Characterization of the mRNA of influenza virus

Interplay between influenza A virus and host factors: targets for antiviral intervention

Influenza A viruses (IAVs) pose a major public health threat worldwide. Recent experience with the 2013 H7N9 outbreak in China and the 2009 "swine flu" pandemic have shown that antiviral vaccines and drugs fall short of controlling the spread of disease in a timely and effective manner. Major problems include rapid emergence of drug-resistant influenza virus strains and the slow process of vaccine production. With the threat of a highly pathogenic H5N1 bird-flu pandemic looming large, it is crucial to develop novel ways of combating influenza A viruses. Targeting the host factors critical for influenza A virus replication has shown promise as a strategy to develop novel antiviral molecules with broad-spectrum protection. In this review, we summarize the role of currently identified host factors that play a critical role in the influenza A virus life cycle and discuss the most promising candidates for anti-influenza therapeutics.

Engineering influenza viral vectors

The influenza virus is a respiratory pathogen with a negative-sense, segmented RNA genome. Construction of recombinant influenza viruses in the laboratory was reported starting in the 1980s. Within a short period of time, pioneer researchers had devised methods that made it possible to construct influenza viral vectors from cDNA plasmid systems. Herein, we discuss the evolution of influenza virus reverse genetics, from helper virus-dependent systems, to helper virus-independent 17-plasmid systems, and all the way to 3- and 1- plasmid systems. Successes in the modification of different gene segments for various applications, including vaccine and gene therapies are highlighted.

An inhibitory activity in human cells restricts the function of an avian-like influenza virus polymerase

Transmission of avian influenza virus into human populations has the potential to cause pandemic outbreaks. A major determinant of species tropism is the identity of amino acid 627 in the PB2 subunit of the heterotrimeric influenza polymerase; glutamic acid predominates in avian PB2, whereas lysine occupies this position in human isolates. We show that a dominant inhibitory activity in human cells potently and selectively restricts the function of polymerases containing an avian-like PB2 with glutamic acid at residue 627. Restricted polymerases fail to assemble into ribonucleoprotein complexes, resulting in decreased genome transcription, replication, and virus production without any significant effect on relative viral infectivity. Understanding the molecular basis of this species-specific restriction should provide strategies to prevent and treat avian influenza outbreaks in humans.

Block to influenza virus replication in cells preirradiated with ultraviolet light

Ultraviolet (uv) irradiation of CEF cells immediately before infection with influenza A (fowl plague) virus inhibited virus growth; no inhibition of the growth of a parainfluenza virus (Newcastle disease virus) could be detected in irradiated cells. The kinetics of inhibition after various doses of uv irradiation were multihit, with an extrapolation number of two. When irradiated cells were allowed to photoreactivate by exposure to visible light for 16 hr their capacity to support influenza virus replication was largely restored; this process was sensitive to caffeine, suggesting that it required DNA repair. In CEF cells exposed to 360 ergs/mm(2) of uv radiation the rate of synthesis of host cellular RNA was reduced by more than 90%, and that of host cellular protein by 40-50%, as judged by incorporation of precursor molecules into an acid-insoluble form. When such irradiated cells were infected with influenza virus all the genome RNA segments were transcribed, but the overall concentration of virus-specific poly (A)-containing cRNA was reduced about 50-fold. Within this population of cRNA molecules, the RNAs coding for late proteins (HA, NA, and M) were reduced in amount relative to the other segments. The rates of synthesis of the M and HA proteins were specifically reduced in uv-irradiated cells, but the rates of synthesis of the P, NP, and NS proteins were only slightly reduced compared to normal cells. Immunofluorescent studies showed that, in uv-irradiated cells, NP migrated into the nucleus early after infection and later migrated out into the cytoplasm, as in normal cells. In contrast to normal cells, no specific immunofluorescence associated with M protein could be observed in uv-irradiated cells. It is concluded that uv-induced damage to host cellular DNA alters the pattern of RNA transcription in CEF cells infected with influenza virus, and that this results in a block to late protein synthesis which stops virus production.

Influenza virus gene expression: control mechanisms at early and late times of infection and nuclear-cytoplasmic transport of virus-specific RNAs

Single-stranded M13 DNAs specific for various influenza virus genomic segments were used to analyze the synthesis of virus-specific RNAs in infected cells. The results show that influenza virus infection is divided into two distinct phases. During the early phase, the syntheses of specific virion RNAs, viral mRNAs, and viral proteins were coupled. Thus, the NS (nonstructural) virion RNA was preferentially synthesized early, leading to the preferential synthesis of NS1 viral mRNA and NS1 protein; in contrast, M (matrix) RNA synthesis was delayed, leading to the delayed synthesis of M1 viral mRNA and M1 protein. This phase lasted for 2.5 h in BHK-21 cells, the time at which the rate of synthesis of all the viral mRNAs was maximal. During the second phase, the synthesis of all the virion RNAs remained at or near maximum until at least 5.5 h postinfection, whereas the rate of synthesis of all the viral mRNAs declined dramatically. By 4.5 h, the rate of synthesis of all the viral mRNAs was 5% of the maximum rate. Viral mRNA and protein syntheses were also not coupled, as the synthesis of all the viral proteins continued at maximum levels, indicating that protein synthesis during this phase was directed principally by previously synthesized viral mRNAs. Short pulses (3 min) with [3H]uridine and nonaqueous fractionation of cells were used to show that influenza virion RNA synthesis occurred in the nucleus, demonstrating that all virus-specific RNA synthesis was nuclear. Virion RNAs, like viral mRNAs, were efficiently transported to the cytoplasm at both early and late times of infection. In contrast, the full-length transcripts of the virion RNAs, which are the templates for virion RNA synthesis, were sequestered in the nucleus. Thus, the template RNAs, which were synthesized only at early times, remained in the nucleus to direct virion RNA synthesis throughout infection. These results enabled us to present an overall scheme for the control of influenza virus gene expression.

Biological characteristics of a cold-adapted influenza A virus mutation residing on a polymerase gene

The biological function of a cold-adapted (ca) mutation residing on the PB2 gene of an influenza A/Ann Arbor/6/60 (A/AA/6/60) ca variant virus in the viral replication cycle at 25 degrees C was studied. The viral polypeptide synthesis of A/AA/6/60 ca variant at 25 degrees C was evident approximately 6 hours earlier than the wild type (wt) virus and yielded twice as many products. The quantitative analysis of viral complementary RNA (cRNA), synthesized in the presence of cycloheximide, revealed that A/AA/6/60 ca variant and a single gene reassortant that contains only the PB2 gene of the ca variant with remaining genes of the wt virus produced equal amount of cRNA at 25 degrees and 33 degrees C, which was an amount approximately four fold greater than the wt virus' cRNA synthesized at 25 degrees C. These results strongly suggest that the ca mutation residing on the PB2 gene of A/AA/6/60 ca variant affects the messenger RNA synthesis at 25 degrees C in the primary transcription.

Transcription and replication of eight RNA segments of influenza virus

A novel quantitation system of both plus- and minus-strand RNAs for all eight genome segments of influenza virus was developed using single-strand cDNAs as the probes for hybridization, and employed for the measurement of various RNA species in influenza virus WSN-infected MDBK cells. The synthesis rate and accumulation level of plus-strand RNAs differed considerably among eight RNA segments and were under temporal control. In contrast, eight vRNA molecules of minus polarity were synthesized coordinately at similar rates. Newly synthesized plus-strand RNAs were rapidly transported into the cytoplasm, particularly during the early phase of virus infection, but vRNAs accumulated in the nuclei until the late infection phase. The present data supported the differential regulation of synthesis and the separate transport between plus- and minus-strand RNAs.

Combined action of mouse alpha and beta interferons in influenza virus-infected macrophages carrying the resistance gene Mx

In mice, the combined action of alpha and beta interferons (IFNs) against influenza viruses is modulated by the host gene Mx. High concentrations of IFN fail to prevent efficiently the replication of influenza A virus in cultured macrophages lacking the gene Mx, whereas cultured macrophages carrying Mx develop strong antiviral activity even at low concentrations of IFN. Several steps in the replication cycle of influenza virus were compared in Mx/Mx and +/+ mouse macrophages treated with IFN-alpha + beta. Uncoating was not affected. A twofold reduction in the accumulation of primary transcripts was observed in IFN-treated macrophages at the highest concentration of IFN regardless of the genetic constitution of the host cell. No evidence was obtained for inhibition of influenza virus translation in macrophages which lacked Mx when treated with IFN-alpha + beta. In contrast, a marked shut-off of influenza virus polypeptide synthesis occurred in Mx-bearing macrophages treated with these IFNs, although the primary transcripts were active in directing the synthesis of viral polypeptides in a cell-free system. We concluded that a specific inhibitory mechanism for influenza virus translation was induced by IFN-alpha + beta in macrophages bearing the resistance gene Mx.

Studies on polysomes synthesizing influenza virus haemagglutinin

A fraction of polysomes synthesizing fowl plague virus (FPV) haemagglutinin (HA) was isolated from an infected chick embryo fibroblast (CEF) culture using a double immunoprecipitation assay. In an immunoprecipitate of HA-synthesizing polysomes (HA precipitate) the content of the HA polypeptide was increased with respect to the M1 + NS1 polypeptides as compared to a preparation of unprecipitated polysomes. In the HA precipitate, besides mRNA coding for HA synthesis, we have detected mRNAs corresponding to genes 1, 2 and 3 coding for high molecular weight P proteins. Studies of a cytoplasmic extract (CE) from FPV-infected CEF cultures in a sucrose density gradient revealed a fraction of polysomes with a sedimentation value of about 500S; the composition of virus-specific polypeptides and mRNA of the fraction was similar to that of the HA precipitate. It is thought that P proteins are synthesized on membrane-bound polysomes located closely to HA-synthesizing polysomes.

Different patterns of replication in influenza virus-infected KB cells

When KB cells were infected either with the fowl plague (FPV) Rostock strain (Hav1N1) or the WSN (H0N1) strain of influenza A virus the yield of cell-associated haemagglutinin and neuraminidase polypeptides was essentially comparable, but virus particles were not produced in the FPV-KB system. WSN virus-infected KB cells synthesized normal amounts of mature virus particles and had all the characteristics of a permissive replication cycle. Biosynthesis and transport of RNP antigen from nucleus to cytoplasm of infected cells were traced by immunofluorescent staining at 4 and 8 hours after the beginning of infection. While the fluorescent-stained material was totally confined to the nuclei in FPV-infected KB cells, RNP antigen migrated out of the nucleus during the replicative cycle of WSN virus in the same host cell. Patterns of virus-specific protein synthesis were studied by pulse-labelling with 35S-methionine. The most significant feature concerned the amplification of synthesis of virus-induced matrix (M) protein which did not occur in FPV-infected cells but occurred normally during WSN infection. The different patterns of replication in the same host cell when infected by different influenza A viruses is discussed.

Nonviral oligonucleotides at the 5' terminus of cytoplasmic influenza viral mRNA deduced from cloned complete genomic sequences

We obtained influenza viral DNA clones containing sequences derived from cytoplasmic viral mRNA and genomic viral RNA. Sequence analysis of terminal nucleotides of five independentlyisolated viral DNA segments showed that additional oligonucleotides were covalently linked to the 5' terminus of viral mRNA transcripts. The sequences of these additional nucleotides varied among DNA clones of the same gene and of different genes as well. These inserts also varied in length, ranging from 6 to 14 nucleotides. The heterogeneity of these sequences suggests that they were derived originally from cellular RNA molecules. These findings provide evidence that cellular RNA sequences are used to prime influenza viral mRNA transcription in infected cells. In addition, the sequences at both termini of vRNA were fully represented in clone pFV 88, indicating that the cloned DNA contained the complete viral gene coding for the hemagglutinin.

Structure of the host-derived sequences present at the 5' ends of influenza virus mRNA

Nucleotide sequence analysis of the terminal virus-coded regions of a clone of the matrix gene of influenza virus indicated that the region corresponding to the 5' end of the mRNA contains an additional 13 non-virus coded nucleotides. Using the dideoxy-chain termination sequencing method with a restriction fragment derived from this clone, we have determined that the 5' ends of matrix gene mRNAs contain a heterogenous sequence of 9-15 nucleotides. In addition, the data indicate that the 3' terminal nucleotide of matrix gene virion RNA is not transcribed into mRNA, transcription of influenza virus-specific sequences commencing with the penultimate nucleotide at the 3' end of viron RNA.

New procedure for the production of influenza virus-specific double-stranded DNA's

A novel technique is described for the production of pure, full-length influenza virus ds DNA's corresponding to each segment of the influenza virus genome, and suitable for molecular cloning and restriction endonuclease mapping. The method involves the synthesis of DNA complementary to both virion (negative strand) and messenger (positive strand) RNA, gel purification and annealing. By avoiding the use of SI nuclease, which often removes the terminal regions of DNA duplexes, the method allows transcription of the total sequence information of influenza virion and messenger RNA's into a ds DNA form.

The smallest genome RNA segment of influenza virus contains two genes that may overlap

The genome of influenza virus consists of eight segments of single-stranded RNA, each of which encodes a different polypeptide. In addition to the eight recognized gene products, the virus specifies a distinct smaller nonstructural polypeptide (NS2), which is translated from a separate species of virus-specific mRNA. The location on the virus genome of the gene encoding this polypeptide was investigated by hybridization of the NS2 mRNA with isolated subgenomic RNA species, and by correlation of the inheritance of a strain-specific NS2 with inheritance of particular genome RNA segments during recombination between two different virus strains. The genetic information for NS2 was found to reside in the smallest genome RNA segment of the virion, which also encodes the NS1 polypeptide. Considering the sizes of the molecules involved, it is likely that the coding sequences for the two polypeptides overlap.

Nuclear accumulation of influenza viral RNA transcripts and the effects of cycloheximide, actinomycin D, and alpha-amanitin

The use of virus-specific (32)P-labeled complementary DNA and (125)I-labeled virion RNA as hybridization probes has allowed us to quantitate the number of molecules of complementary RNA (cRNA) and progeny virion RNA in MDCK cells infected with influenza virus. We compared the distribution of cRNA between the nucleus and the cytoplasm in cycloheximide-treated cells to that found in untreated cells, beginning 1 h after infection. A greater percentage of the total cRNA was detected in the nucleus of the drug-treated cells at all times investigated. For the first 2 h after infection about 50% of the cRNA synthesized in the cycloheximide-treated cells was found in the nucleus. These nuclear cRNA molecules were characterized and shown to be polyadenylated transcripts of each of the genome virion RNA segments. Viral cRNA synthesis was not completely inhibited by the addition of actinomycin D at the beginning of infection, with or without the concomitant addition of cycloheximide. A large fraction (about 90%) of these cRNA sequences were detected in the nucleus. Characterization of these nuclear cRNA molecules showed that they contained polyadenylic acid and represented transcripts of both those segments coding for proteins synthesized predominantly early after infection ("early" proteins) and those virion RNA segments coding for "late" proteins. Also, in vitro translation of these cRNA molecules showed that they were functional virus mRNA's. In contrast to actinomycin D, alpha-amanitin completely inhibited cRNA synthesis when added at the beginning of infection, and addition of this drug after 1.5 h had no effect on further cRNA synthesis.

Nucleotide sequences at the 5' termini of influenza virus RNAs and their transcripts

The results of analyses of the 5'-terminal sequences of Fowl Plague virus RNAs are presented. The first 13 residues of each of the eight RNA molecules which constitute the genome are in the identical sequence 5'AGUAGAAAUUAGG- and this conservation of sequence is shown to extend to other influenza viruses. The 5'-terminal sequences of virion RNA transcripts produced in vitro are also reported and again the first 12 nucleotides of these are identical for all influenza type A transcripts examined in the sequence 5'AGCAAAAGCAGG-. In addition the results of attempts to determine the sequence relationship between vRNAs and the two classes of complementary RNA synthesized in influenza infected cells are described which support the conclusion that influenza messenger RNAs are incomplete transcripts.

The segments of influenza viral mRNA

Influenza viral mRNA, i.e., complementary RNA (cRNA), isolated from infected cells , was resolved into six different species by electrophoresis in 2.1% acrylamide gels containing 6 M urea. The cRNA's were grouped into three size classes: L (large), M (medium-size), and S (small). Similarly, when gels were sliced for analysis, the virion RNA (vRNA) also distributed into six peaks because the three largest vRNA segments were closely spaced and were resolved only when the gels were autoradiographed or stained. Because of their attached polyadenylic acid [poly(A)]sequences, the cRNA segments migrated more slowly than did the corresponding vRNA segments during gel electrophoresis. After removal of the poly(A) by RNase H, the cRNA and vRNA segments comigrated, indicating that they were approximately the same size. One of the cRNA segments, S2, was shown by annealing to contain the genetic information in the vRNA segment with which it comigrated, strongly suggesting that each cRNA segment was transcribed from the vRNA segment of the same size. In contrast to the vRNA segments, which when isolated from virions were present in approximately 1:1 molar ratios, the segments of the isolated cRNA were present in unequal amounts, with the segments M2 and S2 predominating, suggesting that different amounts of the cRNA segments were synthesized in the infected cell. The predominant cRNA segments, M2 and S2, and also the S1 segment, were active as mRNA's in wheat germ extracts. The M2 cRNA was the mRNA for the nucleocapsid protein; S1 for the membrane protein; and S2 for the nonstructural protein NS1.

Use of specific radioactive probes to study transcription and replication of the influenza virus genome

Specific radioactive probes have been obtained for both influenza virion RNA (vRNA) and for its complement (complementary RNA or cRNA): 32P-labeled complementary DNA (cDNA) synthesized with the avian sarcoma virus reverse transcriptase, and [125I]vRNA, respectively. From the kinetics of annealing of these two probes to RNA from canine kidney cells infected with the WSN strain of influenza virus, we have determined the average number of cRNA and vRNA sequences in the nucleus and cytoplasm as a function of time after infection. Immediately after infection, a small amount of vRNA is detected, presumably from the inoculum virus. As expected, the amount of cRNA is insignificant. During the first 1.75 h of infection, the most significant increase observed is in cRNA sequences. Most of these cRNA sequences are found in the cytoplasm, but a significant amount (30%) is found in the nucleus. During this time, a small but significant increase in vRNA is also detected in the nucleus and cytoplasm. From 1.75 to 2.75 h, the absolute amounts of both cRNA and vRNA increase, predominantly in the cytoplasm, with cRNA remaining as the majority species. Subsequently, the amount of vRNA increases with respect to cRNA and becomes the majority species. At 3.75 h, 95% of both cRNA and vRNA are found in the cytoplasm. Addition of actinomycin D at 1.75 h completely suppresses the subsequent ninefold increase in cRNA and does not have a significant effect on the subsequent 14-fold increase in cytoplasmic vRNA. This assay is also able to detect the cRNA produced as a result of primary transcription, operationally defined as the cRNA produced in the presence of 100 mug of cycloheximide per ml added at zero time of infection. Increases in cRNA in the presence of cycloheximide are detectable in both the nucleus and the cytoplasm. Addition of actinomycin D as well as cycloheximide at zero time completely suppresses the appearance of cRNA in the cytoplasm, whereas a large fraction (50%) of the increase in nuclear cRNA still occurs.

Influenza virion transcriptase: synthesis in vitro of large, polyadenylic acid-containing complementary RNA

The influenza virion transcriptase is capable of synthesizing in vitro complementary RNA (cRNA) that is similar in several characteristics to the cRNA synthesized in the infected cell, which is the viral mRNA. Most of the in vitro cRNA is large (approximately 2.5 X 10(5) to 10(6) daltons), similar in size to in vivo cRNA. The in vitro transcripts initiate in adenosine (A) or guanosine (G) at the 5' end, as also appears to be the case with in vivo cRNA (R.M. Krug et al., 1976). The in vitro transcripts contain covalently linked polyadenylate [poly(A)] sequences, which are longer and more heterogeneous than the poly(A) sequences found on in vivo cRNA. The synthesis in vitro of cRNA with these characteristics requires both the proper divalent cation, Mg2+, and a specific dinulceside monophosphage (DNMP), ApG or GpG. These DNMPs stimulate cRNA synthesis about 100-fold in the presence of Mg2+ and act as primers to initiate RNA chains, as demonstrated by the fact that the 5'-phosphorylated derivatives of these DNMP's, 32pApG or 32pGpG, are incroporated at the 5' end of the product RNA. The RNA synthesized in vitro differs from in vivo cRNA in that neither capping nor methylation of the in vitro transcripts has been detected. The virion does contain a methylase activity, as shown by its ability to methylate exogenous methyl-deficient Escherichia coli tRNA.

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.

Characterization of polysome-associated RNA from influenza virus-infected cells

Virus-specific polysome-associated RNA (psRNA) and RNA after dissociation of polysomes were analyzed by direct hybridization with unlabeled viral RNA (vRNA) and complementary RNA (cRNA). psRNA after a 30-min pulse with [3H]uridine contained 28% labeled cRNA, 70% host RNA, and no vRNA. After dissociation, psRNA sedimented heterogeneously. Heavy RNA (greater than 60S), ribosomal subunit RNA (rsuRNA, 30-60S), free mRNA (fmRNA, 10-30S), and light RNA (less than 10S) contained 16%, 54%, 70% and 28% cRNA, respectively, but no vRNA. When actinomycin D (AcD) was added at 2 h postinfection, the nature of the psRNA depended on the concentration of AcD and the condition of the labeling. At AcD concentrations of 1 mug or more per ml, no detectable vRNA or cRNA was associated with polysomes. At 0.2 mug of AcD per ml (a concentration that partially inhibited cRNA synthesis) and 2 h of labeling at 2.5 h postinfection, psRNA contained 40% viral-specific RNA, which included both vRNA and cRNA in almost equal amounts. When polysomes were dissociated, however, viral-specific fm RNA from AcD-treated cells contained exclusively cRNA and no detectable vRNA. Increasing amounts of labeled vRNA were present in the heavy region of the gradient (and in the pellet), which also contained varying amounts of cRNA. The labeled vRNA appears to be associated with polysomes in a cesium chloride density gradient (rho = 1.525 g/ml). Although we have ruled out the trivial explanation of viral ribonucleoprotein contamination,the nature of the complex containing both polysomes and vRNA is unknown.

Influenza viral mRNA contains internal N6-methyladenosine and 5'-terminal 7-methylguanosine in cap structures

Influenza viral complementary RNA (cRNA), i.e., viral mRNA was radioactive when purified from the cytoplasmic fraction of cordycepin-treated canine kidney cells that were incubated with [methyl-3H]methionine during infection. Approximately 55 to 60% of the methyl-3H radioactivity was in internal N6-methyladenosine, a feature distinguishing this mRNA from those viral mRNA's that are known to be synthesized in the cytoplasm. The remaining methyl-3H radioactivity was in 5'-terminal cap structures that consisted of 7-methylguanosine in pyrophosphate linkage to 2'-o-methyladenosine, N6, 2'-O-dimethyladenosine, or 2'-O-methylguanosine. Methylated adenosine was the predominant penultimate nucleoside in caps, suggesting that cRNA synthesis in infected cells initiates preferentially with adenosine at the 5' end. In contrast to cRNA, influenza virion RNA segments extracted from purified virus contained mainly 5'-terminal ppA and no detectable cap structures.

Influenza virus genome consists of eight distinct RNA species

The genomic RNA of the avian influenza A virus, fowl plague, was fractionated into eight species by electrophoresis in polyacrylamide-agarose gels containing 6 M urea. The separated 32P-labeled RNA species were characterized by digestion with RNase T1 and fractionation of the resulting oligonucleotides by two-dimensional gel electrophoresis; this demonstrated that each species has a distinct nucleotide sequence. A tentative correlation of each genome RNA species with the virus protein that it encodes was made.