Absence of Polyadenylic Acid from Reovirus Messenger Ribonucleic Acid

Dynamic gene expression of southern rice black-streaked dwarf virus during its infection in rice plants and vector insects

In this century, a disease caused by southern rice black-streaked dwarf virus (SRBSDV) has resulted in significant loss in rice production in Asia. Aside from infecting rice plants, SRBSDV is transmitted by white-backed planthopper (WBPH) in a persistent propagative manner. Recent studies showed that SRBSDV can dynamically modulate the host cells throughout the infection progress. However, the expression dynamics of the SRBSDV genes during infection remain unclear. Here we established an absolute real-time quantitative PCR method to assess the dynamic of the SRBSDV genes expression in rice plants and planthoppers. Apart from displaying the expression levels of viral genes, we discovered that the expression level of viral genes in insects significantly surpasses that in plant cells. In addition, we identified two nonstructural proteins with unknown functions that exhibit the highest expression levels in plant and insect cells, respectively, which provide possible targets for restraining the disease outbreaks.

Characterization of replication and variations in genome segments of a bat reovirus, BatMRV/B19-02, by RNA-seq in infected Vero-E6 cells

Mammalian orthoreoviruses (MEVs) that can cause enteric, respiratory, and encephalitic infections have been identified in a wide variety of mammalian species. Here, we report a novel MRV type 1 strain detected in Miniopterus schreibersii that may have resulted from reassortment events. Using next-generation RNA sequencing (RNA-seq), we found that the ratios of the RNA levels of the 10 reovirus segments in infected cells were constant during the late stages of infection. We also discovered that the relative abundance of each segment differed. Notably, the relative abundance of M2 (encoding the µ1 protein) and S4 (encoding the σ3 protein) RNAs was higher than that of the others throughout the infection. Additionally, massive junctions were identified. These results support the hypothesis that defective genome segments are generated and that cross-family recombination occurs. These data may further the study of gene function, viral replication, and virus evolution.

Reovirus Nonstructural Protein σNS Acts as an RNA Stability Factor Promoting Viral Genome Replication

Viral nonstructural proteins, which are not packaged into virions, are essential for the replication of most viruses. Reovirus, a nonenveloped, double-stranded RNA (dsRNA) virus, encodes three nonstructural proteins that are required for viral replication and dissemination in the host. The reovirus nonstructural protein σNS is a single-stranded RNA (ssRNA)-binding protein that must be expressed in infected cells for production of viral progeny. However, the activities of σNS during individual steps of the reovirus replication cycle are poorly understood. We explored the function of σNS by disrupting its expression during infection using cells expressing a small interfering RNA (siRNA) targeting the σNS-encoding S3 gene and found that σNS is required for viral genome replication. Using complementary biochemical assays, we determined that σNS forms complexes with viral and nonviral RNAs. We also discovered, using in vitro and cell-based RNA degradation experiments, that σNS increases the RNA half-life. Cryo-electron microscopy revealed that σNS and ssRNAs organize into long, filamentous structures. Collectively, our findings indicate that σNS functions as an RNA-binding protein that increases the viral RNA half-life. These results suggest that σNS forms RNA-protein complexes in preparation for genome replication.IMPORTANCE Following infection, viruses synthesize nonstructural proteins that mediate viral replication and promote dissemination. Viruses from the family Reoviridae encode nonstructural proteins that are required for the formation of progeny viruses. Although nonstructural proteins of different viruses in the family Reoviridae diverge in primary sequence, they are functionally homologous and appear to facilitate conserved mechanisms of dsRNA virus replication. Using in vitro and cell culture approaches, we found that the mammalian reovirus nonstructural protein σNS binds and stabilizes viral RNA and is required for genome synthesis. This work contributes new knowledge about basic mechanisms of dsRNA virus replication and provides a foundation for future studies to determine how viruses in the family Reoviridae assort and replicate their genomes.

De novo assembly of Sockeye salmon kidney transcriptomes reveal a limited early response to piscine reovirus with or without infectious hematopoietic necrosis virus superinfection

Background

Piscine reovirus (PRV) has been associated with the serious disease known as Heart and Skeletal Muscle Inflammation (HSMI) in cultured Atlantic salmon Salmo salar in Norway. PRV is also prevalent in wild and farmed salmon without overt disease manifestations, suggesting multifactorial triggers or PRV variant-specific factors are required to initiate disease. In this study, we explore the head kidney transcriptome of Sockeye salmon Oncorhynchus nerka during early PRV infection to identify host responses in the absence of disease in hopes of elucidating mechanisms by which PRV may directly alter host functions and contribute to the development of a disease state. We further investigate the role of PRV as a coinfecting agent following superinfection with infectious hematopoietic necrosis virus (IHNV) – a highly pathogenic rhabdovirus endemic to the west coast of North America.

Results

Challenge of Sockeye salmon with PRV resulted in high quantities of viral transcripts to become present in the blood and kidney of infected fish without manifestations of disease. De novo transcriptome assembly of over 2.3 billion paired RNA-seq reads from the head kidneys of 36 fish identified more than 320,000 putative unigenes, of which less than 20 were suggested to be differentially expressed in response to PRV at either 2 or 3 weeks post challenge by DESeq2 and edgeR analysis. Of these, only one, Ependymin, was confirmed to be differentially expressed by qPCR in an expanded sample set. In contrast, IHNV induced substantial transcriptional changes (differential expression of > 20,000 unigenes) which included transcripts involved in antiviral and inflammatory response pathways. Prior infection with PRV had no significant effect on host responses to superinfecting IHNV, nor did host responses initiated by IHNV exposure influence increasing PRV loads.

Conclusions

PRV does not substantially alter the head kidney transcriptome of Sockeye salmon during early (2 to 3 week) infection and dissemination in a period of significant increasing viral load, nor does the presence of PRV change the host transcriptional response to an IHNV superinfection. Further, concurrent infections of PRV and IHNV do not appear to significantly influence the infectivity or severity of IHNV associated disease, or conversely, PRV load.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3196-y) contains supplementary material, which is available to authorized users.

Mechanism of interferon action. Expression of reovirus S3 gene in transfected COS cells and subsequent inhibition at the level of protein synthesis by type I but not by type II interferon

The effect of interferon on the expression of the reovirus serotype 1 Lang strain S3 gene was examined in simian COS cells transfected with the expression vector pSVS3 containing the S3 gene under the control of the SV40 late promoter. When COS cells were treated with type I interferon-alpha 24 hr after transfection, the synthesis of the reovirus S3-encoded sigma NS polypeptide was inhibited about 10-fold as compared to that in untreated control cells. By contrast, under the same conditions, neither the plasmid DNA copy number nor the S3 gene mRNA levels were significantly affected by interferon treatment. Type II interferon-gamma, unlike the type I interferons-alpha, did not affect the rate of synthesis of polypeptide sigma NS in pSVS3-transfected cells.

Biosynthesis of reovirus-specified polypeptides. Efficiency of expression of cDNAs of the reovirus S1 and S4 genes in transfected animal cells differs at the level of translation

Full-length cDNAs of the reovirus serotype 1 Lang strain S1 and S4 genes were cloned in Escherichia coli using bacteriophage M13 and expressed in monkey COS cells under the control of the SV40 late promoter using the eukaryotic expression vector pJC119. The s1-encoded sigma 1 and s4-encoded sigma 3 gene products were expressed in transfected COS cells and were indistinguishable from the authentic sigma 1 and sigma 3 polypeptides synthesized in reovirion-infected COS cells. The relative translational efficiencies of the s1 and s4 mRNAs in transfected COS cells were similar to the efficiencies observed in virion-infected cells; the s4 mRNA was translated approximately five times more efficiently than the s1 mRNA. Our results suggest that the differential translation of the reovirus s1 and s4 mRNAs in vivo may be attributed to intrinsic structural properties of the individual mRNAs and is independent of competition with other viral mRNAs.

Inhibition of translation in L-cell lysates by free polyadenylic acid: differences in sensitivity among different mRNAs and possible involvement of an initiation factor

Free polyadenylic acid specifically inhibits in vitro translation of naturally polyadenylated mRNAs in L-cell lysates. The polynucleotide affects the initiation of protein synthesis but has no apparent effect on elongation of polypeptide chains. Reovirus mRNA, naturally devoid of a poly(A) tail, is much less sensitive to this inhibition than are naturally polyadenylated mRNAs. Reovirus mRNA that was polyadenylated in vitro is not more sensitive than normal reovirus mRNA. The degree of inhibition of translation varies for the different reovirus mRNA species. The addition of proteins contained in a high salt wash of ribosomes can mitigate the inhibition of translation of naturally polyadenylated mRNAs by free polyadenylic acid. Altogether these results suggest that the inhibition by polyadenylic acid may be mediated by its interaction with a cellular (initiation) factor. The various sensitivities exhibited by different mRNAs may indicate differences in requirement for this factor.

Genome structure and expression of a defective interfering mutant of the killer virus of yeast

A large internal deletion in M1 double-stranded (ds) RNA from the killer virus of Saccharomyces cerevisiae generates a suppressive (S3) dsRNA molecule. Strains which harbor S3 dsRNA are defective in toxin production and immunity to the toxin. The biochemical defect in expression has been investigated and is apparently due to truncation of the protoxin polypeptide translation reading frame on S3 dsRNA. Transcription in vivo, and in isolated virions in vitro, results in the synthesis of a full-length positive polarity messenger RNA, denoted s. The s transcript contains no long poly(A) tracts as determined by its lack of affinity for oligo(dT)-cellulose, and as inferred by sequence analysis of approximately 87% of the S3 dsRNA genome. These data support a model for template coding of polyadenylate in transcripts derived from the wild-type M1 dsRNA. The orientation of the sequences conserved on S3 dsRNA with respect to M1 dsRNA has been determined. Some of the conserved sequences are likely to be required for the maintenance and replication of these viral dsRNA genomes in S. cerevisiae.

Stability of non-polyadenylated viral mRNAs injected into frog oocytes

The naturally non-polyadenylated mRNAs of reovirus were shown to have a half-life in excess of 3 days when injected into Xenopus laevis oocytes. Hybridization analysis and gel electrophoresis showed that all 10 mRNA species had a similar high stability, despite being translated at widely differing rates. We have confirmed previous findings indicating a role for the 5'-terminal cap structure in determining reovirus mRNA stability [Furuichi et al. (1977) Nature (Lond.) 266, 235-239]. The significance of these results in relation to a general role for poly(A) in messenger RNA function is discussed.

Characterization of RNA polymerase products of Nebraska calf diarrhea virus and SA11 rotavirus

The endogenous RNA polymerase of the calf rotavirus was shown to synthesize single-stranded RNA transcripts of one polarity which were identical in size to the denatured parental double-stranded RNA segments. The transcripts were notable in their absence of polyadenylate sequences. The polymerase activity associated with the cores of calf rotavirus was minimally altered by the reaction, since calf rotavirus cores could be reused after purification, whereas the RNA polymerase products appeared to be released from the virion.

On procaryotic gene expression in eucaryotic systems

Numerous types of interaction between pro- and eucaryotes exist in nature, from the endosymbiosis of some bacteria with unicellular organisms and insects to the complex systems of bacterial flora associated with the skin and intestines of animals and man, and nitrogen-fixation and crown-gall tumor induction in plants. Until recently, such interactions were not thought to include genetic transfer, but an increasing body of evidence points to the probability of similar naturally-occurring exchanges with wide-ranging implications for evolution and genetic manipulation. Experiments to elucidate the possible effects of procaryotic genes in eucaryotic systems have included in vitro and in vivo studies with both plant and animal systems, for instance the translation of bacterial messenger RNAs in the wheat germ and rabbit reticulocyte systems and the introduction of bacterial genes into plant protoplasts, animal cells and whole organisms. In the present paper we have tried to summarize the results of experiments involving the uptake, replication, transcription, translation and integration of procaryotic genes in various eucaryotic systems and to discuss the implications of such findings for basic research as well as for possible biomedical applications. Awareness of the possibility of procaryotic-eucaryotic genetic interactions may help to elucidate unresolved questions in pathology, such as possible involvement of the intestinal flora in carcinogenesis, as well as to provide valuable probes of eucaryotic control mechanisms and new approaches in agricultural genetic engineering.

Virus-Specific RNA Synthesis in Cells Infected by Infectious Pancreatic Necrosis Virus

Pulse-labeling experiments with [ 3 H]uridine revealed that the rate of infections pancreatic necrosis virus-specific RNA synthesis was maximal at 8 to 10 h after infection and was completely diminished by 12 to 14 h. Three forms of RNA intermediates were detected: (i) a putative transcription intermediate (TRI) which comigrated in acrylamide gels with virion double-stranded RNA (dsRNA) after RNase treatment; (ii) a 24S genome length mRNA which could be resolved into two bands by polyacrylamide gel electrophoresis; and (iii) a 14S dsRNA component indistinguishable from virion RNA by gradient centrifugation and gel electrophoresis. The TRI (i) was LiCl precipitable; (ii) sedimented slightly faster and broader (14 to 16S) than the 14S virion dsRNA; (iii) had a lower electrophoretic mobility in acrylamide gels than dsRNA, barely entering acrylamide gels as a heterogenous component; (iv) yielded genome-sized pieces of dsRNA after RNase digestion; and (v) was the most abundant RNA form early in the infectious cycle. The 24S single-stranded RNA was thought to be the viral mRNA since it: (i) became labeled during short pulses; (ii) was found in the polysomal fraction of infected cells; and (iii) hybridized to denatured viral RNA, forming two segments of RNase-resistant RNA that comigrated with virion dsRNA in gels. The 24S mRNA component was formed before the synthesis of dsRNA, and radioactivity could be chased from 24S single-stranded RNA to dsRNA, indicating that 24S RNA may serve as template for the synthesis of complementary strands to form dsRNA. Similar to reovirus, infectious pancreatic necrosis viral 24S mRNA contained no polyadenylic acid tracts.

The effect of cordycepin on the multiplication of Semliki Forest virus and on polyadenylation of viral RNA

Cordycepin (3'-deoxyadenosine), at a concentration of 20 microgram/ml, has a marked effect on Semliki Forest virus multiplication. The appearance of plaque forming units is delayed by about 2 hours and the yield greatly reduced. The incorporation of [3H] uridine into intracellular viral RNAs reaches less than 50 per cent of controls. However, no specific effect on poly (A) synthesis could be detected. The binding efficiency of viral RNAs on nitrocellulose membranes and poly (U) sepharose is not affected by cordycepin. The average poly (A) length of total intracellular viral RNA was calculated on the basis of the ratio of the radioactivity of adenosine-monophosphate: adenosine and found to be about 35 nucleotides in treated and untreated cells.

Synthesis of polyadenylic acid-containing ribonucleic acid during the germination of Neurospora crassa conidia

Ribonucleic acid (RNA) synthesized during the first 1 h of conidial germination (15 to 20, 25 to 30, and 55 to 60 min) has been characterized by sucrose-sodium dodecyl sulfate gradient centrifugation, binding to polyuridylic acid filters, and oligo(dT)-cellulose chromatography. At all labeling periods examined, polyadenylic acid-containing RNA is synthesized, processed, and incorporated into polysomes. Approximately 40% of the labeled RNA sedimenting between 5 and 17S binds to polyuridylic acid filters. RNA which binds to oligo(dT)-cellulose displays a heterogeneous distribution in sucrose-sodium dodecyl sulfate gradients with a major, broad peak at 10-16S. In addition, some polyadenylic acid-containing RNA sediments beyond the 25S marker. Approximately 3% of the [3H]adenosine in pulse-labeled polysomal RNA is in polyadenylic acid segments resistant to pancreatic and T1 ribonucleases.

Ribosome binding to reovirus mRNA in protein synthesis requires 5' terminal 7-methylguanosine

Purified reovirus synthesizes in vitro a mixture of mRNA molecules that contain 5' terminal structures of the type ppG..., GpppG..., and m7GpppGm, the relative amount of each depending upon the presence of S-adenosylmethionine (SAM) or S-adenosylhomocysteine (SAH) in the transcription incubation mixture. Reovirus mRNAs containing 5' termini of the type ppG... and GpppG... can be specifically modified by wheat germ extracts in the presence of SAM to yield the structure m7GpppG...(Muthukrishnan et al., 1975). The mRNA methylase activity is ribosome-independent and is recovered almost entirely in the high speed supernatant fraction of wheat germ extracts. Its activity is inhibited by aurintricarboxylic acid. Ribosome binding experiments with reovirus mRNA and wheat germ extract indicate that only those mRNA molecules containing 5' terminal m7G are capable of participating in the initiation of protein synthesis and subsequent polysome formation. mRNA with unmethylated 5' termini do not form a complex with 40S ribosomal subunits. Discrimination between unmethylated and methylated reovirus mRNA, active in protein synthesis, apparently occurs at or before the formation of 40S-mRNA complexes. T1 or pancreatic RNAase digestion of methylated mRNA bound to 80S ribosomes yields 5' terminal fragments of apparent chain lengths about 32 and 36 nucleotides, respectively. A portion of the T1 RNAase-resistant fragments rebinds to ribosomes to form a nuclease-resistant complex. In contrast, the shorter 5' terminal oligonucleotide m7GpppGmpCpUp(Np)3Gp derived by RNAase T1 digestion of purified reovirus mRNA does not bind to ribosomes. The results suggest that 5' terminal m7G may function as the primary recognition signal for ribosome binding and that wheat germ ribosomes bind very close to the 5' termini of some of the species of methylated reovirus mRNAs.

Synthesis and translation site of light-induced mRNAs in etiolated Euglena gracilis

Poly(a)-mRNA synthesis has been studied in etiolated Euglena gracilis exposed to 1 or 2 h of illumination. 1. Labeling kinetics of mRNAs containing poly(A) sequences, during illumination or after return to darkness, reach a plateau in 10 or 20 min according to nutritional conditions. When the cultures are returned to darkness, the mRNA synthesis decreases rapidly. Thus, the synthesis of these mRNAs (light-induced mRNAs) is dependent on light and their half-life can be evaluated. 2. Cycloheximide induces accumulation of label in poly(A)-containing mRNA; such an accumulation is not observed after addition of lincomycin. Labeling during illumination of mRNA in a chloroplast mutant is similar to that in the wild type strain. These data suggest that the poly(A)-mRNAs synthesized in the two first hours of illumination are translated on cytoplasmic polyribosomes.

Synthesis of all the gene products of the reovirus genome in vivo and in vitro

Sixteen virus-specific polypeptides have been resolved in reovirus-infected mouse L cells by using SDS-polyacrylamide slab gel electrophoresis and autoradiography. Of these, ten have been designated as primary products of the genome by the following criteria: they are present in lysates of infected cells labeled for a short time; they co-migrate on SDS-polyacrylamide slab gels with polypeptides synthesized in cell-free-extracts of wheat germ in response to purified viral mRNA; and their molecular weights correspond to the values expected if all ten reovirus mRNA species are monocistronic. Reovirus mRNA species lack 3' poly(A) but are translated into proteins of the expected size. The pattern of synthesis of the primary gene products observed in vitro mimicks that observed in reovirus-infected cells suggesting that the structure of the mRNA may profoundly influence its translation. The results further indicate that there is little, if any, exclusively regulatory information in the reovirus genome since both in vivo and in vitro, transcripts of the ten genome segments direct the synthesis of ten polypeptides that presumably correspond to the primary gene products. The expression of the reovirus genome thus appears to be complete.

Poly(A) polymerase activity in reovirus

An enzymatic activity which synthesized oligo(A) in vitro was found in highly purified reovirus. The poly(A) polymerase activity was dependent on Mn(2+) and utilized only ATP, whereas the virion-associated RNA polymerase required all four ribonucleoside triphosphates and Mg(2+). Oligo(A) synthesis was demonstrated with complete virions and infectious subviral particles derived from virus by limited chymotrypsin digestion but not with cores, a product of extensive chymotrypsin digestion of virus. The enzymatic product and the oligo(A) from purified virions were isolated by binding to oligo(dT)-cellulose columns. Most of the in vitro product was similar in size and structure to the oligo(A) from purified virions by the criteria of gel electrophoresis, DEAE-cellulose chromatography, end-group analysis, and sensitivity to RNase. The evidence suggests that oligo(A) synthesis is mediated by the poly(A) polymerase during a late step in viral morphogenesis and may result from an alternative activity of the virion-associated transcriptase.