system, almost all ribosomes were active, as evident from the fact that all were found in polysomes when analyzed at the time of linear incorporation, and the molar ratio of ribosomes to mRNA was maintained at 4:1. When AUG(U)(n) was hybridized with poly(A), it could not direct polyphenylalanine synthesis with or without eIF-3 and was a potent inhibitor of the translation of globin mRNA in the presence of eIF-3. When poly(A) containing 10% U was hybridized with AUG(U)(n) and added to the cell-free system, addition of eIF-3 promoted polyphenylalanine synthesis to about 80% of control. Moreover, eIF-3 was seen to shift significantly the melting temperature of globin and synthetic double-stranded RNA. These observations suggest that extraction of ribosomes with 0.5 M KCl may release a ribosomal protein that fractionates with eIF-3. This protein may function in unwinding or melting the secondary structure of mRNA and thus facilitate translation.

Interferon-induced inhibition of protein synthesis in L-cell extracts: an ATP-dependent step in the activation of an inhibitor by double-stranded RNA

The translation of encephalomyocarditis virion RNA in extracts from interferon-treated L-cells is inhibited by the addition of double-stranded RNA (dsRNA) at 400 ng/ml. A similar inhibition in response to dsRNA is seen in control cell extracts supplemented with small amounts of a postribosomal supernatant fraction from interferon-treated cells (interferon cell sap): Neither interferon cell sap nor dsRNA alone is inhibitory in control systems. The inhibition is much reduced if translation is carried out at low ATP concentrations.Conversely, the inhibitory capacity of the interferon cell sap is increased 100-fold if it is preincubated with dsRNA and ATP prior to its addition to the protein-synthesizing system. After this preincubation all detectable dsRNA can be removed without any diminution of the inhibitory activity of the cell sap. These results are compatible with a two-step model for the inhibition in which a pre-inhibitor is activated by dsRNA, the activated inhibitor then interacting with the protein synthesis system to inhibit translation.

Partial purification of a double-stranded RNA specific ribonuclease (RNAse D) from Krebs II ascites cells

In a search for eucaryotic enzymes which might process the heterogenous nuclear RNA (HnRNA) from animal cells into messenger RNA, a ribonuclease called RNAse D analogous to E. coli RNAse III in its ability to cleave specifically synthetic or viral double-stranded polyribonucleotides has been detected and extensively purified from the cytosol of Krebs II mouse ascites cells. The purification procedure involved cellular fractionation followed by DEAE-and CM-cellulose chromatography and resulted in an RNAas D preparation contaminated with trace amounts of single-strand specific RNAse (equivalent to less than 0.3 ng per ml) as assayed against poly (rC). Significant levels of RNAse H activity against poly (rA)-poly (dT) were still present in these preparations.

Cellular protein synthesis shutoff by mengovirus: translation of nonviral and viral mRNA's in extracts from uninfected and infected Ehrlich ascites tumor cells

The mechanism whereby picornaviruses inhibit host protein synthesis while their own synthetic processes proceed unabated has remained elusive. One of our approaches to this problem was to study the ability of cell-free extracts derived from uninfected and mengovirus-infected Ehrlich ascites tumor cells to translate viral and nonviral mRNA's under various conditions of incubation. Our results indicate that viral messengers (from mengovirus and encephalomyocarditis virus) and cellular messengers [L cell and Ehrlich ascites tumor poly(A)-containing mRNA's, rabbit globin mRNA, and chicken embryo lens crystallin mRNA] are translated equally well in both extracts. We also examined the simultaneous translation of viral and nonviral mRNA's in extracts from uninfected Ehrlich ascites tumor cells. Our results indicate that under certain conditions mengovirus RNA can suppress completely the translation of globin mRNA. The significance of these results in terms of the shutoff of host protein synthesis is discussed.

Protein synthesis in BHK-21 cells infected with semliki forest virus

[3H]leucine-labeled proteins synthesized in BHK-21 cells infected with Semliki Forest virus were fractionated by polyacrylamide gel electrophoresis (PAGE). Cellular and virus-specific proteins were identified by difference analysis of the PAGE profiles. The specific activity of intracellular [3H-A1leucine was determined. Two alterations of protein synthesis, which develop with different time courses, were discerned. (i) In infected cultures an inhibition of overall protein synthesis to about 25% of the protein synthesis in mock-infected cultures develops between about 1 and 4 h postinfection (p.i.). (ii) The relative amount of virus-specific polypeptides versus cellular polypeptides increases after infection. About 80% of the proteins synthesized at 4 h p.i. are cellular proteins. Since significant amounts of nontranslocating robosomes in polyribosomes were not detected up to 7 h p.i., the inhibition of protein synthesis is not caused by inactivation of about 75% of all polyribosomes but by a decreased protein synthetic activity of the majority of polyribosomes. Indirect evidence indicates that an inhibition of elongation and/or release of protein synthesis develops in infected cells, which is sufficient to account for the observed inhibition of protein synthesis. Inhibition of over-all protein synthesis developed when virus-specific RNA began to accumulate at the maximal rate. This relationship was observed during virus multiplication at 37, 30, and 25 C. A possible mechanism by which synthesis of virus-specific RNA in the cytoplasm could inhibit cellular protein synthesis is discussed. Indirect evidence and analysis of polyribosomal RNA show that the increased synthesis of virus-specific protein is brought about by a substitution of cellular by viral mRNA in the polyribosomes.

Cleavage of adenovirus messenger RNA and of 28S and 18S ribosomal RNA by RNase III

Escherichia coli ribonuclease III cleaves adenovirus messenger RNA and mammalian 28S and 18S ribosomal RNA. Fragmentation is not random, but in each case a specific collection of products is generated. This points to the potential use of the enzyme as a tool for specific fragmentation of RNA. Cleavage by RNase III abolishes the capability of adenovirus messenger RNA to direct cell-free synthesis of virus polypeptides.

Blocks in elongation and initiation of protein synthesis induced by interferon treatment in mouse L cells

Synthesis of polypeptide chains coded by exogenous messenger RNAs is inhibited in cell-free extracts from interferon-treated mouse L cells, due to a "deficiency" in some specific tRNA species. A detailed analysis shows that polypeptide chain elongation is blocked and incomplete chains are formed. After a few minutes, however, initiation of new polypeptide chains is also blocked. Messenger RNA still binds to ribosomes but initiator Met-tRNA(FMET) binding is inhibited. The block in initiation appears to be secondary to the block in elongation.

Distinct ribonuclease H activities in calf thymus

Three enzymes with ribonuclease H activity are present in calf thymus. They have been separated on the basis of chromatographic behaviour and molecular weight. They are further distinguished from one another by their ionic requirements and sensitivity to the -SH reagent N-ethylmaleimide. Two of these enzymes are classified as ribonuclease H, the third is obtained in a fraction which possesses ribonuclease H activity but also degrades double-stranded RNA and poly(rA). No association between any of the enzymes and cellular DNA polymerases could be demonstrated.

Translation of Rous sarcoma virus RNA in a cell-free system from ascites Krebs II cells

The template activities of the 60-70S RNA complex and of the 30-40S subunit RNA species of Rous sarcoma virus were tested in a cell-free protein-synthesizing system from mouse ascites Krebs II cells. Stimulation of protein synthesis over the endogenous background was about 2-fold with 30-40S viral RNA and about 1.3-fold with 60-70S viral RNA as template. Analysis by sodium dodecyl sulfate-gel electrophoresis showed that the predominant polypeptide synthesized in vitro in response to 30-40S RNA of Rous sarcoma virus had a molecular weight of 75,000-80,000. This polypeptide could be precipitated by antiserum against the group-specific antigens of the virus, although its molecular weight is higher than that of virion group-specific antigen proteins. Analysis of tryptic digests of the protein made in vitro indicates similarity to tryptic digests from authentic virion group-specific proteins. It is concluded that part of the RNA from Rous sarcoma virus is translated in vitro into a high-molecular-weight protein, perhaps a precursor of the virion group-specific proteins.

RNA synthesis in cells infected with herpes simplex virus. IX. Evidence for accumulation of abundant symmetric transcripts in nuclei

RNA extracted from nuclei of 8-h infected cells drove approximately 50% of herpes virus DNA into DNA-RNA hybrid. The same RNA, preannealed under conditions which allowed base pairing to take place, drove only 35% of the DNA into DNA-RNA hybrid; further annealing of the RNA did not diminish the amount of RNA sequences remaining available for subsequent hybridization with DNA. Upon denaturation of the preannealed RNA, the RNA sequences sequestered during preannealing became available again for hybridization with DNA. The base pairing that occurred during preincubation of the RNA was inter-molecular, since it was RNA concentration dependent and was not affected by limited alkaline hydrolysis. The nuclear viral transcripts that remained available for hybridization, after preannealing of the RNA, were subset of the RNA sequences that accumulated in the cytoplasm of infected cells. In addition, a small amount (derived from 5% or less of the viral DNA) of complementary transcripts was detected in the cytoplasm.

Viral infection and host defense

Double-stranded RNA, made as an intermediary substance in the replication of most, if not all, viruses, may play a much more important role in the pathogenesis and the recovery from virus infections than has hitherto been suspected. Apparently, dsRNA is used by both the challenge virus and the host cell in an attempt to gain "molecular control." Double-stranded RNA exerts a set of effects, which may be well balanced, not only at the level of the individual cell but also at the complex assemblage of these cells termed the organism (Fig. 1). In the cell, interferon synthesis is triggered, although interferon mRNA translation may not occur if dsRNA shuts off protein synthesis too quickly. In the whole organism, the disease severity will depend on how certain toxic reactions evoked by infection (such as cell necrosis and fever) are counterbalanced by an increase in the host defense mechanisms (for example, immune responsiveness and interferon production). Many aspects of the response, relating to either progress of, or recovery from, the disease, can be explained on the basis of a dsRNA. In addition to drawing attention to the biodynamic role of dsRNA, our hypothesis suggests specific experimental vectors designed to enhance our information on the molecular basis of the morbid process which occurs with viral infection. Finally, we suggest that, although the dsRNA molecule may be viewed as a rather simple unit structure, the opportunity for further diversity in the biological activity of a given dsRNA molecule always exists. Namely, each deviation from a perfectly double-helical arrangement introduces the possibility for emphasizing one biological reactivity at the expense of another. This latter structure-activity property may partially account for the extreme apparent diversity, commonly encountered, in the presentations of virologic illness. Appendix note added in proof. Subsequent to submission of this text, we have found that the potent mitogen effect of dsRNA for lymphocytes (murine and human) is also exquisitively sensitive to the fidelity in base pairing of the input polymer pair (59). For example, infrequent "loops" (one nucleotide per 20 base pairs) in an otherwise perfectly helical rI(n) (.) rC(n) molecule [for example, rI(n) (.) r(C(19,)U)(n)] strongly changes its mitogenic properties. This observation, which supports our thesis that a "fine structure" term can be developed for other reactions triggered by dsRNA's in biological systems, emphasizes that diverse biological effects may be encountered with an ostensibly uniform family of dsRNA's.

Pancreatic ribonuclease: enzymic and physiological properties of a cross-linked dimer

Monomeric ribonuclease A has very low activity toward typically double-stranded RNA's; the dimeric form of ribonuclease A obtained by cross linking the enzyme by dimethyl suberimidate has more than 78 times the activity of the monomer toward polyadenylate . polyuridylate and 440 times the activity of the monomer toward the double-stranded RNA of a virus from Penicillium chrysogenum. The half-life of the dimer in the bloodstream of the rat is 12 times that of the mononmer.

Encephalomyocarditis virus infection of mouse plasmacytoma cells. I. Inhibition of cellular protein synthesis

Mouse plasmacytoma ascites tumor cells (MOPC 460) were efficiently infected with encephalomyocarditis virus. Inhibition of host protein synthesis was evident after 2 h and complete by 4 h postinfection. The mechanism by which virus infection results in inhibition of host cell protein synthesis was studied in vitro. Cell-free protein-synthesizing systems, prepared from uninfected and infected cells, were found to be equally active with respect to their abilities to translate cellular and viral mRNAs. The plasmacytoma cell-free system was also shown to be insensitive to the addition of double-stranded viral RNA. Host cellular mRNA was isolated from uninfected and infected cells. No difference in the amount or size distribution of the mRNA was detected. However, the mRNA from infected cells was translated only 46 to 49% as actively as that from uninfected cells. mRNA isolated from cells in which initiation of protein synthesis was inhibited with pactamycin was similarly inactivated. Simultaneous addition of viral RNA and cellular mRNA to the plasmacytoma cell-free system resulted in a complete suppression of the translation of the cellular message, whereas viral RNA was translated normally.

Effect of poliovirus double-stranded RNA on viral and host-cell protein synthesis

Cell-free protein-synthesizing systems that initiate on endogenous messenger RNA have been developed from uninfected and poliovirus-infected HeLa cells. Poliovirus double-stranded RNA is an effective inhibitor of protein synthesis in these extracts, and both cell-directed and virus-specific protein synthesis are equally sensitive to the inhibitory action of double-stranded RNA. The concentrations of double-stranded RNA required for inhibition are not achieved in the infected cell at early times after infection when host-cell shut-off occurs, but rather are achieved only late in infection when virus-specific protein synthesis begins to decline. This indicates that double-stranded RNA does not act as a direct agent to inhibit host cell protein synthesis following infection by poliovirus. The possible significance of inhibition by double-stranded RNA of poliovirus-specific protein synthesis is discussed.

Formation of Sindbis virus capsid protein in mammalian cell-free extracts programmed with viral messenger RNA

Extracts from Krebs II ascites cells and rabbit reticulocytes effectively synthesize viral proteins with Sindbis viral mRNA isolated from Sindbis-infected BHK cells. The major product is identical to Sindbis capsid protein on the basis of its electrophoretic mobility in sodium dodecyl sulfate-acrylamide gels and two-dimensional tryptic-peptide fingerprints. Various amounts of several additional discrete polypeptides are formed, depending on the components of the cell-free extracts. One of these polypeptides may be a prematurely terminated part of the viral-capsid protein, while another is larger in molecular weight than capsid protein but contains the capsid tryptic peptides. Several of the proteins formed in vitro also are detected in extracts of Sindbis-infected BHK cells labeled with [(35)S]methionine. The three proteins found in Sindbis virions are postulated to originate by proteolytic cleavage from a larger molecular weight polypeptide precursor that is translated from a polycistronic mRNA presumed to contain a single site for initiation of protein synthesis. The two in vitro systems appear to translate this polycistronic viral mRNA to yield specific viral capsid although no evidence was found for post-translational proteolysis. Other mechanisms for production of the capsid protein in the cell-free extracts are considered, and some of these may function in the viral-infected cell where unusually large amounts of viral capsid proteins are frequently detected.

Fractionation of nucleic acids from Penicillium chrysogenum and associated ribonucleic acid viruses by selective exclusion and retention in agarose gels

Double-stranded nucleic acids from a strain of Penicillium chrysogenum containing RNA viruses were isolated by agarose-gel filtration, and separated into DNA and double-stranded RNA fractions by agarose-gel chromatography in 2.5m-NaCl. The DNA fraction contained less than 1% alkali-labile polynucleotides, and sedimented homogeneously at 8-10S in alkaline sucrose gradients. In CsCl gradients it tended to band in the density region of 1.66-1.72g/ml. It had a ;melting' temperature (T(m)) of 75 degrees C in 0.015m-NaCl-0.0015m-trisodium citrate, corresponding to 51.5mol% of G+C. The double-stranded RNA fraction did not contain detectable DNA. It could not band in CsCl up to a density of 1.78g/ml, and mainly consisted of a 14-15S RNA species with a T(m) of 88.5 degrees C in the above solvent, and a G+C content of 49.3 mol%.